mirror of
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(v1.0.1.9005) as.mo() improvements
This commit is contained in:
@@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.0.1.9004
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Date: 2020-03-14
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Version: 1.0.1.9005
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Date: 2020-04-13
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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16
NAMESPACE
16
NAMESPACE
@@ -2,16 +2,22 @@
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S3method("[",ab)
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S3method("[",disk)
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S3method("[",mic)
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S3method("[",mo)
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S3method("[<-",ab)
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S3method("[<-",disk)
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S3method("[<-",mic)
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S3method("[<-",mo)
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S3method("[<-",rsi)
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S3method("[[",ab)
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S3method("[[",disk)
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S3method("[[",mic)
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S3method("[[",mo)
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S3method("[[<-",ab)
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S3method("[[<-",disk)
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S3method("[[<-",mic)
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S3method("[[<-",mo)
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S3method("[[<-",rsi)
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S3method(as.data.frame,ab)
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S3method(as.data.frame,disk)
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S3method(as.data.frame,mo)
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@@ -26,7 +32,9 @@ S3method(barplot,mic)
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S3method(barplot,rsi)
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S3method(c,ab)
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S3method(c,disk)
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S3method(c,mic)
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S3method(c,mo)
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S3method(c,rsi)
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S3method(droplevels,mic)
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S3method(droplevels,rsi)
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S3method(format,bug_drug_combinations)
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@@ -216,16 +224,22 @@ export(susceptibility)
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export(theme_rsi)
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exportMethods("[.ab")
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exportMethods("[.disk")
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exportMethods("[.mic")
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exportMethods("[.mo")
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exportMethods("[<-.ab")
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exportMethods("[<-.disk")
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exportMethods("[<-.mic")
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exportMethods("[<-.mo")
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exportMethods("[<-.rsi")
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exportMethods("[[.ab")
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exportMethods("[[.disk")
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exportMethods("[[.mic")
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exportMethods("[[.mo")
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exportMethods("[[<-.ab")
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exportMethods("[[<-.disk")
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exportMethods("[[<-.mic")
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exportMethods("[[<-.mo")
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exportMethods("[[<-.rsi")
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exportMethods(as.data.frame.ab)
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exportMethods(as.data.frame.disk)
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exportMethods(as.data.frame.mo)
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@@ -236,7 +250,9 @@ exportMethods(barplot.mic)
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exportMethods(barplot.rsi)
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exportMethods(c.ab)
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exportMethods(c.disk)
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exportMethods(c.mic)
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exportMethods(c.mo)
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exportMethods(c.rsi)
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exportMethods(droplevels.mic)
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exportMethods(droplevels.rsi)
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exportMethods(format.bug_drug_combinations)
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14
NEWS.md
14
NEWS.md
@@ -1,12 +1,22 @@
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# AMR 1.0.1.9004
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## <small>Last updated: 14-Mar-2020</small>
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# AMR 1.0.1.9005
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## <small>Last updated: 13-Apr-2020</small>
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### New
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* Support for easy principal component analysis for AMR, using the new `pca()` function
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* Plotting biplots for principal component analysis using the new `ggplot_pca()` function
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### Changed
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* Improvements for the algorithm used by `as.mo()` (and consequently all `mo_*` functions, that use `as.mo()` internally):
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* Support for codes ending with `SPE` for species, like `"ESCSPE"` for *Escherichia coli*
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* Support for any encoding, which means that any language-specific character with accents can be used for input
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* Support for more arbitrary IDs used in laboratory information systems
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* Small fix for preventing viruses being treated as bacteria
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* Small fix for preventing contamination and lack of growth being treated as valid microorganisms
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* Added more abbreviations to the `antibiotics` data set
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### Other
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* Support for the upcoming `dplyr` version 1.0.0
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* More robust assigning for classes `rsi` and `mic`
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# AMR 1.0.1
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39
R/data.R
39
R/data.R
@@ -19,11 +19,11 @@
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Data sets with ~550 antimicrobials
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#' Data sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` antimicrobials
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#'
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#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
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#' @format
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#' ### For the [antibiotics] data set: a [`data.frame`] with 452 observations and 14 variables:
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#' ### For the [antibiotics] data set: a [`data.frame`] with `r nrow(antibiotics)` observations and `r ncol(antibiotics)` variables:
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#' - `ab`\cr Antibiotic ID as used in this package (like `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
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#' - `cid`\cr Compound ID as found in PubChem
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@@ -39,7 +39,7 @@
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#' - `iv_units`\cr Units of `iv_ddd`
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#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
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#'
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#' ### For the [antivirals] data set: a [`data.frame`] with 102 observations and 9 variables:
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#' ### For the [antivirals] data set: a [`data.frame`] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
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#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
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#' - `cid`\cr Compound ID as found in PubChem
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#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
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@@ -71,11 +71,11 @@
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#' @rdname antibiotics
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"antivirals"
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#' Data set with ~70,000 microorganisms
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#' Data set with `r format(nrow(microorganisms), big.mark = ",")` microorganisms
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#'
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#' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using [as.mo()].
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#' @inheritSection catalogue_of_life Catalogue of Life
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#' @format A [`data.frame`] with 69,447 observations and 17 variables:
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#' @format A [`data.frame`] with `r format(nrow(microorganisms), big.mark = ",")` observations and `r ncol(microorganisms)` variables:
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#' - `mo`\cr ID of microorganism as used by this package
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#' - `col_id`\cr Catalogue of Life ID
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#' - `fullname`\cr Full name, like `"Escherichia coli"`
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@@ -92,8 +92,8 @@
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#' - 3 entries of *Trichomonas* (*Trichomonas vaginalis*, and its family and genus)
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#' - 1 entry of *Blastocystis* (*Blastocystis hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
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#' - 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
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#' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not in the Catalogue of Life
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#' - 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
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#' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
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#' - `r format(nrow(filter(microorganisms, source == "DSMZ")), big.mark = ",")` species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
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#'
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#' ### Direct download
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#' This data set is available as 'flat file' for use even without R - you can find the file here:
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@@ -122,7 +122,7 @@ catalogue_of_life <- list(
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#'
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#' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by [as.mo()].
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#' @inheritSection catalogue_of_life Catalogue of Life
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#' @format A [`data.frame`] with 24,246 observations and 5 variables:
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#' @format A [`data.frame`] with `r format(nrow(microorganisms.old), big.mark = ",")` observations and `r ncol(microorganisms.old)` variables:
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#' - `col_id`\cr Catalogue of Life ID that was originally given
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#' - `col_id_new`\cr New Catalogue of Life ID that responds to an entry in the [microorganisms] data set
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#' - `fullname`\cr Old full taxonomic name of the microorganism
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@@ -136,7 +136,7 @@ catalogue_of_life <- list(
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#' Translation table for common microorganism codes
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#'
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#' A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with [set_mo_source()]. They will all be searched when using [as.mo()] and consequently all the [`mo_*`][mo_property()] functions.
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#' @format A [`data.frame`] with 5,450 observations and 2 variables:
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#' @format A [`data.frame`] with `r format(nrow(microorganisms.codes), big.mark = ",")` observations and `r ncol(microorganisms.codes)` variables:
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#' - `code`\cr Commonly used code of a microorganism
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#' - `mo`\cr ID of the microorganism in the [microorganisms] data set
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#' @inheritSection catalogue_of_life Catalogue of Life
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@@ -144,10 +144,10 @@ catalogue_of_life <- list(
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#' @seealso [as.mo()] [microorganisms]
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"microorganisms.codes"
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#' Data set with 2,000 example isolates
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#' Data set with `r format(nrow(example_isolates), big.mark = ",")` example isolates
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#'
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#' A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read [the tutorial on our website](https://msberends.gitlab.io/AMR/articles/AMR.html).
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#' @format A [`data.frame`] with 2,000 observations and 49 variables:
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#' A data set containing `r format(nrow(example_isolates), big.mark = ",")` microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read [the tutorial on our website](https://msberends.gitlab.io/AMR/articles/AMR.html).
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#' @format A [`data.frame`] with `r format(nrow(example_isolates), big.mark = ",")` observations and `r ncol(example_isolates)` variables:
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#' - `date`\cr date of receipt at the laboratory
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#' - `hospital_id`\cr ID of the hospital, from A to D
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#' - `ward_icu`\cr logical to determine if ward is an intensive care unit
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@@ -157,14 +157,14 @@ catalogue_of_life <- list(
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#' - `gender`\cr gender of the patient
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#' - `patient_id`\cr ID of the patient
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#' - `mo`\cr ID of microorganism created with [as.mo()], see also [microorganisms]
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#' - `PEN:RIF`\cr 40 different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()]
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#' - `PEN:RIF`\cr `r sum(sapply(example_isolates, is.rsi))` different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()]
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#' @inheritSection AMR Read more on our website!
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"example_isolates"
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#' Data set with unclean data
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#'
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#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
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#' @format A [`data.frame`] with 3,000 observations and 8 variables:
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#' A data set containing `r format(nrow(example_isolates_unclean), big.mark = ",")` microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
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#' @format A [`data.frame`] with `r format(nrow(example_isolates_unclean), big.mark = ",")` observations and `r ncol(example_isolates_unclean)` variables:
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#' - `patient_id`\cr ID of the patient
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#' - `date`\cr date of receipt at the laboratory
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#' - `hospital`\cr ID of the hospital, from A to C
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@@ -173,10 +173,10 @@ catalogue_of_life <- list(
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#' @inheritSection AMR Read more on our website!
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"example_isolates_unclean"
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#' Data set with 500 isolates - WHONET example
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#' Data set with `r format(nrow(WHONET), big.mark = ",")` isolates - WHONET example
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#'
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#' This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our [example_isolates] data set.
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#' @format A [`data.frame`] with 500 observations and 53 variables:
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#' @format A [`data.frame`] with `r format(nrow(WHONET), big.mark = ",")` observations and `r ncol(WHONET)` variables:
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#' - `Identification number`\cr ID of the sample
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#' - `Specimen number`\cr ID of the specimen
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#' - `Organism`\cr Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using [as.mo()].
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@@ -202,14 +202,14 @@ catalogue_of_life <- list(
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#' - `Inducible clindamycin resistance`\cr Clindamycin can be induced?
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#' - `Comment`\cr Other comments
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#' - `Date of data entry`\cr Date this data was entered in WHONET
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#' - `AMP_ND10:CIP_EE`\cr 27 different antibiotics. You can lookup the abbreviatons in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()].
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#' - `AMP_ND10:CIP_EE`\cr `r sum(sapply(WHONET, is.rsi))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()].
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#' @inheritSection AMR Read more on our website!
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"WHONET"
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#' Data set for R/SI interpretation
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#'
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#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
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#' @format A [`data.frame`] with 13,975 observations and 9 variables:
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#' @format A [`data.frame`] with `r format(nrow(rsi_translation), big.mark = ",")` observations and `r ncol(rsi_translation)` variables:
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#' - `guideline`\cr Name of the guideline
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#' - `method`\cr Either "MIC" or "DISK"
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#' - `site`\cr Body site, e.g. "Oral" or "Respiratory"
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@@ -219,6 +219,7 @@ catalogue_of_life <- list(
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#' - `disk_dose`\cr Dose of the used disk diffusion method
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#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
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#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
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#' - `uti`\cr A logical value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
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#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
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#' @inheritSection AMR Read more on our website!
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"rsi_translation"
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3
R/disk.R
3
R/disk.R
@@ -159,6 +159,7 @@ vec_ptype_full.disk <- function(x, ...) {
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#' @export
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#' @noRd
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"[<-.disk" <- function(i, j, ..., value) {
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value <- as.disk(value)
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y <- NextMethod()
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attributes(y) <- attributes(i)
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y
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@@ -167,6 +168,7 @@ vec_ptype_full.disk <- function(x, ...) {
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#' @export
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#' @noRd
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"[[<-.disk" <- function(i, j, ..., value) {
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value <- as.disk(value)
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y <- NextMethod()
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attributes(y) <- attributes(i)
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y
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@@ -176,6 +178,7 @@ vec_ptype_full.disk <- function(x, ...) {
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#' @noRd
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c.disk <- function(x, ...) {
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y <- NextMethod()
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y <- as.disk(y)
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attributes(y) <- attributes(x)
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y
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}
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@@ -21,7 +21,7 @@
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#' PCA biplot with `ggplot2`
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#'
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#' This function is to produce a `ggplot2` variant of a so-called [biplot](https://en.wikipedia.org/wiki/Biplot) for PCA (principal component analysis), but is more flexible and more appealing than the base \R [biplot()] function.
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#' Produces a `ggplot2` variant of a so-called [biplot](https://en.wikipedia.org/wiki/Biplot) for PCA (principal component analysis), but is more flexible and more appealing than the base \R [biplot()] function.
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#' @inheritSection lifecycle Maturing lifecycle
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#' @param x an object returned by [pca()], [prcomp()] or [princomp()]
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#' @inheritParams stats::biplot.prcomp
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||||
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43
R/mic.R
43
R/mic.R
@@ -254,3 +254,46 @@ pillar_shaft.mic <- function(x, ...) {
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out[is.na(x)] <- pillar::style_na(NA)
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pillar::new_pillar_shaft_simple(out, align = "right", min_width = 4)
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}
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#' @exportMethod [.mic
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#' @export
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#' @noRd
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"[.mic" <- function(x, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @exportMethod [[.mic
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#' @export
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#' @noRd
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"[[.mic" <- function(x, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @exportMethod [<-.mic
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#' @export
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#' @noRd
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"[<-.mic" <- function(i, j, ..., value) {
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value <- as.mic(value)
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y <- NextMethod()
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attributes(y) <- attributes(i)
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y
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}
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#' @exportMethod [[<-.mic
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#' @export
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#' @noRd
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"[[<-.mic" <- function(i, j, ..., value) {
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value <- as.mic(value)
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y <- NextMethod()
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||||
attributes(y) <- attributes(i)
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y
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}
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#' @exportMethod c.mic
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#' @export
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#' @noRd
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c.mic <- function(x, ...) {
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y <- NextMethod()
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||||
attributes(y) <- attributes(i)
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||||
y
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||||
}
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||||
|
||||
47
R/mo.R
47
R/mo.R
@@ -177,8 +177,14 @@ as.mo <- function(x,
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|
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check_dataset_integrity()
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|
||||
# start off with replaced language-specific non-ASCII characters with ASCII characters
|
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x <- parse_encoding(x)
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||||
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# WHONET: xxx = no growth
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x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
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# Laboratory systems: remove entries like "no growth" etc
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x[trimws2(x) %like% "(no .*growth|keine? .*wachtstum|geen .*groei|no .*crecimientonon|sem .*crescimento|pas .*croissance)"] <- NA_character_
|
||||
x[trimws2(x) %like% "^(no|not|kein|geen|niet|non|sem) [a-z]+"] <- "UNKNOWN"
|
||||
|
||||
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
|
||||
|
||||
@@ -256,9 +262,15 @@ exec_as.mo <- function(x,
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
# start off with replaced language-specific non-ASCII characters with ASCII characters
|
||||
x <- parse_encoding(x)
|
||||
|
||||
# WHONET: xxx = no growth
|
||||
x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
|
||||
|
||||
# Laboratory systems: remove entries like "no growth" etc
|
||||
x[trimws2(x) %like% "(no .*growth|keine? .*wachtstum|geen .*groei|no .*crecimientonon|sem .*crescimento|pas .*croissance)"] <- NA_character_
|
||||
x[trimws2(x) %like% "^(no|not|kein|geen|niet|non|sem) [a-z]+"] <- "UNKNOWN"
|
||||
|
||||
if (initial_search == TRUE) {
|
||||
options(mo_failures = NULL)
|
||||
options(mo_uncertainties = NULL)
|
||||
@@ -298,7 +310,7 @@ exec_as.mo <- function(x,
|
||||
|
||||
x_input <- x
|
||||
# already strip leading and trailing spaces
|
||||
x <- trimws(x, which = "both")
|
||||
x <- trimws(x)
|
||||
# only check the uniques, which is way faster
|
||||
x <- unique(x)
|
||||
# remove empty values (to later fill them in again with NAs)
|
||||
@@ -417,7 +429,7 @@ exec_as.mo <- function(x,
|
||||
strip_whitespace <- function(x, dyslexia_mode) {
|
||||
# all whitespaces (tab, new lines, etc.) should be one space
|
||||
# and spaces before and after should be omitted
|
||||
trimmed <- trimws(gsub("[\\s]+", " ", x, perl = TRUE), which = "both")
|
||||
trimmed <- trimws2(x)
|
||||
# also, make sure the trailing and leading characters are a-z or 0-9
|
||||
# in case of non-regex
|
||||
if (dyslexia_mode == FALSE) {
|
||||
@@ -439,8 +451,9 @@ exec_as.mo <- function(x,
|
||||
# remove spp and species
|
||||
x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x)
|
||||
x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x)
|
||||
x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x) # when ending in SPE instead of SPP and preceded by 2-4 characters
|
||||
x <- strip_whitespace(x, dyslexia_mode)
|
||||
|
||||
|
||||
x_backup_without_spp <- x
|
||||
x_species <- paste(x, "species")
|
||||
# translate to English for supported languages of mo_property
|
||||
@@ -454,6 +467,8 @@ exec_as.mo <- function(x,
|
||||
x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x)
|
||||
x <- gsub("(schimmels?|mofo|molde|stampo|moisissure|fungi)[a-z]*", "fungus", x)
|
||||
x <- gsub("fungus[ph|f]rya", "fungiphrya", x)
|
||||
# no contamination
|
||||
x <- gsub("(contamination|kontamination|mengflora|contaminaci.n|contamina..o)", "", x)
|
||||
# remove non-text in case of "E. coli" except dots and spaces
|
||||
x <- trimws(gsub("[^.a-zA-Z0-9/ \\-]+", " ", x))
|
||||
# but make sure that dots are followed by a space
|
||||
@@ -680,8 +695,8 @@ exec_as.mo <- function(x,
|
||||
next
|
||||
}
|
||||
|
||||
if (x_backup_without_spp[i] %like_case% "virus") {
|
||||
# there is no fullname like virus, so don't try to coerce it
|
||||
if (x_backup_without_spp[i] %like_case% "(virus|viridae)") {
|
||||
# there is no fullname like virus or viridae, so don't try to coerce it
|
||||
x[i] <- NA_character_
|
||||
next
|
||||
}
|
||||
@@ -1467,7 +1482,8 @@ exec_as.mo <- function(x,
|
||||
if (n_distinct(failures) > 1) {
|
||||
plural <- c("values", "them", "were")
|
||||
}
|
||||
total_failures <- length(x_input[as.character(x_input) %in% as.character(failures) & !x_input %in% c(NA, NULL, NaN)])
|
||||
x_input_clean <- trimws2(x_input)
|
||||
total_failures <- length(x_input_clean[as.character(x_input_clean) %in% as.character(failures) & !x_input %in% c(NA, NULL, NaN)])
|
||||
total_n <- length(x_input[!x_input %in% c(NA, NULL, NaN)])
|
||||
msg <- paste0(nr2char(n_distinct(failures)), " unique ", plural[1],
|
||||
" (covering ", percentage(total_failures / total_n),
|
||||
@@ -1475,7 +1491,7 @@ exec_as.mo <- function(x,
|
||||
if (n_distinct(failures) <= 10) {
|
||||
msg <- paste0(msg, ": ", paste('"', unique(failures), '"', sep = "", collapse = ", "))
|
||||
}
|
||||
msg <- paste0(msg, ". Use mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` parameter if needed (see ?as.mo).")
|
||||
msg <- paste0(msg, ".\nUse mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` parameter if needed (see ?as.mo).")
|
||||
warning(red(paste0("\n", msg)),
|
||||
call. = FALSE,
|
||||
immediate. = TRUE) # thus will always be shown, even if >= warnings
|
||||
@@ -1787,6 +1803,7 @@ as.data.frame.mo <- function(x, ...) {
|
||||
"[<-.mo" <- function(i, j, ..., value) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
# must only contain valid MOs
|
||||
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
|
||||
as.character(microorganisms.translation$mo_old)))
|
||||
}
|
||||
@@ -1796,6 +1813,7 @@ as.data.frame.mo <- function(x, ...) {
|
||||
"[[<-.mo" <- function(i, j, ..., value) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
# must only contain valid MOs
|
||||
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
|
||||
as.character(microorganisms.translation$mo_old)))
|
||||
}
|
||||
@@ -1805,6 +1823,7 @@ as.data.frame.mo <- function(x, ...) {
|
||||
c.mo <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
# must only contain valid MOs
|
||||
class_integrity_check(y, "microorganism code", c(as.character(microorganisms$mo),
|
||||
as.character(microorganisms.translation$mo_old)))
|
||||
}
|
||||
@@ -1949,3 +1968,15 @@ levenshtein_fraction <- function(input, output) {
|
||||
# self-made score between 0 and 1 (for % certainty, so 0 means huge distance, 1 means no distance)
|
||||
(base::nchar(output) - 0.5 * levenshtein) / nchar(output)
|
||||
}
|
||||
|
||||
trimws2 <- function(x) {
|
||||
trimws(gsub("[\\s]+", " ", x, perl = TRUE))
|
||||
}
|
||||
|
||||
parse_encoding <- function(x) {
|
||||
tryCatch({
|
||||
parsed <- iconv(x, to = "UTF-8")
|
||||
parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
|
||||
gsub('"', "", parsed, fixed = TRUE)
|
||||
}, error = function(e) stop(e$message, call. = FALSE))
|
||||
}
|
||||
|
||||
31
R/rsi.R
31
R/rsi.R
@@ -226,7 +226,7 @@ as.rsi.mic <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST",
|
||||
uti <- rep(uti, length(x))
|
||||
}
|
||||
|
||||
message(blue(paste0("=> Interpreting MIC values of column `", bold(ab), "` (",
|
||||
message(blue(paste0("=> Interpreting MIC values of `", bold(ab), "` (",
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ") using guideline ", bold(guideline_coerced), " ... ")),
|
||||
appendLF = FALSE)
|
||||
@@ -263,7 +263,7 @@ as.rsi.disk <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST"
|
||||
uti <- rep(uti, length(x))
|
||||
}
|
||||
|
||||
message(blue(paste0("=> Interpreting disk zones of column `", bold(ab), "` (",
|
||||
message(blue(paste0("=> Interpreting disk zones of `", bold(ab), "` (",
|
||||
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ") using guideline ", bold(guideline_coerced), " ... ")),
|
||||
appendLF = FALSE)
|
||||
@@ -682,3 +682,30 @@ pillar_shaft.rsi <- function(x, ...) {
|
||||
out[x == "R"] <- bgRed(white(" R "))
|
||||
pillar::new_pillar_shaft_simple(out, align = "left", width = 3)
|
||||
}
|
||||
|
||||
#' @exportMethod [<-.rsi
|
||||
#' @export
|
||||
#' @noRd
|
||||
"[<-.rsi" <- function(i, j, ..., value) {
|
||||
value <- as.rsi(value)
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
y
|
||||
}
|
||||
#' @exportMethod [[<-.rsi
|
||||
#' @export
|
||||
#' @noRd
|
||||
"[[<-.rsi" <- function(i, j, ..., value) {
|
||||
value <- as.rsi(value)
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
y
|
||||
}
|
||||
#' @exportMethod c.rsi
|
||||
#' @export
|
||||
#' @noRd
|
||||
c.rsi <- function(x, ...) {
|
||||
y <- unlist(lapply(list(...), as.character))
|
||||
x <- as.character(x)
|
||||
as.rsi(c(x, y))
|
||||
}
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -301,7 +301,7 @@ antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]] <- list(c("clo
|
||||
antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]], "CFC")) # cefaclor old WHONET4 code
|
||||
antibiotics[which(antibiotics$ab == "AMX"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "AMX"), "synonyms"][[1]], "Amoxy")))
|
||||
# 'Polymixin B' (POL) and 'Polymyxin B' (PLB) both exist, so:
|
||||
antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "POL", "Polymixin", "Polymixin B"))
|
||||
antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "POL", "Polymixin", "Polymixin B", "Poly B"))
|
||||
antibiotics <- filter(antibiotics, ab != "POL")
|
||||
# 'Latamoxef' (LTM) and 'Moxalactam (Latamoxef)' (MOX) both exist, so:
|
||||
antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c("MOX", "moxa"))
|
||||
@@ -323,7 +323,19 @@ antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]] <
|
||||
antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]], "cftz"))
|
||||
antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]], "cfpi"))
|
||||
antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt"))
|
||||
antibiotics[which(antibiotics$ab == as.ab("cotrimoxazol")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cotrimoxazol")), "abbreviations"][[1]], "trsx"))
|
||||
# More GLIMS codes
|
||||
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz"))
|
||||
antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr"))
|
||||
antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "cftx"))
|
||||
antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]], "cfrx"))
|
||||
antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]], "cfzl"))
|
||||
antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]], "cfxt"))
|
||||
antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "pipc"))
|
||||
antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "PIPC"))
|
||||
antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "COTRIM"))
|
||||
antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "trsx"))
|
||||
antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "PIPTAZ"))
|
||||
antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pita"))
|
||||
# ESBL E-test codes:
|
||||
antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
|
||||
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))
|
||||
@@ -351,7 +363,6 @@ old_sym <- old_sym[!old_sym %in% c("Cotrimoxazole", "Bactrimel")]
|
||||
antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] <- list(old_sym)
|
||||
antibiotics[which(antibiotics$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole"))))
|
||||
|
||||
|
||||
## new ATC codes
|
||||
# ceftaroline
|
||||
antibiotics[which(antibiotics$ab == "CPT"), "atc"] <- "J01DI02"
|
||||
@@ -362,7 +373,6 @@ antibiotics[which(antibiotics$ab == "BPR"), "atc"] <- "J01DI01"
|
||||
|
||||
# typo
|
||||
antibiotics[which(antibiotics$ab == "RXT"), "name"] <- "Roxithromycin"
|
||||
|
||||
antibiotics[which(antibiotics$ab == "PEN"), "atc"] <- "J01CE01"
|
||||
|
||||
|
||||
@@ -408,8 +418,15 @@ antibiotics <- antibiotics %>%
|
||||
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
|
||||
class(antibiotics$ab) <- "ab"
|
||||
|
||||
# make all abbreviations and synonyms lower case, unique and alphabetically sorted
|
||||
for (i in 1:nrow(antibiotics)) {
|
||||
abb <- sort(unique(tolower(antibiotics[i, "abbreviations"][[1]])))
|
||||
syn <- sort(unique(tolower(antibiotics[i, "synonyms"][[1]])))
|
||||
antibiotics[i, "abbreviations"][[1]] <- ifelse(length(abb[!abb == ""]) == 0, list(""), list(abb))
|
||||
antibiotics[i, "synonyms"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(syn))
|
||||
}
|
||||
|
||||
# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
|
||||
|
||||
dim(antibiotics) # for R/data.R
|
||||
usethis::use_data(antibiotics, overwrite = TRUE)
|
||||
rm(antibiotics)
|
||||
|
||||
@@ -890,6 +890,5 @@ rm(microorganisms.translation)
|
||||
devtools::load_all(".")
|
||||
|
||||
# TO DO AFTER THIS
|
||||
# * Update the year and dim()s in R/data.R
|
||||
# * Rerun data-raw/reproduction_of_rsi_translation.R
|
||||
# * Run unit tests
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@@ -17,23 +17,27 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="https://msberends.gitlab.io/AMR/apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="https://msberends.gitlab.io/AMR/bootstrap-toc.css">
|
||||
<script src="https://msberends.gitlab.io/AMR/bootstrap-toc.js"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
|
||||
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<!-- pkgdown -->
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<body>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
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</span>
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</div>
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@@ -477,6 +480,12 @@ END OF TERMS AND CONDITIONS
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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@@ -487,7 +496,7 @@ END OF TERMS AND CONDITIONS
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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@@ -12,15 +12,14 @@
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<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
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<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
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<script src="../extra.js"></script><meta property="og:title" content="How to conduct AMR analysis">
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<meta name="twitter:card" content="summary">
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<meta property="og:description" content="AMR">
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<meta property="og:image" content="/logo.svg">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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@@ -39,7 +38,7 @@
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||||
</button>
|
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<span class="navbar-brand">
|
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -75,6 +74,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -179,7 +185,7 @@
|
||||
<h1>How to conduct AMR analysis</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">23 February 2020</h4>
|
||||
<h4 class="date">17 March 2020</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>AMR.Rmd</code></div>
|
||||
@@ -188,7 +194,7 @@
|
||||
|
||||
|
||||
|
||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 23 February 2020.</p>
|
||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 17 March 2020.</p>
|
||||
<div id="introduction" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#introduction" class="anchor"></a>Introduction</h1>
|
||||
@@ -219,21 +225,21 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2020-02-23</td>
|
||||
<td align="center">2020-03-17</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2020-02-23</td>
|
||||
<td align="center">2020-03-17</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2020-02-23</td>
|
||||
<td align="center">2020-03-17</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@@ -294,24 +300,24 @@
|
||||
<div id="put-everything-together" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#put-everything-together" class="anchor"></a>Put everything together</h2>
|
||||
<p>Using the <code><a href="https://dplyr.tidyverse.org/reference/sample.html">sample()</a></code> function, we can randomly select items from all objects we defined earlier. To let our fake data reflect reality a bit, we will also approximately define the probabilities of bacteria and the antibiotic results with the <code>prob</code> parameter.</p>
|
||||
<p>Using the <code><a href="https://rdrr.io/r/base/sample.html">sample()</a></code> function, we can randomly select items from all objects we defined earlier. To let our fake data reflect reality a bit, we will also approximately define the probabilities of bacteria and the antibiotic results with the <code>prob</code> parameter.</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>sample_size <-<span class="st"> </span><span class="dv">20000</span></span>
|
||||
<span id="cb7-2"><a href="#cb7-2"></a>data <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">date =</span> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(dates, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>),</span>
|
||||
<span id="cb7-3"><a href="#cb7-3"></a> <span class="dt">patient_id =</span> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(patients, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>),</span>
|
||||
<span id="cb7-4"><a href="#cb7-4"></a> <span class="dt">hospital =</span> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(hospitals, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-2"><a href="#cb7-2"></a>data <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">date =</span> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(dates, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>),</span>
|
||||
<span id="cb7-3"><a href="#cb7-3"></a> <span class="dt">patient_id =</span> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(patients, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>),</span>
|
||||
<span id="cb7-4"><a href="#cb7-4"></a> <span class="dt">hospital =</span> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(hospitals, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-5"><a href="#cb7-5"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.30</span>, <span class="fl">0.35</span>, <span class="fl">0.15</span>, <span class="fl">0.20</span>)),</span>
|
||||
<span id="cb7-6"><a href="#cb7-6"></a> <span class="dt">bacteria =</span> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(bacteria, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-6"><a href="#cb7-6"></a> <span class="dt">bacteria =</span> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(bacteria, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-7"><a href="#cb7-7"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.50</span>, <span class="fl">0.25</span>, <span class="fl">0.15</span>, <span class="fl">0.10</span>)),</span>
|
||||
<span id="cb7-8"><a href="#cb7-8"></a> <span class="dt">AMX =</span> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(ab_interpretations, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-8"><a href="#cb7-8"></a> <span class="dt">AMX =</span> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(ab_interpretations, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-9"><a href="#cb7-9"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.60</span>, <span class="fl">0.05</span>, <span class="fl">0.35</span>)),</span>
|
||||
<span id="cb7-10"><a href="#cb7-10"></a> <span class="dt">AMC =</span> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(ab_interpretations, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-10"><a href="#cb7-10"></a> <span class="dt">AMC =</span> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(ab_interpretations, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-11"><a href="#cb7-11"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.75</span>, <span class="fl">0.10</span>, <span class="fl">0.15</span>)),</span>
|
||||
<span id="cb7-12"><a href="#cb7-12"></a> <span class="dt">CIP =</span> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(ab_interpretations, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-12"><a href="#cb7-12"></a> <span class="dt">CIP =</span> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(ab_interpretations, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-13"><a href="#cb7-13"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.80</span>, <span class="fl">0.00</span>, <span class="fl">0.20</span>)),</span>
|
||||
<span id="cb7-14"><a href="#cb7-14"></a> <span class="dt">GEN =</span> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(ab_interpretations, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-14"><a href="#cb7-14"></a> <span class="dt">GEN =</span> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(ab_interpretations, <span class="dt">size =</span> sample_size, <span class="dt">replace =</span> <span class="ot">TRUE</span>,</span>
|
||||
<span id="cb7-15"><a href="#cb7-15"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.92</span>, <span class="fl">0.00</span>, <span class="fl">0.08</span>)))</span></code></pre></div>
|
||||
<p>Using the <code><a href="https://dplyr.tidyverse.org/reference/join.html">left_join()</a></code> function from the <code>dplyr</code> package, we can ‘map’ the gender to the patient ID using the <code>patients_table</code> object we created earlier:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>data <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/join.html">left_join</a></span>(patients_table)</span></code></pre></div>
|
||||
<p>Using the <code><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html">left_join()</a></code> function from the <code>dplyr</code> package, we can ‘map’ the gender to the patient ID using the <code>patients_table</code> object we created earlier:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>data <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html">left_join</a></span>(patients_table)</span></code></pre></div>
|
||||
<p>The resulting data set contains 20,000 blood culture isolates. With the <code><a href="https://rdrr.io/r/utils/head.html">head()</a></code> function we can preview the first 6 rows of this data set:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(data)</span></code></pre></div>
|
||||
<table class="table">
|
||||
@@ -328,9 +334,20 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-10-31</td>
|
||||
<td align="center">B4</td>
|
||||
<td align="center">2013-12-05</td>
|
||||
<td align="center">H6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2015-04-13</td>
|
||||
<td align="center">I3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -338,60 +355,49 @@
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-02-24</td>
|
||||
<td align="center">E10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-11-04</td>
|
||||
<td align="center">G1</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-10-08</td>
|
||||
<td align="center">V4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">2011-10-12</td>
|
||||
<td align="center">Z1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-02-16</td>
|
||||
<td align="center">K6</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<tr class="even">
|
||||
<td align="center">2011-11-05</td>
|
||||
<td align="center">D1</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-05-28</td>
|
||||
<td align="center">N6</td>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-12-28</td>
|
||||
<td align="center">B7</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-07-25</td>
|
||||
<td align="center">F8</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -423,16 +429,16 @@ Unique: 2</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">M</td>
|
||||
<td align="right">10,361</td>
|
||||
<td align="right">51.81%</td>
|
||||
<td align="right">10,361</td>
|
||||
<td align="right">51.81%</td>
|
||||
<td align="right">10,489</td>
|
||||
<td align="right">52.45%</td>
|
||||
<td align="right">10,489</td>
|
||||
<td align="right">52.45%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,639</td>
|
||||
<td align="right">48.20%</td>
|
||||
<td align="right">9,511</td>
|
||||
<td align="right">47.56%</td>
|
||||
<td align="right">20,000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@@ -472,7 +478,7 @@ Unique: 2</p>
|
||||
<span id="cb15-3"><a href="#cb15-3"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></span>
|
||||
<span id="cb15-4"><a href="#cb15-4"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></span>
|
||||
<span id="cb15-5"><a href="#cb15-5"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></span></code></pre></div>
|
||||
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1"></a>data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb16-2"><a href="#cb16-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</span></code></pre></div>
|
||||
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
|
||||
@@ -482,7 +488,7 @@ Unique: 2</p>
|
||||
<div id="first-weighted-isolates" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
|
||||
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient Q2, sorted on date:</p>
|
||||
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient A2, sorted on date:</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">isolate</th>
|
||||
@@ -498,10 +504,10 @@ Unique: 2</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-02-26</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-01-14</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -509,32 +515,32 @@ Unique: 2</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-03-25</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-06-29</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-05-23</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-07-21</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-05-24</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-08-18</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -542,10 +548,10 @@ Unique: 2</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-09-08</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-11-16</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -553,32 +559,32 @@ Unique: 2</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2011-03-19</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2011-01-29</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2011-04-02</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2011-03-30</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2011-04-05</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2011-04-08</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@@ -586,19 +592,19 @@ Unique: 2</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-11-13</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2011-05-09</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-11-28</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2011-07-16</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -634,10 +640,10 @@ Unique: 2</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-02-26</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-01-14</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -646,23 +652,23 @@ Unique: 2</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-03-25</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-06-29</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-05-23</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-07-21</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
@@ -670,44 +676,68 @@ Unique: 2</p>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-05-24</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-08-18</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-09-08</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2010-11-16</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2011-03-19</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2011-01-29</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2011-04-02</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2011-03-30</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2011-04-08</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-05-09</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -717,21 +747,9 @@ Unique: 2</p>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2011-04-05</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-11-13</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-07-16</td>
|
||||
<td align="center">A2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -740,25 +758,13 @@ Unique: 2</p>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-11-28</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Instead of 2, now 7 isolates are flagged. In total, 74.8% of all isolates are marked ‘first weighted’ - 46.4% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
|
||||
<p>Instead of 2, now 6 isolates are flagged. In total, 75.8% of all isolates are marked ‘first weighted’ - 47.3% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
|
||||
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1"></a>data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb19-2"><a href="#cb19-2"></a><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</span></code></pre></div>
|
||||
<p>So we end up with 14,960 isolates for analysis.</p>
|
||||
<p>So we end up with 15,159 isolates for analysis.</p>
|
||||
<p>We can remove unneeded columns:</p>
|
||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a>data_1st <-<span class="st"> </span>data_1st <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb20-2"><a href="#cb20-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(first, keyab))</span></code></pre></div>
|
||||
@@ -782,9 +788,24 @@ Unique: 2</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-10-31</td>
|
||||
<td align="center">B4</td>
|
||||
<td align="center">2013-12-05</td>
|
||||
<td align="center">H6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2015-04-13</td>
|
||||
<td align="center">I3</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@@ -796,76 +817,61 @@ Unique: 2</p>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-02-24</td>
|
||||
<td align="center">E10</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-11-04</td>
|
||||
<td align="center">G1</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-10-08</td>
|
||||
<td align="center">V4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">2011-10-12</td>
|
||||
<td align="center">Z1</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-11-05</td>
|
||||
<td align="center">D1</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-02-16</td>
|
||||
<td align="center">K6</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2014-05-28</td>
|
||||
<td align="center">N6</td>
|
||||
<td align="center">2017-12-28</td>
|
||||
<td align="center">B7</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-07-25</td>
|
||||
<td align="center">F8</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
@@ -890,8 +896,8 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1"></a>data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus, species)</span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 14,960<br>
|
||||
Available: 14,960 (100%, NA: 0 = 0%)<br>
|
||||
Length: 15,159<br>
|
||||
Available: 15,159 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@@ -908,33 +914,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">7,397</td>
|
||||
<td align="right">49.45%</td>
|
||||
<td align="right">7,397</td>
|
||||
<td align="right">49.45%</td>
|
||||
<td align="right">7,543</td>
|
||||
<td align="right">49.76%</td>
|
||||
<td align="right">7,543</td>
|
||||
<td align="right">49.76%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">3,685</td>
|
||||
<td align="right">24.63%</td>
|
||||
<td align="right">11,082</td>
|
||||
<td align="right">74.08%</td>
|
||||
<td align="right">3,783</td>
|
||||
<td align="right">24.96%</td>
|
||||
<td align="right">11,326</td>
|
||||
<td align="right">74.71%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,361</td>
|
||||
<td align="right">15.78%</td>
|
||||
<td align="right">13,443</td>
|
||||
<td align="right">89.86%</td>
|
||||
<td align="right">2,316</td>
|
||||
<td align="right">15.28%</td>
|
||||
<td align="right">13,642</td>
|
||||
<td align="right">89.99%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,517</td>
|
||||
<td align="right">10.14%</td>
|
||||
<td align="right">14,960</td>
|
||||
<td align="right">10.01%</td>
|
||||
<td align="right">15,159</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@@ -946,7 +952,7 @@ Longest: 24</p>
|
||||
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
|
||||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
||||
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1"></a>data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX)</span>
|
||||
<span id="cb24-2"><a href="#cb24-2"></a><span class="co"># [1] 0.4635695</span></span></code></pre></div>
|
||||
<span id="cb24-2"><a href="#cb24-2"></a><span class="co"># [1] 0.4593311</span></span></code></pre></div>
|
||||
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a>data_1st <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb25-2"><a href="#cb25-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%>%</span><span class="st"> </span></span>
|
||||
@@ -959,19 +965,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.4490022</td>
|
||||
<td align="center">0.4554126</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.4746786</td>
|
||||
<td align="center">0.4619586</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.4505104</td>
|
||||
<td align="center">0.4566170</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.4760039</td>
|
||||
<td align="center">0.4625695</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -989,23 +995,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.4490022</td>
|
||||
<td align="center">4510</td>
|
||||
<td align="center">0.4554126</td>
|
||||
<td align="center">4508</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.4746786</td>
|
||||
<td align="center">5134</td>
|
||||
<td align="center">0.4619586</td>
|
||||
<td align="center">5310</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.4505104</td>
|
||||
<td align="center">2253</td>
|
||||
<td align="center">0.4566170</td>
|
||||
<td align="center">2282</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.4760039</td>
|
||||
<td align="center">3063</td>
|
||||
<td align="center">0.4625695</td>
|
||||
<td align="center">3059</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1025,27 +1031,27 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.9251048</td>
|
||||
<td align="center">0.8952278</td>
|
||||
<td align="center">0.9928349</td>
|
||||
<td align="center">0.9241681</td>
|
||||
<td align="center">0.8932785</td>
|
||||
<td align="center">0.9935039</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.9169413</td>
|
||||
<td align="center">0.9083718</td>
|
||||
<td align="center">0.9947264</td>
|
||||
<td align="center">0.9215557</td>
|
||||
<td align="center">0.9004614</td>
|
||||
<td align="center">0.9953856</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.9305292</td>
|
||||
<td align="center">0.9158752</td>
|
||||
<td align="center">0.9937585</td>
|
||||
<td align="center">0.9188475</td>
|
||||
<td align="center">0.9254560</td>
|
||||
<td align="center">0.9939202</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.6027107</td>
|
||||
<td align="center">0.6178756</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.6027107</td>
|
||||
<td align="center">0.6178756</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@@ -1158,7 +1164,7 @@ Longest: 24</p>
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@@ -1206,7 +1212,7 @@ Longest: 24</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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@@ -186,7 +185,7 @@
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<h1>How to apply EUCAST rules</h1>
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<h4 class="author">Matthijs S. Berends</h4>
|
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|
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<h4 class="date">14 March 2020</h4>
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<h4 class="date">17 March 2020</h4>
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<div class="hidden name"><code>EUCAST.Rmd</code></div>
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@@ -368,7 +367,7 @@
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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@@ -75,6 +74,13 @@
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Predict antimicrobial resistance
|
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Conduct principal component analysis for AMR
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@@ -179,7 +185,7 @@
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<h1>How to determine multi-drug resistance (MDR)</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">23 February 2020</h4>
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<h4 class="date">17 March 2020</h4>
|
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<div class="hidden name"><code>MDR.Rmd</code></div>
|
||||
@@ -274,7 +280,7 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="co"># a helper function to get a random vector with values S, I and R</span></span>
|
||||
<span id="cb3-2"><a href="#cb3-2"></a><span class="co"># with the probabilities 50% - 10% - 40%</span></span>
|
||||
<span id="cb3-3"><a href="#cb3-3"></a>sample_rsi <-<span class="st"> </span><span class="cf">function</span>() {</span>
|
||||
<span id="cb3-4"><a href="#cb3-4"></a> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</span>
|
||||
<span id="cb3-4"><a href="#cb3-4"></a> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</span>
|
||||
<span id="cb3-5"><a href="#cb3-5"></a> <span class="dt">size =</span> <span class="dv">5000</span>,</span>
|
||||
<span id="cb3-6"><a href="#cb3-6"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</span>
|
||||
<span id="cb3-7"><a href="#cb3-7"></a> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</span>
|
||||
@@ -298,19 +304,19 @@ Unique: 2</p>
|
||||
<p>The data set now looks like this:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</span>
|
||||
<span id="cb5-2"><a href="#cb5-2"></a><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span id="cb5-3"><a href="#cb5-3"></a><span class="co"># 1 S R S R R I</span></span>
|
||||
<span id="cb5-4"><a href="#cb5-4"></a><span class="co"># 2 S R S S R S</span></span>
|
||||
<span id="cb5-5"><a href="#cb5-5"></a><span class="co"># 3 I S R R S R</span></span>
|
||||
<span id="cb5-6"><a href="#cb5-6"></a><span class="co"># 4 S S S S S R</span></span>
|
||||
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># 5 S S S I R R</span></span>
|
||||
<span id="cb5-8"><a href="#cb5-8"></a><span class="co"># 6 I I R R S S</span></span>
|
||||
<span id="cb5-3"><a href="#cb5-3"></a><span class="co"># 1 S R R I R R</span></span>
|
||||
<span id="cb5-4"><a href="#cb5-4"></a><span class="co"># 2 I R R R S R</span></span>
|
||||
<span id="cb5-5"><a href="#cb5-5"></a><span class="co"># 3 R R R S R S</span></span>
|
||||
<span id="cb5-6"><a href="#cb5-6"></a><span class="co"># 4 S S R R R S</span></span>
|
||||
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># 5 S R S R S S</span></span>
|
||||
<span id="cb5-8"><a href="#cb5-8"></a><span class="co"># 6 R S S S R S</span></span>
|
||||
<span id="cb5-9"><a href="#cb5-9"></a><span class="co"># kanamycin</span></span>
|
||||
<span id="cb5-10"><a href="#cb5-10"></a><span class="co"># 1 S</span></span>
|
||||
<span id="cb5-11"><a href="#cb5-11"></a><span class="co"># 2 I</span></span>
|
||||
<span id="cb5-11"><a href="#cb5-11"></a><span class="co"># 2 S</span></span>
|
||||
<span id="cb5-12"><a href="#cb5-12"></a><span class="co"># 3 R</span></span>
|
||||
<span id="cb5-13"><a href="#cb5-13"></a><span class="co"># 4 R</span></span>
|
||||
<span id="cb5-14"><a href="#cb5-14"></a><span class="co"># 5 R</span></span>
|
||||
<span id="cb5-15"><a href="#cb5-15"></a><span class="co"># 6 I</span></span></code></pre></div>
|
||||
<span id="cb5-15"><a href="#cb5-15"></a><span class="co"># 6 R</span></span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a><span class="kw"><a href="../reference/mdro.html">mdro</a></span>(my_TB_data, <span class="dt">guideline =</span> <span class="st">"TB"</span>)</span></code></pre></div>
|
||||
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
|
||||
@@ -339,40 +345,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3274</td>
|
||||
<td align="right">65.48%</td>
|
||||
<td align="right">3274</td>
|
||||
<td align="right">65.48%</td>
|
||||
<td align="right">3312</td>
|
||||
<td align="right">66.24%</td>
|
||||
<td align="right">3312</td>
|
||||
<td align="right">66.24%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">651</td>
|
||||
<td align="right">13.02%</td>
|
||||
<td align="right">3925</td>
|
||||
<td align="right">78.50%</td>
|
||||
<td align="right">634</td>
|
||||
<td align="right">12.68%</td>
|
||||
<td align="right">3946</td>
|
||||
<td align="right">78.92%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">612</td>
|
||||
<td align="right">12.24%</td>
|
||||
<td align="right">4537</td>
|
||||
<td align="right">90.74%</td>
|
||||
<td align="right">554</td>
|
||||
<td align="right">11.08%</td>
|
||||
<td align="right">4500</td>
|
||||
<td align="right">90.00%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">288</td>
|
||||
<td align="right">5.76%</td>
|
||||
<td align="right">4825</td>
|
||||
<td align="right">96.50%</td>
|
||||
<td align="right">291</td>
|
||||
<td align="right">5.82%</td>
|
||||
<td align="right">4791</td>
|
||||
<td align="right">95.82%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">175</td>
|
||||
<td align="right">3.50%</td>
|
||||
<td align="right">209</td>
|
||||
<td align="right">4.18%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@@ -381,7 +387,7 @@ Unique: 5</p>
|
||||
</div>
|
||||
</div>
|
||||
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||||
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|
||||
|
||||
@@ -394,7 +400,7 @@ Unique: 5</p>
|
||||
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|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -12,21 +12,21 @@
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
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@@ -183,12 +183,12 @@
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</header><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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||||
<h1>How to conduct principal component analysis (PCA) for AMR</h1>
|
||||
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">14 March 2020</h4>
|
||||
|
||||
<h4 class="date">13 April 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>PCA.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
@@ -204,124 +204,117 @@
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#transforming" class="anchor"></a>Transforming</h1>
|
||||
<p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(AMR)</span>
|
||||
<span id="cb1-2"><a href="#cb1-2"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</span>
|
||||
<span id="cb1-3"><a href="#cb1-3"></a><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">glimpse</a></span>(example_isolates)</span>
|
||||
<span id="cb1-4"><a href="#cb1-4"></a><span class="co"># Observations: 2,000</span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5"></a><span class="co"># Variables: 49</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># $ date <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002…</span></span>
|
||||
<span id="cb1-7"><a href="#cb1-7"></a><span class="co"># $ hospital_id <fct> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B,…</span></span>
|
||||
<span id="cb1-8"><a href="#cb1-8"></a><span class="co"># $ ward_icu <lgl> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, T…</span></span>
|
||||
<span id="cb1-9"><a href="#cb1-9"></a><span class="co"># $ ward_clinical <lgl> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, F…</span></span>
|
||||
<span id="cb1-10"><a href="#cb1-10"></a><span class="co"># $ ward_outpatient <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALS…</span></span>
|
||||
<span id="cb1-11"><a href="#cb1-11"></a><span class="co"># $ age <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 7…</span></span>
|
||||
<span id="cb1-12"><a href="#cb1-12"></a><span class="co"># $ gender <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…</span></span>
|
||||
<span id="cb1-13"><a href="#cb1-13"></a><span class="co"># $ patient_id <chr> "A77334", "A77334", "067927", "067927", "067927", "06…</span></span>
|
||||
<span id="cb1-14"><a href="#cb1-14"></a><span class="co"># $ mo <mo> B_ESCHR_COLI, B_ESCHR_COLI, B_STPHY_EPDR, B_STPHY_EPDR…</span></span>
|
||||
<span id="cb1-15"><a href="#cb1-15"></a><span class="co"># $ PEN <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span></span>
|
||||
<span id="cb1-16"><a href="#cb1-16"></a><span class="co"># $ OXA <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-17"><a href="#cb1-17"></a><span class="co"># $ FLC <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span></span>
|
||||
<span id="cb1-18"><a href="#cb1-18"></a><span class="co"># $ AMX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-19"><a href="#cb1-19"></a><span class="co"># $ AMC <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span></span>
|
||||
<span id="cb1-20"><a href="#cb1-20"></a><span class="co"># $ AMP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-21"><a href="#cb1-21"></a><span class="co"># $ TZP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-22"><a href="#cb1-22"></a><span class="co"># $ CZO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-23"><a href="#cb1-23"></a><span class="co"># $ FEP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-24"><a href="#cb1-24"></a><span class="co"># $ CXM <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span></span>
|
||||
<span id="cb1-25"><a href="#cb1-25"></a><span class="co"># $ FOX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-26"><a href="#cb1-26"></a><span class="co"># $ CTX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span></span>
|
||||
<span id="cb1-27"><a href="#cb1-27"></a><span class="co"># $ CAZ <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span></span>
|
||||
<span id="cb1-28"><a href="#cb1-28"></a><span class="co"># $ CRO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span></span>
|
||||
<span id="cb1-29"><a href="#cb1-29"></a><span class="co"># $ GEN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-30"><a href="#cb1-30"></a><span class="co"># $ TOB <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span></span>
|
||||
<span id="cb1-31"><a href="#cb1-31"></a><span class="co"># $ AMK <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-32"><a href="#cb1-32"></a><span class="co"># $ KAN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-33"><a href="#cb1-33"></a><span class="co"># $ TMP <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span></span>
|
||||
<span id="cb1-34"><a href="#cb1-34"></a><span class="co"># $ SXT <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span></span>
|
||||
<span id="cb1-35"><a href="#cb1-35"></a><span class="co"># $ NIT <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-36"><a href="#cb1-36"></a><span class="co"># $ FOS <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-37"><a href="#cb1-37"></a><span class="co"># $ LNZ <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></span>
|
||||
<span id="cb1-38"><a href="#cb1-38"></a><span class="co"># $ CIP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span></span>
|
||||
<span id="cb1-39"><a href="#cb1-39"></a><span class="co"># $ MFX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-40"><a href="#cb1-40"></a><span class="co"># $ VAN <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span></span>
|
||||
<span id="cb1-41"><a href="#cb1-41"></a><span class="co"># $ TEC <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></span>
|
||||
<span id="cb1-42"><a href="#cb1-42"></a><span class="co"># $ TCY <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span></span>
|
||||
<span id="cb1-43"><a href="#cb1-43"></a><span class="co"># $ TGC <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-44"><a href="#cb1-44"></a><span class="co"># $ DOX <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span></span>
|
||||
<span id="cb1-45"><a href="#cb1-45"></a><span class="co"># $ ERY <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span></span>
|
||||
<span id="cb1-46"><a href="#cb1-46"></a><span class="co"># $ CLI <rsi> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span id="cb1-47"><a href="#cb1-47"></a><span class="co"># $ AZM <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span></span>
|
||||
<span id="cb1-48"><a href="#cb1-48"></a><span class="co"># $ IPM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span></span>
|
||||
<span id="cb1-49"><a href="#cb1-49"></a><span class="co"># $ MEM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-50"><a href="#cb1-50"></a><span class="co"># $ MTR <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-51"><a href="#cb1-51"></a><span class="co"># $ CHL <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-52"><a href="#cb1-52"></a><span class="co"># $ COL <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span></span>
|
||||
<span id="cb1-53"><a href="#cb1-53"></a><span class="co"># $ MUP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span></span>
|
||||
<span id="cb1-54"><a href="#cb1-54"></a><span class="co"># $ RIF <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/reexports.html">glimpse</a></span>(<span class="no">example_isolates</span>)
|
||||
<span class="co"># Rows: 2,000</span>
|
||||
<span class="co"># Columns: 49</span>
|
||||
<span class="co"># $ date <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002…</span>
|
||||
<span class="co"># $ hospital_id <fct> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B,…</span>
|
||||
<span class="co"># $ ward_icu <lgl> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, T…</span>
|
||||
<span class="co"># $ ward_clinical <lgl> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, F…</span>
|
||||
<span class="co"># $ ward_outpatient <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALS…</span>
|
||||
<span class="co"># $ age <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 7…</span>
|
||||
<span class="co"># $ gender <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…</span>
|
||||
<span class="co"># $ patient_id <chr> "A77334", "A77334", "067927", "067927", "067927", "06…</span>
|
||||
<span class="co"># $ mo <mo> B_ESCHR_COLI, B_ESCHR_COLI, B_STPHY_EPDR, B_STPHY_EPDR…</span>
|
||||
<span class="co"># $ PEN <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ OXA <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FLC <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
|
||||
<span class="co"># $ AMX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ AMC <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
|
||||
<span class="co"># $ AMP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TZP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CZO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FEP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CXM <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
|
||||
<span class="co"># $ FOX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CTX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ CAZ <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
|
||||
<span class="co"># $ CRO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ GEN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TOB <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
|
||||
<span class="co"># $ AMK <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ KAN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ TMP <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
|
||||
<span class="co"># $ SXT <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
|
||||
<span class="co"># $ NIT <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ FOS <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ LNZ <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
|
||||
<span class="co"># $ CIP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
|
||||
<span class="co"># $ MFX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ VAN <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ TEC <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
|
||||
<span class="co"># $ TCY <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
|
||||
<span class="co"># $ TGC <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ DOX <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
|
||||
<span class="co"># $ ERY <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ CLI <rsi> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ AZM <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
|
||||
<span class="co"># $ IPM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
|
||||
<span class="co"># $ MEM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ MTR <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ CHL <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ COL <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
|
||||
<span class="co"># $ MUP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
|
||||
<span class="co"># $ RIF <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span></pre></body></html></div>
|
||||
<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>resistance_data <-<span class="st"> </span>example_isolates <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="dt">order =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(mo), <span class="co"># group on anything, like order</span></span>
|
||||
<span id="cb2-3"><a href="#cb2-3"></a> <span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span><span class="st"> </span><span class="co"># and genus as we do here</span></span>
|
||||
<span id="cb2-4"><a href="#cb2-4"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span>(is.rsi, resistance) <span class="op">%>%</span><span class="st"> </span><span class="co"># then get resistance of all drugs</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(order, genus, AMC, CXM, CTX, </span>
|
||||
<span id="cb2-6"><a href="#cb2-6"></a> CAZ, GEN, TOB, TMP, SXT) <span class="co"># and select only relevant columns</span></span>
|
||||
<span id="cb2-7"><a href="#cb2-7"></a></span>
|
||||
<span id="cb2-8"><a href="#cb2-8"></a><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(resistance_data)</span>
|
||||
<span id="cb2-9"><a href="#cb2-9"></a><span class="co"># # A tibble: 6 x 10</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10"></a><span class="co"># # Groups: order [2]</span></span>
|
||||
<span id="cb2-11"><a href="#cb2-11"></a><span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span></span>
|
||||
<span id="cb2-12"><a href="#cb2-12"></a><span class="co"># <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
|
||||
<span id="cb2-13"><a href="#cb2-13"></a><span class="co"># 1 (unknown orde… Micrococcoides NA NA NA NA NA NA NA NA</span></span>
|
||||
<span id="cb2-14"><a href="#cb2-14"></a><span class="co"># 2 Actinomycetal… Actinomyces NA NA NA NA NA NA NA NA</span></span>
|
||||
<span id="cb2-15"><a href="#cb2-15"></a><span class="co"># 3 Actinomycetal… Corynebacterium NA NA NA NA NA NA NA NA</span></span>
|
||||
<span id="cb2-16"><a href="#cb2-16"></a><span class="co"># 4 Actinomycetal… Dermabacter NA NA NA NA NA NA NA NA</span></span>
|
||||
<span id="cb2-17"><a href="#cb2-17"></a><span class="co"># 5 Actinomycetal… Micrococcus NA NA NA NA NA NA NA NA</span></span>
|
||||
<span id="cb2-18"><a href="#cb2-18"></a><span class="co"># 6 Actinomycetal… Propionibacter… NA NA NA NA NA NA NA NA</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">resistance_data</span> <span class="kw"><-</span> <span class="no">example_isolates</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">order</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">mo</span>), <span class="co"># group on anything, like order</span>
|
||||
<span class="kw">genus</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>)) <span class="kw">%>%</span> <span class="co"># and genus as we do here</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span>(<span class="no">is.rsi</span>, <span class="no">resistance</span>) <span class="kw">%>%</span> <span class="co"># then get resistance of all drugs</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">order</span>, <span class="no">genus</span>, <span class="no">AMC</span>, <span class="no">CXM</span>, <span class="no">CTX</span>,
|
||||
<span class="no">CAZ</span>, <span class="no">GEN</span>, <span class="no">TOB</span>, <span class="no">TMP</span>, <span class="no">SXT</span>) <span class="co"># and select only relevant columns</span>
|
||||
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">resistance_data</span>)
|
||||
<span class="co"># # A tibble: 6 x 10</span>
|
||||
<span class="co"># # Groups: order [2]</span>
|
||||
<span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span>
|
||||
<span class="co"># <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl></span>
|
||||
<span class="co"># 1 (unknown orde… Micrococcoides NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 2 Actinomycetal… Actinomyces NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 3 Actinomycetal… Corynebacterium NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 4 Actinomycetal… Dermabacter NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 5 Actinomycetal… Micrococcus NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 6 Actinomycetal… Propionibacter… NA NA NA NA NA NA NA NA</span></pre></body></html></div>
|
||||
</div>
|
||||
<div id="perform-principal-component-analysis" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#perform-principal-component-analysis" class="anchor"></a>Perform principal component analysis</h1>
|
||||
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>pca_result <-<span class="st"> </span><span class="kw"><a href="../reference/pca.html">pca</a></span>(resistance_data)</span>
|
||||
<span id="cb3-2"><a href="#cb3-2"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: Columns selected for PCA: AMC/CXM/CTX/CAZ/GEN/TOB/TMP/SXT.</span></span>
|
||||
<span id="cb3-3"><a href="#cb3-3"></a><span class="co"># Total observations available: 7.</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">pca_result</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span>(<span class="no">resistance_data</span>)
|
||||
<span class="co"># NOTE: Columns selected for PCA: AMC/CXM/CTX/CAZ/GEN/TOB/TMP/SXT.</span>
|
||||
<span class="co"># Total observations available: 7.</span></pre></body></html></div>
|
||||
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(pca_result)</span>
|
||||
<span id="cb4-2"><a href="#cb4-2"></a><span class="co"># Importance of components:</span></span>
|
||||
<span id="cb4-3"><a href="#cb4-3"></a><span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
|
||||
<span id="cb4-4"><a href="#cb4-4"></a><span class="co"># Standard deviation 2.1580 1.6783 0.61282 0.33017 0.20150 0.03190 2.123e-16</span></span>
|
||||
<span id="cb4-5"><a href="#cb4-5"></a><span class="co"># Proportion of Variance 0.5821 0.3521 0.04694 0.01363 0.00508 0.00013 0.000e+00</span></span>
|
||||
<span id="cb4-6"><a href="#cb4-6"></a><span class="co"># Cumulative Proportion 0.5821 0.9342 0.98117 0.99480 0.99987 1.00000 1.000e+00</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">pca_result</span>)
|
||||
<span class="co"># Importance of components:</span>
|
||||
<span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span>
|
||||
<span class="co"># Standard deviation 2.1580 1.6783 0.61282 0.33017 0.20150 0.03190 2.123e-16</span>
|
||||
<span class="co"># Proportion of Variance 0.5821 0.3521 0.04694 0.01363 0.00508 0.00013 0.000e+00</span>
|
||||
<span class="co"># Cumulative Proportion 0.5821 0.9342 0.98117 0.99480 0.99987 1.00000 1.000e+00</span></pre></body></html></div>
|
||||
<p>Good news. The first two components explain a total of 93.4% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
|
||||
</div>
|
||||
<div id="plotting-the-results" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#plotting-the-results" class="anchor"></a>Plotting the results</h1>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span>(pca_result)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span>(<span class="no">pca_result</span>)</pre></body></html></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
|
||||
<p>But we can’t see the explanation of the points. Perhaps this works better with the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a><span class="kw"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(pca_result)</span></code></pre></div>
|
||||
<p>But we can’t see the explanation of the points. Perhaps this works better with our new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
|
||||
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>)</pre></body></html></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-6-1.png" width="750"></p>
|
||||
<p>You can also print an ellipse per group, and edit the appearance:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="kw"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(pca_result, <span class="dt">ellipse =</span> <span class="ot">TRUE</span>) <span class="op">+</span></span>
|
||||
<span id="cb7-2"><a href="#cb7-2"></a><span class="st"> </span>ggplot2<span class="op">::</span><span class="kw"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="dt">title =</span> <span class="st">"An AMR/PCA biplot!"</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><html><body><pre class="r">
|
||||
<span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span>(<span class="no">pca_result</span>, <span class="kw">ellipse</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +
|
||||
<span class="kw pkg">ggplot2</span><span class="kw ns">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span>(<span class="kw">title</span> <span class="kw">=</span> <span class="st">"An AMR/PCA biplot!"</span>)</pre></body></html></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
|
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|
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</div>
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<div id="tocnav">
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<h2 class="hasAnchor">
|
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<a href="#tocnav" class="anchor"></a>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
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<li><a href="#introduction">Introduction</a></li>
|
||||
<li><a href="#transforming">Transforming</a></li>
|
||||
<li><a href="#perform-principal-component-analysis">Perform principal component analysis</a></li>
|
||||
<li><a href="#plotting-the-results">Plotting the results</a></li>
|
||||
</ul>
|
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<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
|
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</nav>
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@@ -332,7 +325,7 @@
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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@@ -39,7 +38,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
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</span>
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</div>
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@@ -75,6 +74,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
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</li>
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<li>
|
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<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
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Conduct principal component analysis for AMR
|
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</a>
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</li>
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<li>
|
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<a href="../articles/MDR.html">
|
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<span class="fa fa-skull-crossbones"></span>
|
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@@ -179,7 +185,7 @@
|
||||
<h1>How to import data from SPSS / SAS / Stata</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">23 February 2020</h4>
|
||||
<h4 class="date">17 March 2020</h4>
|
||||
|
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|
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<div class="hidden name"><code>SPSS.Rmd</code></div>
|
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@@ -377,7 +383,7 @@
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@@ -399,7 +405,7 @@
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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</span>
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@@ -75,6 +74,13 @@
|
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Predict antimicrobial resistance
|
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<a href="../articles/PCA.html">
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Conduct principal component analysis for AMR
|
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<a href="../articles/MDR.html">
|
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<span class="fa fa-skull-crossbones"></span>
|
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@@ -179,7 +185,7 @@
|
||||
<h1>How to work with WHONET data</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">23 February 2020</h4>
|
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<h4 class="date">17 March 2020</h4>
|
||||
|
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|
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<div class="hidden name"><code>WHONET.Rmd</code></div>
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@@ -379,7 +385,7 @@ Unique: 3</p>
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@@ -392,7 +398,7 @@ Unique: 3</p>
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||||
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||||
<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
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||||
<script src="../extra.js"></script><meta property="og:title" content="Benchmarks">
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||||
<meta property="og:description" content="">
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||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png">
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<meta name="twitter:card" content="summary">
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||||
<meta property="og:description" content="AMR">
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||||
<meta property="og:image" content="/logo.svg">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -186,7 +185,7 @@
|
||||
<h1>Benchmarks</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">14 March 2020</h4>
|
||||
<h4 class="date">17 March 2020</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>benchmarks.Rmd</code></div>
|
||||
@@ -220,21 +219,36 @@
|
||||
<span id="cb2-16"><a href="#cb2-16"></a> <span class="dt">times =</span> <span class="dv">10</span>)</span>
|
||||
<span id="cb2-17"><a href="#cb2-17"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</span>
|
||||
<span id="cb2-18"><a href="#cb2-18"></a><span class="co"># Unit: milliseconds</span></span>
|
||||
<span id="cb2-19"><a href="#cb2-19"></a><span class="co"># expr min lq mean median uq max neval</span></span>
|
||||
<span id="cb2-20"><a href="#cb2-20"></a><span class="co"># as.mo("sau") 8.9 9.3 9.6 9.6 9.9 10 10</span></span>
|
||||
<span id="cb2-21"><a href="#cb2-21"></a><span class="co"># as.mo("stau") 41.0 41.0 51.0 43.0 67.0 74 10</span></span>
|
||||
<span id="cb2-22"><a href="#cb2-22"></a><span class="co"># as.mo("STAU") 39.0 41.0 49.0 42.0 56.0 72 10</span></span>
|
||||
<span id="cb2-23"><a href="#cb2-23"></a><span class="co"># as.mo("staaur") 9.0 9.2 9.7 9.5 9.9 11 10</span></span>
|
||||
<span id="cb2-24"><a href="#cb2-24"></a><span class="co"># as.mo("STAAUR") 9.5 9.8 24.0 21.0 38.0 45 10</span></span>
|
||||
<span id="cb2-25"><a href="#cb2-25"></a><span class="co"># as.mo("S. aureus") 15.0 16.0 26.0 18.0 38.0 61 10</span></span>
|
||||
<span id="cb2-26"><a href="#cb2-26"></a><span class="co"># as.mo("S aureus") 15.0 15.0 17.0 16.0 17.0 21 10</span></span>
|
||||
<span id="cb2-27"><a href="#cb2-27"></a><span class="co"># as.mo("Staphylococcus aureus") 5.2 5.6 8.4 6.0 6.5 30 10</span></span>
|
||||
<span id="cb2-28"><a href="#cb2-28"></a><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 640.0 690.0 710.0 710.0 720.0 760 10</span></span>
|
||||
<span id="cb2-29"><a href="#cb2-29"></a><span class="co"># as.mo("Sthafilokkockus aaureuz") 350.0 360.0 420.0 400.0 490.0 510 10</span></span>
|
||||
<span id="cb2-30"><a href="#cb2-30"></a><span class="co"># as.mo("MRSA") 9.2 9.3 16.0 10.0 10.0 49 10</span></span>
|
||||
<span id="cb2-31"><a href="#cb2-31"></a><span class="co"># as.mo("VISA") 25.0 27.0 46.0 56.0 57.0 60 10</span></span>
|
||||
<span id="cb2-32"><a href="#cb2-32"></a><span class="co"># as.mo("VRSA") 26.0 27.0 39.0 28.0 32.0 120 10</span></span>
|
||||
<span id="cb2-33"><a href="#cb2-33"></a><span class="co"># as.mo(22242419) 120.0 140.0 170.0 140.0 150.0 410 10</span></span></code></pre></div>
|
||||
<span id="cb2-19"><a href="#cb2-19"></a><span class="co"># expr min lq mean median uq max</span></span>
|
||||
<span id="cb2-20"><a href="#cb2-20"></a><span class="co"># as.mo("sau") 9.1 9.5 12.0 9.8 10.0 34.0</span></span>
|
||||
<span id="cb2-21"><a href="#cb2-21"></a><span class="co"># as.mo("stau") 38.0 41.0 55.0 41.0 42.0 160.0</span></span>
|
||||
<span id="cb2-22"><a href="#cb2-22"></a><span class="co"># as.mo("STAU") 41.0 41.0 50.0 44.0 63.0 67.0</span></span>
|
||||
<span id="cb2-23"><a href="#cb2-23"></a><span class="co"># as.mo("staaur") 8.6 8.8 9.4 9.4 9.6 10.0</span></span>
|
||||
<span id="cb2-24"><a href="#cb2-24"></a><span class="co"># as.mo("STAAUR") 8.6 8.8 12.0 9.3 9.8 37.0</span></span>
|
||||
<span id="cb2-25"><a href="#cb2-25"></a><span class="co"># as.mo("S. aureus") 14.0 15.0 51.0 27.0 43.0 250.0</span></span>
|
||||
<span id="cb2-26"><a href="#cb2-26"></a><span class="co"># as.mo("S aureus") 14.0 15.0 16.0 15.0 16.0 18.0</span></span>
|
||||
<span id="cb2-27"><a href="#cb2-27"></a><span class="co"># as.mo("Staphylococcus aureus") 5.1 5.3 5.7 5.5 6.0 6.6</span></span>
|
||||
<span id="cb2-28"><a href="#cb2-28"></a><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 640.0 670.0 700.0 690.0 730.0 760.0</span></span>
|
||||
<span id="cb2-29"><a href="#cb2-29"></a><span class="co"># as.mo("Sthafilokkockus aaureuz") 370.0 380.0 420.0 400.0 440.0 510.0</span></span>
|
||||
<span id="cb2-30"><a href="#cb2-30"></a><span class="co"># as.mo("MRSA") 8.6 8.7 11.0 9.1 9.6 32.0</span></span>
|
||||
<span id="cb2-31"><a href="#cb2-31"></a><span class="co"># as.mo("VISA") 24.0 25.0 38.0 38.0 50.0 53.0</span></span>
|
||||
<span id="cb2-32"><a href="#cb2-32"></a><span class="co"># as.mo("VRSA") 24.0 25.0 49.0 37.0 52.0 150.0</span></span>
|
||||
<span id="cb2-33"><a href="#cb2-33"></a><span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 160.0 160.0</span></span>
|
||||
<span id="cb2-34"><a href="#cb2-34"></a><span class="co"># neval</span></span>
|
||||
<span id="cb2-35"><a href="#cb2-35"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-36"><a href="#cb2-36"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-37"><a href="#cb2-37"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-38"><a href="#cb2-38"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-39"><a href="#cb2-39"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-40"><a href="#cb2-40"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-41"><a href="#cb2-41"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-42"><a href="#cb2-42"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-43"><a href="#cb2-43"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-44"><a href="#cb2-44"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-45"><a href="#cb2-45"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-46"><a href="#cb2-46"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-47"><a href="#cb2-47"></a><span class="co"># 10</span></span>
|
||||
<span id="cb2-48"><a href="#cb2-48"></a><span class="co"># 10</span></span></code></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second.</p>
|
||||
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
|
||||
@@ -246,19 +260,19 @@
|
||||
<span id="cb3-6"><a href="#cb3-6"></a> <span class="dt">times =</span> <span class="dv">10</span>)</span>
|
||||
<span id="cb3-7"><a href="#cb3-7"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(M.semesiae, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</span>
|
||||
<span id="cb3-8"><a href="#cb3-8"></a><span class="co"># Unit: milliseconds</span></span>
|
||||
<span id="cb3-9"><a href="#cb3-9"></a><span class="co"># expr min lq mean median uq</span></span>
|
||||
<span id="cb3-10"><a href="#cb3-10"></a><span class="co"># as.mo("metsem") 1485.000 1507.000 1524.00 1519.000 1538.000</span></span>
|
||||
<span id="cb3-11"><a href="#cb3-11"></a><span class="co"># as.mo("METSEM") 1371.000 1495.000 1557.00 1567.000 1633.000</span></span>
|
||||
<span id="cb3-12"><a href="#cb3-12"></a><span class="co"># as.mo("M. semesiae") 16.010 16.310 25.38 16.480 42.840</span></span>
|
||||
<span id="cb3-13"><a href="#cb3-13"></a><span class="co"># as.mo("M. semesiae") 15.700 15.900 16.74 16.370 17.480</span></span>
|
||||
<span id="cb3-14"><a href="#cb3-14"></a><span class="co"># as.mo("Methanosarcina semesiae") 5.885 6.116 11.79 6.347 8.155</span></span>
|
||||
<span id="cb3-9"><a href="#cb3-9"></a><span class="co"># expr min lq mean median uq</span></span>
|
||||
<span id="cb3-10"><a href="#cb3-10"></a><span class="co"># as.mo("metsem") 1530.00 1561.000 1618.00 1620.000 1665.000</span></span>
|
||||
<span id="cb3-11"><a href="#cb3-11"></a><span class="co"># as.mo("METSEM") 1482.00 1523.000 1544.00 1555.000 1567.000</span></span>
|
||||
<span id="cb3-12"><a href="#cb3-12"></a><span class="co"># as.mo("M. semesiae") 15.01 16.140 27.85 17.080 43.620</span></span>
|
||||
<span id="cb3-13"><a href="#cb3-13"></a><span class="co"># as.mo("M. semesiae") 15.54 16.200 19.30 16.570 17.040</span></span>
|
||||
<span id="cb3-14"><a href="#cb3-14"></a><span class="co"># as.mo("Methanosarcina semesiae") 6.05 6.307 9.35 6.437 7.649</span></span>
|
||||
<span id="cb3-15"><a href="#cb3-15"></a><span class="co"># max neval</span></span>
|
||||
<span id="cb3-16"><a href="#cb3-16"></a><span class="co"># 1577.00 10</span></span>
|
||||
<span id="cb3-17"><a href="#cb3-17"></a><span class="co"># 1663.00 10</span></span>
|
||||
<span id="cb3-18"><a href="#cb3-18"></a><span class="co"># 48.53 10</span></span>
|
||||
<span id="cb3-19"><a href="#cb3-19"></a><span class="co"># 18.55 10</span></span>
|
||||
<span id="cb3-20"><a href="#cb3-20"></a><span class="co"># 32.92 10</span></span></code></pre></div>
|
||||
<p>That takes 5.5 times as much time on average. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
|
||||
<span id="cb3-16"><a href="#cb3-16"></a><span class="co"># 1710.00 10</span></span>
|
||||
<span id="cb3-17"><a href="#cb3-17"></a><span class="co"># 1586.00 10</span></span>
|
||||
<span id="cb3-18"><a href="#cb3-18"></a><span class="co"># 50.39 10</span></span>
|
||||
<span id="cb3-19"><a href="#cb3-19"></a><span class="co"># 42.95 10</span></span>
|
||||
<span id="cb3-20"><a href="#cb3-20"></a><span class="co"># 33.42 10</span></span></code></pre></div>
|
||||
<p>That takes 5.7 times as much time on average. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
|
||||
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Methanosarcina semesiae</em> (which is uncommon):</p>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="900"></p>
|
||||
<p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
@@ -292,8 +306,8 @@
|
||||
<span id="cb4-24"><a href="#cb4-24"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</span>
|
||||
<span id="cb4-25"><a href="#cb4-25"></a><span class="co"># Unit: milliseconds</span></span>
|
||||
<span id="cb4-26"><a href="#cb4-26"></a><span class="co"># expr min lq mean median uq max neval</span></span>
|
||||
<span id="cb4-27"><a href="#cb4-27"></a><span class="co"># mo_name(x) 542 585 605 601 614 738 100</span></span></code></pre></div>
|
||||
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.6 seconds (600 ms). You only lose time on your unique input values.</p>
|
||||
<span id="cb4-27"><a href="#cb4-27"></a><span class="co"># mo_name(x) 572 626 648 645 666 792 100</span></span></code></pre></div>
|
||||
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.64 seconds (644 ms). You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@@ -305,10 +319,10 @@
|
||||
<span id="cb5-4"><a href="#cb5-4"></a> <span class="dt">times =</span> <span class="dv">10</span>)</span>
|
||||
<span id="cb5-5"><a href="#cb5-5"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</span>
|
||||
<span id="cb5-6"><a href="#cb5-6"></a><span class="co"># Unit: milliseconds</span></span>
|
||||
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># expr min lq mean median uq max neval</span></span>
|
||||
<span id="cb5-8"><a href="#cb5-8"></a><span class="co"># A 6.760 6.900 7.43 7.070 7.540 9.290 10</span></span>
|
||||
<span id="cb5-9"><a href="#cb5-9"></a><span class="co"># B 14.200 14.400 18.80 14.900 16.000 51.500 10</span></span>
|
||||
<span id="cb5-10"><a href="#cb5-10"></a><span class="co"># C 0.586 0.726 0.74 0.757 0.763 0.804 10</span></span></code></pre></div>
|
||||
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># expr min lq mean median uq max neval</span></span>
|
||||
<span id="cb5-8"><a href="#cb5-8"></a><span class="co"># A 6.730 6.860 7.110 6.950 7.170 8.47 10</span></span>
|
||||
<span id="cb5-9"><a href="#cb5-9"></a><span class="co"># B 14.500 14.800 18.100 15.500 15.900 43.10 10</span></span>
|
||||
<span id="cb5-10"><a href="#cb5-10"></a><span class="co"># C 0.726 0.753 0.821 0.791 0.882 1.04 10</span></span></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0008 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a>run_it <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</span>
|
||||
<span id="cb6-2"><a href="#cb6-2"></a> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</span>
|
||||
@@ -322,14 +336,14 @@
|
||||
<span id="cb6-10"><a href="#cb6-10"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</span>
|
||||
<span id="cb6-11"><a href="#cb6-11"></a><span class="co"># Unit: milliseconds</span></span>
|
||||
<span id="cb6-12"><a href="#cb6-12"></a><span class="co"># expr min lq mean median uq max neval</span></span>
|
||||
<span id="cb6-13"><a href="#cb6-13"></a><span class="co"># A 0.374 0.381 0.389 0.389 0.395 0.416 10</span></span>
|
||||
<span id="cb6-14"><a href="#cb6-14"></a><span class="co"># B 0.404 0.411 0.422 0.421 0.425 0.452 10</span></span>
|
||||
<span id="cb6-15"><a href="#cb6-15"></a><span class="co"># C 0.615 0.711 0.726 0.730 0.751 0.861 10</span></span>
|
||||
<span id="cb6-16"><a href="#cb6-16"></a><span class="co"># D 0.405 0.409 0.429 0.428 0.435 0.485 10</span></span>
|
||||
<span id="cb6-17"><a href="#cb6-17"></a><span class="co"># E 0.381 0.384 0.392 0.390 0.394 0.429 10</span></span>
|
||||
<span id="cb6-18"><a href="#cb6-18"></a><span class="co"># F 0.365 0.366 0.379 0.375 0.383 0.419 10</span></span>
|
||||
<span id="cb6-19"><a href="#cb6-19"></a><span class="co"># G 0.362 0.372 0.378 0.380 0.388 0.391 10</span></span>
|
||||
<span id="cb6-20"><a href="#cb6-20"></a><span class="co"># H 0.378 0.381 0.403 0.387 0.393 0.556 10</span></span></code></pre></div>
|
||||
<span id="cb6-13"><a href="#cb6-13"></a><span class="co"># A 0.348 0.398 0.405 0.404 0.419 0.438 10</span></span>
|
||||
<span id="cb6-14"><a href="#cb6-14"></a><span class="co"># B 0.407 0.416 0.461 0.426 0.490 0.667 10</span></span>
|
||||
<span id="cb6-15"><a href="#cb6-15"></a><span class="co"># C 0.701 0.745 0.757 0.754 0.769 0.814 10</span></span>
|
||||
<span id="cb6-16"><a href="#cb6-16"></a><span class="co"># D 0.435 0.440 0.497 0.464 0.569 0.588 10</span></span>
|
||||
<span id="cb6-17"><a href="#cb6-17"></a><span class="co"># E 0.351 0.397 0.435 0.419 0.489 0.520 10</span></span>
|
||||
<span id="cb6-18"><a href="#cb6-18"></a><span class="co"># F 0.358 0.385 0.396 0.393 0.420 0.430 10</span></span>
|
||||
<span id="cb6-19"><a href="#cb6-19"></a><span class="co"># G 0.322 0.363 0.409 0.401 0.450 0.508 10</span></span>
|
||||
<span id="cb6-20"><a href="#cb6-20"></a><span class="co"># H 0.340 0.372 0.384 0.385 0.403 0.432 10</span></span></code></pre></div>
|
||||
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div id="results-in-other-languages" class="section level3">
|
||||
@@ -356,18 +370,18 @@
|
||||
<span id="cb7-18"><a href="#cb7-18"></a><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</span>
|
||||
<span id="cb7-19"><a href="#cb7-19"></a><span class="co"># Unit: milliseconds</span></span>
|
||||
<span id="cb7-20"><a href="#cb7-20"></a><span class="co"># expr min lq mean median uq max neval</span></span>
|
||||
<span id="cb7-21"><a href="#cb7-21"></a><span class="co"># en 24.76 26.92 35.44 27.70 31.93 143.10 100</span></span>
|
||||
<span id="cb7-22"><a href="#cb7-22"></a><span class="co"># de 26.46 28.18 33.90 29.51 30.51 64.85 100</span></span>
|
||||
<span id="cb7-23"><a href="#cb7-23"></a><span class="co"># nl 32.40 34.89 39.79 35.94 37.28 75.95 100</span></span>
|
||||
<span id="cb7-24"><a href="#cb7-24"></a><span class="co"># es 26.41 28.80 34.46 29.56 31.58 67.56 100</span></span>
|
||||
<span id="cb7-25"><a href="#cb7-25"></a><span class="co"># it 26.44 28.52 35.22 29.30 30.37 156.00 100</span></span>
|
||||
<span id="cb7-26"><a href="#cb7-26"></a><span class="co"># fr 26.24 28.09 34.78 29.52 31.23 65.88 100</span></span>
|
||||
<span id="cb7-27"><a href="#cb7-27"></a><span class="co"># pt 26.28 28.32 36.00 29.49 32.22 66.76 100</span></span></code></pre></div>
|
||||
<span id="cb7-21"><a href="#cb7-21"></a><span class="co"># en 25.28 26.99 33.53 27.88 29.51 61.96 100</span></span>
|
||||
<span id="cb7-22"><a href="#cb7-22"></a><span class="co"># de 26.99 29.27 36.92 30.02 33.09 160.30 100</span></span>
|
||||
<span id="cb7-23"><a href="#cb7-23"></a><span class="co"># nl 32.37 34.58 40.59 35.88 37.10 67.43 100</span></span>
|
||||
<span id="cb7-24"><a href="#cb7-24"></a><span class="co"># es 27.54 29.14 34.40 29.88 31.45 61.89 100</span></span>
|
||||
<span id="cb7-25"><a href="#cb7-25"></a><span class="co"># it 26.77 28.79 34.28 29.73 31.30 69.41 100</span></span>
|
||||
<span id="cb7-26"><a href="#cb7-26"></a><span class="co"># fr 27.01 28.81 34.96 29.39 30.79 161.10 100</span></span>
|
||||
<span id="cb7-27"><a href="#cb7-27"></a><span class="co"># pt 26.76 28.85 34.13 29.69 31.74 63.08 100</span></span></code></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
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@@ -380,7 +394,7 @@
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- headroom.js -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<!-- pkgdown -->
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<link href="../pkgdown.css" rel="stylesheet">
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<meta property="og:title" content="Articles" />
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</head>
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<body>
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<body data-spy="scroll" data-target="#toc">
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<div class="container template-article-index">
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<header>
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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@@ -78,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
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</span>
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</div>
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@@ -229,16 +232,24 @@
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<h3>All vignettes</h3>
|
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<p class="section-desc"></p>
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<ul>
|
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<li><a href="AMR.html">How to conduct AMR analysis</a></li>
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<li><a href="EUCAST.html">How to apply EUCAST rules</a></li>
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<li><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></li>
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<li><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></li>
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<li><a href="SPSS.html">How to import data from SPSS / SAS / Stata</a></li>
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<li><a href="WHONET.html">How to work with WHONET data</a></li>
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<li><a href="benchmarks.html">Benchmarks</a></li>
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<li><a href="resistance_predict.html">How to predict antimicrobial resistance</a></li>
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</ul>
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<dl>
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<dt><a href="AMR.html">How to conduct AMR analysis</a></dt>
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<dd></dt>
|
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<dt><a href="EUCAST.html">How to apply EUCAST rules</a></dt>
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<dd></dt>
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<dt><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></dt>
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<dd></dt>
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<dt><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></dt>
|
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<dd></dt>
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<dt><a href="SPSS.html">How to import data from SPSS / SAS / Stata</a></dt>
|
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<dd></dt>
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<dt><a href="WHONET.html">How to work with WHONET data</a></dt>
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<dd></dt>
|
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<dt><a href="benchmarks.html">Benchmarks</a></dt>
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<dd></dt>
|
||||
<dt><a href="resistance_predict.html">How to predict antimicrobial resistance</a></dt>
|
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<dd></dt>
|
||||
</dl>
|
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</div>
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</div>
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</div>
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@@ -250,7 +261,7 @@
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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@@ -12,15 +12,14 @@
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@@ -39,7 +38,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
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</span>
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</div>
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||||
|
||||
@@ -75,6 +74,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
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||||
Conduct principal component analysis for AMR
|
||||
</a>
|
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</li>
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||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -179,7 +185,7 @@
|
||||
<h1>How to predict antimicrobial resistance</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">23 February 2020</h4>
|
||||
<h4 class="date">17 March 2020</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
|
||||
@@ -334,7 +340,7 @@
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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@@ -355,7 +361,7 @@
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -17,23 +17,27 @@
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|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="bootstrap-toc.css">
|
||||
<script src="bootstrap-toc.js"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="pkgdown.css" rel="stylesheet">
|
||||
@@ -45,8 +49,7 @@
|
||||
<script src="extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="Citation and Authors" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -64,7 +67,7 @@
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-citation-authors">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -78,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -223,14 +226,10 @@
|
||||
<div class="contents col-md-9">
|
||||
<div class="page-header">
|
||||
<h1>Citation</h1>
|
||||
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
|
||||
</div>
|
||||
|
||||
<p>Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2019).
|
||||
“AMR - An R Package for Working with Antimicrobial Resistance Data.”
|
||||
<em>bioRxiv</em>.
|
||||
<a href="https://doi.org/10.1101/810622">https://doi.org/10.1101/810622</a>.
|
||||
</p>
|
||||
<p>Berends MS, Luz CF et al. (2019). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622</p>
|
||||
<pre>@Article{,
|
||||
title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
|
||||
author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
|
||||
@@ -246,27 +245,27 @@
|
||||
|
||||
<ul class="list-unstyled">
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a></strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7620-1800' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
|
||||
<p><strong><a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a></strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7620-1800' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
|
||||
<p><strong><a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
|
||||
<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
|
||||
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -311,7 +310,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
60
docs/bootstrap-toc.css
vendored
Normal file
60
docs/bootstrap-toc.css
vendored
Normal file
@@ -0,0 +1,60 @@
|
||||
/*!
|
||||
* Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
|
||||
* Copyright 2015 Aidan Feldman
|
||||
* Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
|
||||
|
||||
/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
|
||||
|
||||
/* All levels of nav */
|
||||
nav[data-toggle='toc'] .nav > li > a {
|
||||
display: block;
|
||||
padding: 4px 20px;
|
||||
font-size: 13px;
|
||||
font-weight: 500;
|
||||
color: #767676;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav > li > a:hover,
|
||||
nav[data-toggle='toc'] .nav > li > a:focus {
|
||||
padding-left: 19px;
|
||||
color: #563d7c;
|
||||
text-decoration: none;
|
||||
background-color: transparent;
|
||||
border-left: 1px solid #563d7c;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav > .active > a,
|
||||
nav[data-toggle='toc'] .nav > .active:hover > a,
|
||||
nav[data-toggle='toc'] .nav > .active:focus > a {
|
||||
padding-left: 18px;
|
||||
font-weight: bold;
|
||||
color: #563d7c;
|
||||
background-color: transparent;
|
||||
border-left: 2px solid #563d7c;
|
||||
}
|
||||
|
||||
/* Nav: second level (shown on .active) */
|
||||
nav[data-toggle='toc'] .nav .nav {
|
||||
display: none; /* Hide by default, but at >768px, show it */
|
||||
padding-bottom: 10px;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav .nav > li > a {
|
||||
padding-top: 1px;
|
||||
padding-bottom: 1px;
|
||||
padding-left: 30px;
|
||||
font-size: 12px;
|
||||
font-weight: normal;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav .nav > li > a:hover,
|
||||
nav[data-toggle='toc'] .nav .nav > li > a:focus {
|
||||
padding-left: 29px;
|
||||
}
|
||||
nav[data-toggle='toc'] .nav .nav > .active > a,
|
||||
nav[data-toggle='toc'] .nav .nav > .active:hover > a,
|
||||
nav[data-toggle='toc'] .nav .nav > .active:focus > a {
|
||||
padding-left: 28px;
|
||||
font-weight: 500;
|
||||
}
|
||||
|
||||
/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
|
||||
nav[data-toggle='toc'] .nav > .active > ul {
|
||||
display: block;
|
||||
}
|
||||
159
docs/bootstrap-toc.js
vendored
Normal file
159
docs/bootstrap-toc.js
vendored
Normal file
@@ -0,0 +1,159 @@
|
||||
/*!
|
||||
* Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
|
||||
* Copyright 2015 Aidan Feldman
|
||||
* Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
|
||||
(function() {
|
||||
'use strict';
|
||||
|
||||
window.Toc = {
|
||||
helpers: {
|
||||
// return all matching elements in the set, or their descendants
|
||||
findOrFilter: function($el, selector) {
|
||||
// http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
|
||||
// http://stackoverflow.com/a/12731439/358804
|
||||
var $descendants = $el.find(selector);
|
||||
return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
|
||||
},
|
||||
|
||||
generateUniqueIdBase: function(el) {
|
||||
var text = $(el).text();
|
||||
var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
|
||||
return anchor || el.tagName.toLowerCase();
|
||||
},
|
||||
|
||||
generateUniqueId: function(el) {
|
||||
var anchorBase = this.generateUniqueIdBase(el);
|
||||
for (var i = 0; ; i++) {
|
||||
var anchor = anchorBase;
|
||||
if (i > 0) {
|
||||
// add suffix
|
||||
anchor += '-' + i;
|
||||
}
|
||||
// check if ID already exists
|
||||
if (!document.getElementById(anchor)) {
|
||||
return anchor;
|
||||
}
|
||||
}
|
||||
},
|
||||
|
||||
generateAnchor: function(el) {
|
||||
if (el.id) {
|
||||
return el.id;
|
||||
} else {
|
||||
var anchor = this.generateUniqueId(el);
|
||||
el.id = anchor;
|
||||
return anchor;
|
||||
}
|
||||
},
|
||||
|
||||
createNavList: function() {
|
||||
return $('<ul class="nav"></ul>');
|
||||
},
|
||||
|
||||
createChildNavList: function($parent) {
|
||||
var $childList = this.createNavList();
|
||||
$parent.append($childList);
|
||||
return $childList;
|
||||
},
|
||||
|
||||
generateNavEl: function(anchor, text) {
|
||||
var $a = $('<a></a>');
|
||||
$a.attr('href', '#' + anchor);
|
||||
$a.text(text);
|
||||
var $li = $('<li></li>');
|
||||
$li.append($a);
|
||||
return $li;
|
||||
},
|
||||
|
||||
generateNavItem: function(headingEl) {
|
||||
var anchor = this.generateAnchor(headingEl);
|
||||
var $heading = $(headingEl);
|
||||
var text = $heading.data('toc-text') || $heading.text();
|
||||
return this.generateNavEl(anchor, text);
|
||||
},
|
||||
|
||||
// Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
|
||||
getTopLevel: function($scope) {
|
||||
for (var i = 1; i <= 6; i++) {
|
||||
var $headings = this.findOrFilter($scope, 'h' + i);
|
||||
if ($headings.length > 1) {
|
||||
return i;
|
||||
}
|
||||
}
|
||||
|
||||
return 1;
|
||||
},
|
||||
|
||||
// returns the elements for the top level, and the next below it
|
||||
getHeadings: function($scope, topLevel) {
|
||||
var topSelector = 'h' + topLevel;
|
||||
|
||||
var secondaryLevel = topLevel + 1;
|
||||
var secondarySelector = 'h' + secondaryLevel;
|
||||
|
||||
return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
|
||||
},
|
||||
|
||||
getNavLevel: function(el) {
|
||||
return parseInt(el.tagName.charAt(1), 10);
|
||||
},
|
||||
|
||||
populateNav: function($topContext, topLevel, $headings) {
|
||||
var $context = $topContext;
|
||||
var $prevNav;
|
||||
|
||||
var helpers = this;
|
||||
$headings.each(function(i, el) {
|
||||
var $newNav = helpers.generateNavItem(el);
|
||||
var navLevel = helpers.getNavLevel(el);
|
||||
|
||||
// determine the proper $context
|
||||
if (navLevel === topLevel) {
|
||||
// use top level
|
||||
$context = $topContext;
|
||||
} else if ($prevNav && $context === $topContext) {
|
||||
// create a new level of the tree and switch to it
|
||||
$context = helpers.createChildNavList($prevNav);
|
||||
} // else use the current $context
|
||||
|
||||
$context.append($newNav);
|
||||
|
||||
$prevNav = $newNav;
|
||||
});
|
||||
},
|
||||
|
||||
parseOps: function(arg) {
|
||||
var opts;
|
||||
if (arg.jquery) {
|
||||
opts = {
|
||||
$nav: arg
|
||||
};
|
||||
} else {
|
||||
opts = arg;
|
||||
}
|
||||
opts.$scope = opts.$scope || $(document.body);
|
||||
return opts;
|
||||
}
|
||||
},
|
||||
|
||||
// accepts a jQuery object, or an options object
|
||||
init: function(opts) {
|
||||
opts = this.helpers.parseOps(opts);
|
||||
|
||||
// ensure that the data attribute is in place for styling
|
||||
opts.$nav.attr('data-toggle', 'toc');
|
||||
|
||||
var $topContext = this.helpers.createChildNavList(opts.$nav);
|
||||
var topLevel = this.helpers.getTopLevel(opts.$scope);
|
||||
var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
|
||||
this.helpers.populateNav($topContext, topLevel, $headings);
|
||||
}
|
||||
};
|
||||
|
||||
$(function() {
|
||||
$('nav[data-toggle="toc"]').each(function(i, el) {
|
||||
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Toc.init($nav);
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<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
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<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
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<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
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<script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
|
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<script src="extra.js"></script><meta property="og:title" content="Antimicrobial Resistance Analysis">
|
||||
<meta property="og:description" content="Functions to simplify the analysis and prediction of Antimicrobial
|
||||
@@ -23,14 +24,13 @@
|
||||
using evidence-based methods, like those defined by Leclercq et al. (2013)
|
||||
<doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory
|
||||
Standards Institute (2014) <isbn: 1-56238-899-1>.">
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png">
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<meta name="twitter:card" content="summary">
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg">
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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<body data-spy="scroll" data-target="#toc">
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<div class="container template-home">
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<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
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<div class="container">
|
||||
@@ -43,7 +43,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -201,11 +201,10 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
||||
<p><code>AMR</code> is a free and open-source <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
|
||||
<p>We created this package for both routine data analysis and academic research (as part of our PhD theses) at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
|
||||
<div class="main-content">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
|
||||
<strong>Used in more than 100 countries</strong><br>
|
||||
Since its first public release in early 2018, this package has been downloaded from more than 100 countries <small>(as of March 2020, <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge, to see the names of the countries.</p>
|
||||
<div class="main-content">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in more than 100 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from more than 100 countries <small>(as of March 2020, <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge, to see the names of the countries.
|
||||
</p>
|
||||
<br><br>
|
||||
</div>
|
||||
<div id="partners" class="section level4">
|
||||
@@ -213,11 +212,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
||||
<a href="#partners" class="anchor"></a>Partners</h4>
|
||||
<p>The development of this package is part of, related to, or made possible by:</p>
|
||||
<div align="center">
|
||||
<a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a>
|
||||
<a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a>
|
||||
<a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice"><img src="./logo_certe.png" class="partner_logo"></a>
|
||||
<a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a>
|
||||
<a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a>
|
||||
<a href="https://www.rug.nl" title="University of Groningen"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><img src="./logo_interreg.png" class="partner_logo"></a>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
@@ -265,7 +260,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
|
||||
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R from CRAN by using the command:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"AMR"</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"AMR"</span>)</pre></div>
|
||||
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> > <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
|
||||
</div>
|
||||
@@ -273,8 +268,8 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
|
||||
<p>The latest and unpublished development version can be installed with (<strong>precaution: may be unstable</strong>):</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"remotes"</span>)</span>
|
||||
<span id="cb2-2"><a href="#cb2-2"></a>remotes<span class="op">::</span><span class="kw"><a href="https://remotes.r-lib.org/reference/install_gitlab.html">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"remotes"</span>)
|
||||
<span class="kw pkg">remotes</span><span class="kw ns">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_gitlab.html">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="get-started" class="section level3">
|
||||
@@ -384,12 +379,14 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<div class="links">
|
||||
<h2>Links</h2>
|
||||
<ul class="list-unstyled">
|
||||
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=AMR">https://cloud.r-project.org/package=AMR</a>
|
||||
</li>
|
||||
<li>Browse source code at <br><a href="https://gitlab.com/msberends/AMR/">https://gitlab.com/msberends/AMR/</a>
|
||||
</li>
|
||||
<li>Report a bug at <br><a href="https://gitlab.com/msberends/AMR/issues">https://gitlab.com/msberends/AMR/issues</a>
|
||||
</li>
|
||||
</ul>
|
||||
@@ -412,17 +409,17 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
||||
<h2>Developers</h2>
|
||||
<ul class="list-unstyled">
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
|
||||
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
|
||||
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
|
||||
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
|
||||
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
|
||||
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
|
||||
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li><a href="authors.html">All authors...</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
@@ -436,7 +433,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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</div>
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</footer>
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@@ -17,23 +17,27 @@
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|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -45,8 +49,7 @@
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="Changelog" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -64,7 +67,7 @@
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-news">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -78,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -222,17 +225,17 @@
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Changelog <small></small></h1>
|
||||
|
||||
<h1 data-toc-skip>Changelog <small></small></h1>
|
||||
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1019004" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-1019004" class="anchor"></a>AMR 1.0.1.9004<small> Unreleased </small>
|
||||
<div id="amr-1019005" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.0.1.9005">
|
||||
<a href="#amr-1019005" class="anchor"></a>AMR 1.0.1.9005<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-14-mar-2020" class="section level2">
|
||||
<div id="last-updated-13-apr-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-14-mar-2020" class="anchor"></a><small>Last updated: 14-Mar-2020</small>
|
||||
<a href="#last-updated-13-apr-2020" class="anchor"></a><small>Last updated: 13-Apr-2020</small>
|
||||
</h2>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@@ -242,31 +245,50 @@
|
||||
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
|
||||
<ul>
|
||||
<li>Support for codes ending with <code>SPE</code> for species, like <code>"ESCSPE"</code> for <em>Escherichia coli</em>
|
||||
</li>
|
||||
<li>Support for any encoding, which means that any language-specific character with accents can be used for input</li>
|
||||
<li>Support for more arbitrary IDs used in laboratory information systems</li>
|
||||
<li>Small fix for preventing viruses being treated as bacteria</li>
|
||||
<li>Small fix for preventing contamination and lack of growth being treated as valid microorganisms</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Added more abbreviations to the <code>antibiotics</code> data set</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Support for the upcoming <code>dplyr</code> version 1.0.0</li>
|
||||
<li>More robust assigning for classes <code>rsi</code> and <code>mic</code>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-101" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="1.0.1">
|
||||
<a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small>
|
||||
</h1>
|
||||
<div id="changed" class="section level3">
|
||||
<div id="changed-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-1" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
|
||||
<li>
|
||||
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>yourdata <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb1-2"><a href="#cb1-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(antibiotic1<span class="op">:</span>antibiotic25), as.rsi, <span class="dt">mo =</span> <span class="st">"E. coli"</span>)</span>
|
||||
<span id="cb1-3"><a href="#cb1-3"></a></span>
|
||||
<span id="cb1-4"><a href="#cb1-4"></a>yourdata <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(antibiotic1<span class="op">:</span>antibiotic25), as.rsi, <span class="dt">mo =</span> .<span class="op">$</span>mybacteria)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb1"><pre class="r"><span class="no">yourdata</span> <span class="kw">%>%</span>
|
||||
<span class="fu">mutate_at</span>(<span class="fu">vars</span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="st">"E. coli"</span>)
|
||||
|
||||
<span class="no">yourdata</span> <span class="kw">%>%</span>
|
||||
<span class="fu">mutate_at</span>(<span class="fu">vars</span>(<span class="no">antibiotic1</span>:<span class="no">antibiotic25</span>), <span class="no">as.rsi</span>, <span class="kw">mo</span> <span class="kw">=</span> <span class="no">.</span>$<span class="no">mybacteria</span>)</pre></div>
|
||||
</li>
|
||||
<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
|
||||
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
|
||||
@@ -275,7 +297,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-100" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="1.0.0">
|
||||
<a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small>
|
||||
</h1>
|
||||
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
|
||||
@@ -289,21 +311,21 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="kw"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)</span>
|
||||
<span id="cb2-2"><a href="#cb2-2"></a><span class="co">#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span></span>
|
||||
<span id="cb2-3"><a href="#cb2-3"></a><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)</span>
|
||||
<span id="cb2-4"><a href="#cb2-4"></a><span class="co">#> [1] "Ampicillin"</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5"></a><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"21066-6"</span>)</span>
|
||||
<span id="cb2-6"><a href="#cb2-6"></a><span class="co">#> [1] "J01CA01"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
|
||||
<span class="co">#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)
|
||||
<span class="co">#> [1] "Ampicillin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"21066-6"</span>)
|
||||
<span class="co">#> [1] "J01CA01"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="kw"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)</span>
|
||||
<span id="cb3-2"><a href="#cb3-2"></a><span class="co">#> [1] 115329001 3092008 113961008</span></span>
|
||||
<span id="cb3-3"><a href="#cb3-3"></a><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="dv">115329001</span>)</span>
|
||||
<span id="cb3-4"><a href="#cb3-4"></a><span class="co">#> [1] "Staphylococcus aureus"</span></span>
|
||||
<span id="cb3-5"><a href="#cb3-5"></a><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="dv">115329001</span>)</span>
|
||||
<span id="cb3-6"><a href="#cb3-6"></a><span class="co">#> [1] "Gram-positive"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
|
||||
<span class="co">#> [1] 115329001 3092008 113961008</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="fl">115329001</span>)
|
||||
<span class="co">#> [1] "Staphylococcus aureus"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="fl">115329001</span>)
|
||||
<span class="co">#> [1] "Gram-positive"</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@@ -350,7 +372,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-090" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.9.0">
|
||||
<a href="#amr-090" class="anchor"></a>AMR 0.9.0<small> 2019-11-29 </small>
|
||||
</h1>
|
||||
<div id="breaking" class="section level3">
|
||||
@@ -361,9 +383,9 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="cf">if</span> (<span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(somebugs) <span class="op">==</span><span class="st"> "Enterobacteriaceae"</span>) ...</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="no">...</span></pre></div>
|
||||
<p>then please adjust this to:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="cf">if</span> (<span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(somebugs) <span class="op">==</span><span class="st"> "Enterobacterales"</span>) ...</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="no">somebugs</span>) <span class="kw">==</span> <span class="st">"Enterobacterales"</span>) <span class="no">...</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@@ -375,12 +397,12 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</span>
|
||||
<span id="cb6-2"><a href="#cb6-2"></a>example_isolates <span class="op">%>%</span></span>
|
||||
<span id="cb6-3"><a href="#cb6-3"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="dt">bug =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(mo)) <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb6-4"><a href="#cb6-4"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX),</span>
|
||||
<span id="cb6-5"><a href="#cb6-5"></a> <span class="dt">amox_clav =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMC)) <span class="op">%>%</span></span>
|
||||
<span id="cb6-6"><a href="#cb6-6"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(amoxicillin) <span class="op">|</span><span class="st"> </span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(amox_clav))</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
|
||||
<span class="no">example_isolates</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">bug</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">mo</span>)) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="kw">amoxicillin</span> <span class="kw">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMX</span>),
|
||||
<span class="kw">amox_clav</span> <span class="kw">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="no">AMC</span>)) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(!<span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="no">amoxicillin</span>) <span class="kw">|</span> !<span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="no">amox_clav</span>))</pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).</p>
|
||||
@@ -402,16 +424,16 @@
|
||||
<li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
|
||||
<li>
|
||||
<p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,</span>
|
||||
<span id="cb7-2"><a href="#cb7-2"></a> <span class="st">"staphylokok aureuz"</span>))</span>
|
||||
<span id="cb7-3"><a href="#cb7-3"></a><span class="co">#> Warning: </span></span>
|
||||
<span id="cb7-4"><a href="#cb7-4"></a><span class="co">#> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span></span>
|
||||
<span id="cb7-5"><a href="#cb7-5"></a><span class="co">#> Class 'mo'</span></span>
|
||||
<span id="cb7-6"><a href="#cb7-6"></a><span class="co">#> [1] B_STPHY_AURS B_STPHY_AURS</span></span>
|
||||
<span id="cb7-7"><a href="#cb7-7"></a></span>
|
||||
<span id="cb7-8"><a href="#cb7-8"></a><span class="kw"><a href="../reference/as.mo.html">mo_uncertainties</a></span>()</span>
|
||||
<span id="cb7-9"><a href="#cb7-9"></a><span class="co">#> "Stafylococcus aureus" -> Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)</span></span>
|
||||
<span id="cb7-10"><a href="#cb7-10"></a><span class="co">#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
|
||||
<span class="st">"staphylokok aureuz"</span>))
|
||||
<span class="co">#> Warning: </span>
|
||||
<span class="co">#> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
|
||||
<span class="co">#> Class 'mo'</span>
|
||||
<span class="co">#> [1] B_STPHY_AURS B_STPHY_AURS</span>
|
||||
|
||||
<span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span>()
|
||||
<span class="co">#> "Stafylococcus aureus" -> Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)</span>
|
||||
<span class="co">#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@@ -450,7 +472,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-080" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.8.0">
|
||||
<a href="#amr-080" class="anchor"></a>AMR 0.8.0<small> 2019-10-15 </small>
|
||||
</h1>
|
||||
<div id="breaking-1" class="section level3">
|
||||
@@ -459,22 +481,22 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a><span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(..., <span class="dt">include_unknown =</span> <span class="ot">TRUE</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb8"><pre class="r"><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">...</span>, <span class="kw">include_unknown</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></div>
|
||||
<p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a><span class="co"># how it works in base R:</span></span>
|
||||
<span id="cb9-2"><a href="#cb9-2"></a>x <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)</span>
|
||||
<span id="cb9-3"><a href="#cb9-3"></a>x[<span class="dv">1</span>] <-<span class="st"> "B"</span></span>
|
||||
<span id="cb9-4"><a href="#cb9-4"></a><span class="co">#> Warning message:</span></span>
|
||||
<span id="cb9-5"><a href="#cb9-5"></a><span class="co">#> invalid factor level, NA generated</span></span>
|
||||
<span id="cb9-6"><a href="#cb9-6"></a></span>
|
||||
<span id="cb9-7"><a href="#cb9-7"></a><span class="co"># how it now works similarly for classes 'mo' and 'ab':</span></span>
|
||||
<span id="cb9-8"><a href="#cb9-8"></a>x <-<span class="st"> </span><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</span>
|
||||
<span id="cb9-9"><a href="#cb9-9"></a>x[<span class="dv">1</span>] <-<span class="st"> "testvalue"</span></span>
|
||||
<span id="cb9-10"><a href="#cb9-10"></a><span class="co">#> Warning message:</span></span>
|
||||
<span id="cb9-11"><a href="#cb9-11"></a><span class="co">#> invalid microorganism code, NA generated</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb9"><pre class="r"><span class="co"># how it works in base R:</span>
|
||||
<span class="no">x</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
|
||||
<span class="no">x</span>[<span class="fl">1</span>] <span class="kw"><-</span> <span class="st">"B"</span>
|
||||
<span class="co">#> Warning message:</span>
|
||||
<span class="co">#> invalid factor level, NA generated</span>
|
||||
|
||||
<span class="co"># how it now works similarly for classes 'mo' and 'ab':</span>
|
||||
<span class="no">x</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="no">x</span>[<span class="fl">1</span>] <span class="kw"><-</span> <span class="st">"testvalue"</span>
|
||||
<span class="co">#> Warning message:</span>
|
||||
<span class="co">#> invalid microorganism code, NA generated</span></pre></div>
|
||||
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
|
||||
</li>
|
||||
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
@@ -487,62 +509,62 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1"></a>x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates)</span>
|
||||
<span id="cb10-2"><a href="#cb10-2"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></span>
|
||||
<span id="cb10-3"><a href="#cb10-3"></a>x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</span>
|
||||
<span id="cb10-4"><a href="#cb10-4"></a><span class="co">#> mo ab S I R total</span></span>
|
||||
<span id="cb10-5"><a href="#cb10-5"></a><span class="co">#> 1 A. baumannii AMC 0 0 3 3</span></span>
|
||||
<span id="cb10-6"><a href="#cb10-6"></a><span class="co">#> 2 A. baumannii AMK 0 0 0 0</span></span>
|
||||
<span id="cb10-7"><a href="#cb10-7"></a><span class="co">#> 3 A. baumannii AMP 0 0 3 3</span></span>
|
||||
<span id="cb10-8"><a href="#cb10-8"></a><span class="co">#> 4 A. baumannii AMX 0 0 3 3</span></span>
|
||||
<span id="cb10-9"><a href="#cb10-9"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></span>
|
||||
<span id="cb10-10"><a href="#cb10-10"></a></span>
|
||||
<span id="cb10-11"><a href="#cb10-11"></a><span class="co"># change the transformation with the FUN argument to anything you like:</span></span>
|
||||
<span id="cb10-12"><a href="#cb10-12"></a>x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates, <span class="dt">FUN =</span> mo_gramstain)</span>
|
||||
<span id="cb10-13"><a href="#cb10-13"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></span>
|
||||
<span id="cb10-14"><a href="#cb10-14"></a>x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</span>
|
||||
<span id="cb10-15"><a href="#cb10-15"></a><span class="co">#> mo ab S I R total</span></span>
|
||||
<span id="cb10-16"><a href="#cb10-16"></a><span class="co">#> 1 Gram-negative AMC 469 89 174 732</span></span>
|
||||
<span id="cb10-17"><a href="#cb10-17"></a><span class="co">#> 2 Gram-negative AMK 251 0 2 253</span></span>
|
||||
<span id="cb10-18"><a href="#cb10-18"></a><span class="co">#> 3 Gram-negative AMP 227 0 405 632</span></span>
|
||||
<span id="cb10-19"><a href="#cb10-19"></a><span class="co">#> 4 Gram-negative AMX 227 0 405 632</span></span>
|
||||
<span id="cb10-20"><a href="#cb10-20"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb10"><pre class="r"><span class="no">x</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="no">example_isolates</span>)
|
||||
<span class="co">#> NOTE: Using column `mo` as input for `col_mo`.</span>
|
||||
<span class="no">x</span>[<span class="fl">1</span>:<span class="fl">4</span>, ]
|
||||
<span class="co">#> mo ab S I R total</span>
|
||||
<span class="co">#> 1 A. baumannii AMC 0 0 3 3</span>
|
||||
<span class="co">#> 2 A. baumannii AMK 0 0 0 0</span>
|
||||
<span class="co">#> 3 A. baumannii AMP 0 0 3 3</span>
|
||||
<span class="co">#> 4 A. baumannii AMX 0 0 3 3</span>
|
||||
<span class="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
|
||||
|
||||
<span class="co"># change the transformation with the FUN argument to anything you like:</span>
|
||||
<span class="no">x</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="no">example_isolates</span>, <span class="kw">FUN</span> <span class="kw">=</span> <span class="no">mo_gramstain</span>)
|
||||
<span class="co">#> NOTE: Using column `mo` as input for `col_mo`.</span>
|
||||
<span class="no">x</span>[<span class="fl">1</span>:<span class="fl">4</span>, ]
|
||||
<span class="co">#> mo ab S I R total</span>
|
||||
<span class="co">#> 1 Gram-negative AMC 469 89 174 732</span>
|
||||
<span class="co">#> 2 Gram-negative AMK 251 0 2 253</span>
|
||||
<span class="co">#> 3 Gram-negative AMP 227 0 405 632</span>
|
||||
<span class="co">#> 4 Gram-negative AMX 227 0 405 632</span>
|
||||
<span class="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span></pre></div>
|
||||
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a><span class="kw"><a href="https://rdrr.io/r/base/format.html">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb11"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="no">x</span>, <span class="kw">combine_IR</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1"></a><span class="co"># --------------------------------------------------------------------</span></span>
|
||||
<span id="cb12-2"><a href="#cb12-2"></a><span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span></span>
|
||||
<span id="cb12-3"><a href="#cb12-3"></a><span class="co"># ----------------------- -----------------------</span></span>
|
||||
<span id="cb12-4"><a href="#cb12-4"></a><span class="co"># Drug A Drug B include as include as include as include as</span></span>
|
||||
<span id="cb12-5"><a href="#cb12-5"></a><span class="co"># numerator denominator numerator denominator</span></span>
|
||||
<span id="cb12-6"><a href="#cb12-6"></a><span class="co"># -------- -------- ---------- ----------- ---------- -----------</span></span>
|
||||
<span id="cb12-7"><a href="#cb12-7"></a><span class="co"># S or I S or I X X X X</span></span>
|
||||
<span id="cb12-8"><a href="#cb12-8"></a><span class="co"># R S or I X X X X</span></span>
|
||||
<span id="cb12-9"><a href="#cb12-9"></a><span class="co"># <NA> S or I X X - -</span></span>
|
||||
<span id="cb12-10"><a href="#cb12-10"></a><span class="co"># S or I R X X X X</span></span>
|
||||
<span id="cb12-11"><a href="#cb12-11"></a><span class="co"># R R - X - X</span></span>
|
||||
<span id="cb12-12"><a href="#cb12-12"></a><span class="co"># <NA> R - - - -</span></span>
|
||||
<span id="cb12-13"><a href="#cb12-13"></a><span class="co"># S or I <NA> X X - -</span></span>
|
||||
<span id="cb12-14"><a href="#cb12-14"></a><span class="co"># R <NA> - - - -</span></span>
|
||||
<span id="cb12-15"><a href="#cb12-15"></a><span class="co"># <NA> <NA> - - - -</span></span>
|
||||
<span id="cb12-16"><a href="#cb12-16"></a><span class="co"># --------------------------------------------------------------------</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb12"><pre class="r"># --------------------------------------------------------------------
|
||||
# only_all_tested = FALSE only_all_tested = TRUE
|
||||
# ----------------------- -----------------------
|
||||
# Drug A Drug B include as include as include as include as
|
||||
# numerator denominator numerator denominator
|
||||
# -------- -------- ---------- ----------- ---------- -----------
|
||||
# S or I S or I X X X X
|
||||
# R S or I X X X X
|
||||
# <na> S or I X X - -
|
||||
# S or I R X X X X
|
||||
# R R - X - X
|
||||
# <na> R - - - -
|
||||
# S or I <na> X X - -
|
||||
# R <na> - - - -
|
||||
# <na><na> - - - -
|
||||
# --------------------------------------------------------------------</na></na></na></na></na></na></pre></div>
|
||||
<p>Since this is a major change, usage of the old <code>also_single_tested</code> will throw an informative error that it has been replaced by <code>only_all_tested</code>.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a><span class="co"># (run this on your own console, as this page does not support colour printing)</span></span>
|
||||
<span id="cb13-2"><a href="#cb13-2"></a><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</span>
|
||||
<span id="cb13-3"><a href="#cb13-3"></a>example_isolates <span class="op">%>%</span></span>
|
||||
<span id="cb13-4"><a href="#cb13-4"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb13-5"><a href="#cb13-5"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb13"><pre class="r"><span class="co"># (run this on your own console, as this page does not support colour printing)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)
|
||||
<span class="no">example_isolates</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">mo</span>:<span class="no">AMC</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-1" class="section level3">
|
||||
<div id="changed-2" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-1" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-2" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
|
||||
<ul>
|
||||
@@ -604,7 +626,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-071" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.7.1">
|
||||
<a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
|
||||
</h1>
|
||||
<div id="new-4" class="section level4">
|
||||
@@ -613,14 +635,14 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1"></a>septic_patients <span class="op">%>%</span></span>
|
||||
<span id="cb14-2"><a href="#cb14-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(AMX, CIP) <span class="op">%>%</span></span>
|
||||
<span id="cb14-3"><a href="#cb14-3"></a><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">rsi_df</a></span>()</span>
|
||||
<span id="cb14-4"><a href="#cb14-4"></a><span class="co"># antibiotic interpretation value isolates</span></span>
|
||||
<span id="cb14-5"><a href="#cb14-5"></a><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></span>
|
||||
<span id="cb14-6"><a href="#cb14-6"></a><span class="co"># 2 Amoxicillin R 0.5557364 683</span></span>
|
||||
<span id="cb14-7"><a href="#cb14-7"></a><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></span>
|
||||
<span id="cb14-8"><a href="#cb14-8"></a><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb14"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">AMX</span>, <span class="no">CIP</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span>()
|
||||
<span class="co"># antibiotic interpretation value isolates</span>
|
||||
<span class="co"># 1 Amoxicillin SI 0.4442636 546</span>
|
||||
<span class="co"># 2 Amoxicillin R 0.5557364 683</span>
|
||||
<span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span>
|
||||
<span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
|
||||
@@ -638,20 +660,20 @@
|
||||
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
|
||||
</ul>
|
||||
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</span>
|
||||
<span id="cb15-2"><a href="#cb15-2"></a><span class="co"># B_ESCHR_COL</span></span>
|
||||
<span id="cb15-3"><a href="#cb15-3"></a><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</span>
|
||||
<span id="cb15-4"><a href="#cb15-4"></a><span class="co"># "Escherichia coli"</span></span>
|
||||
<span id="cb15-5"><a href="#cb15-5"></a><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</span>
|
||||
<span id="cb15-6"><a href="#cb15-6"></a><span class="co"># "Gram-negative"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb15"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
|
||||
<span class="co"># B_ESCHR_COL</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)
|
||||
<span class="co"># "Escherichia coli"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)
|
||||
<span class="co"># "Gram-negative"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-2" class="section level4">
|
||||
<div id="changed-3" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-2" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-3" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></code> are now lowercase</li>
|
||||
<li>Fixed bug in translation of microorganism names</li>
|
||||
@@ -685,7 +707,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-070" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.7.0">
|
||||
<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
|
||||
</h1>
|
||||
<div id="new-5" class="section level4">
|
||||
@@ -698,9 +720,9 @@
|
||||
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-3" class="section level4">
|
||||
<div id="changed-4" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-3" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-4" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</p></li>
|
||||
<li><p>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</p></li>
|
||||
@@ -745,14 +767,14 @@
|
||||
<li><p>when all values are unique it now shows a message instead of a warning</p></li>
|
||||
<li>
|
||||
<p>support for boxplots:</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1"></a>septic_patients <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb16-2"><a href="#cb16-2"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb16-3"><a href="#cb16-3"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</span>
|
||||
<span id="cb16-4"><a href="#cb16-4"></a><span class="co"># grouped boxplots:</span></span>
|
||||
<span id="cb16-5"><a href="#cb16-5"></a>septic_patients <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb16-6"><a href="#cb16-6"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb16-7"><a href="#cb16-7"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span></span>
|
||||
<span id="cb16-8"><a href="#cb16-8"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb16"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">age</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
|
||||
<span class="co"># grouped boxplots:</span>
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital_id</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">age</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@@ -782,12 +804,12 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-061" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.6.1">
|
||||
<a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small>
|
||||
</h1>
|
||||
<div id="changed-4" class="section level4">
|
||||
<div id="changed-5" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-4" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-5" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
|
||||
</li>
|
||||
@@ -796,7 +818,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-060" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.6.0">
|
||||
<a href="#amr-060" class="anchor"></a>AMR 0.6.0<small> 2019-03-27 </small>
|
||||
</h1>
|
||||
<p><strong>New website!</strong></p>
|
||||
@@ -836,32 +858,32 @@
|
||||
</li>
|
||||
<li>
|
||||
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</span>
|
||||
<span id="cb17-2"><a href="#cb17-2"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</span>
|
||||
<span id="cb17-3"><a href="#cb17-3"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</span>
|
||||
<span id="cb17-4"><a href="#cb17-4"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</span>
|
||||
<span id="cb17-5"><a href="#cb17-5"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</span>
|
||||
<span id="cb17-6"><a href="#cb17-6"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</span>
|
||||
<span id="cb17-7"><a href="#cb17-7"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</span>
|
||||
<span id="cb17-8"><a href="#cb17-8"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</span>
|
||||
<span id="cb17-9"><a href="#cb17-9"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</span>
|
||||
<span id="cb17-10"><a href="#cb17-10"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</span>
|
||||
<span id="cb17-11"><a href="#cb17-11"></a><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb17"><pre class="r"><span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</pre></div>
|
||||
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
|
||||
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1"></a>septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</span>
|
||||
<span id="cb18-2"><a href="#cb18-2"></a><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></span>
|
||||
<span id="cb18-3"><a href="#cb18-3"></a>septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</span>
|
||||
<span id="cb18-4"><a href="#cb18-4"></a><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb18"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>)
|
||||
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="kw">result</span> <span class="kw">=</span> <span class="st">"R"</span>, <span class="kw">scope</span> <span class="kw">=</span> <span class="st">"all"</span>)
|
||||
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1"></a>ab_property -><span class="st"> </span><span class="kw">atc_property</span>()</span>
|
||||
<span id="cb19-2"><a href="#cb19-2"></a>ab_name -><span class="st"> </span><span class="kw">atc_name</span>()</span>
|
||||
<span id="cb19-3"><a href="#cb19-3"></a>ab_official -><span class="st"> </span><span class="kw">atc_official</span>()</span>
|
||||
<span id="cb19-4"><a href="#cb19-4"></a>ab_trivial_nl -><span class="st"> </span><span class="kw">atc_trivial_nl</span>()</span>
|
||||
<span id="cb19-5"><a href="#cb19-5"></a>ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</span>
|
||||
<span id="cb19-6"><a href="#cb19-6"></a>ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</span>
|
||||
<span id="cb19-7"><a href="#cb19-7"></a>ab_tradenames -><span class="st"> </span><span class="kw">atc_tradenames</span>()</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb19"><pre class="r"><span class="no">ab_property</span> <span class="kw">-></span> <span class="fu">atc_property</span>()
|
||||
<span class="no">ab_name</span> <span class="kw">-></span> <span class="fu">atc_name</span>()
|
||||
<span class="no">ab_official</span> <span class="kw">-></span> <span class="fu">atc_official</span>()
|
||||
<span class="no">ab_trivial_nl</span> <span class="kw">-></span> <span class="fu">atc_trivial_nl</span>()
|
||||
<span class="no">ab_certe</span> <span class="kw">-></span> <span class="fu">atc_certe</span>()
|
||||
<span class="no">ab_umcg</span> <span class="kw">-></span> <span class="fu">atc_umcg</span>()
|
||||
<span class="no">ab_tradenames</span> <span class="kw">-></span> <span class="fu">atc_tradenames</span>()</pre></div>
|
||||
<p>These functions use <code>as.atc()</code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</p>
|
||||
</li>
|
||||
<li><p>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</p></li>
|
||||
@@ -874,28 +896,28 @@
|
||||
<li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</p></li>
|
||||
<li>
|
||||
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1"></a>x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</span>
|
||||
<span id="cb20-2"><a href="#cb20-2"></a><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(x)</span>
|
||||
<span id="cb20-3"><a href="#cb20-3"></a><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb20"><pre class="r"><span class="no">x</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="no">septic_patients</span>, <span class="kw">col_ab</span> <span class="kw">=</span> <span class="st">"amox"</span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(<span class="no">x</span>)
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="no">x</span>)</pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1"></a>septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</span>
|
||||
<span id="cb21-2"><a href="#cb21-2"></a><span class="co"># or</span></span>
|
||||
<span id="cb21-3"><a href="#cb21-3"></a><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb21"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%>%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">...</span>)
|
||||
<span class="co"># or</span>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)</pre></div>
|
||||
<p>is equal to:</p>
|
||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1"></a>septic_patients <span class="op">%>%</span></span>
|
||||
<span id="cb22-2"><a href="#cb22-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></span>
|
||||
<span id="cb22-3"><a href="#cb22-3"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></span>
|
||||
<span id="cb22-4"><a href="#cb22-4"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>only_firsts)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb22"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">only_firsts</span> <span class="kw">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="no">septic_patients</span>, <span class="no">...</span>)) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="no">only_firsts</span> <span class="kw">==</span> <span class="fl">TRUE</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">only_firsts</span>)</pre></div>
|
||||
</li>
|
||||
<li><p>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code></p></li>
|
||||
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-5" class="section level4">
|
||||
<div id="changed-6" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-5" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-6" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
|
||||
<ul>
|
||||
@@ -915,33 +937,33 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1"></a><span class="co"># mo_fullname() uses as.mo() internally</span></span>
|
||||
<span id="cb23-2"><a href="#cb23-2"></a></span>
|
||||
<span id="cb23-3"><a href="#cb23-3"></a><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</span>
|
||||
<span id="cb23-4"><a href="#cb23-4"></a><span class="co">#> [1] "Staphylococcus aureus"</span></span>
|
||||
<span id="cb23-5"><a href="#cb23-5"></a></span>
|
||||
<span id="cb23-6"><a href="#cb23-6"></a><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</span>
|
||||
<span id="cb23-7"><a href="#cb23-7"></a><span class="co">#> [1] "Staphylococcus kloosii"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb23"><pre class="r"><span class="co"># mo_fullname() uses as.mo() internally</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)
|
||||
<span class="co">#> [1] "Staphylococcus aureus"</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)
|
||||
<span class="co">#> [1] "Staphylococcus kloosii"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
|
||||
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb24-1"><a href="#cb24-1"></a><span class="co"># equal:</span></span>
|
||||
<span id="cb24-2"><a href="#cb24-2"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</span>
|
||||
<span id="cb24-3"><a href="#cb24-3"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</span>
|
||||
<span id="cb24-4"><a href="#cb24-4"></a></span>
|
||||
<span id="cb24-5"><a href="#cb24-5"></a><span class="co"># also equal:</span></span>
|
||||
<span id="cb24-6"><a href="#cb24-6"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</span>
|
||||
<span id="cb24-7"><a href="#cb24-7"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb24"><pre class="r"><span class="co"># equal:</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">2</span>)
|
||||
|
||||
<span class="co"># also equal:</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">FALSE</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">...</span>, <span class="kw">allow_uncertain</span> <span class="kw">=</span> <span class="fl">0</span>)</pre></div>
|
||||
<p>Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</p>
|
||||
</li>
|
||||
<li><p>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em></p></li>
|
||||
<li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
|
||||
<li>
|
||||
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</span>
|
||||
<span id="cb25-2"><a href="#cb25-2"></a><span class="co"># Warning: </span></span>
|
||||
<span id="cb25-3"><a href="#cb25-3"></a><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></span>
|
||||
<span id="cb25-4"><a href="#cb25-4"></a><span class="co">#> [1] "(género desconocido)"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb25"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>)
|
||||
<span class="co"># Warning: </span>
|
||||
<span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
|
||||
<span class="co">#> [1] "(género desconocido)"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Fix for vector containing only empty values</p></li>
|
||||
<li><p>Finds better results when input is in other languages</p></li>
|
||||
@@ -986,19 +1008,19 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1"></a><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></span>
|
||||
<span id="cb26-2"><a href="#cb26-2"></a><span class="co"># OLD WAY</span></span>
|
||||
<span id="cb26-3"><a href="#cb26-3"></a>septic_patients <span class="op">%>%</span></span>
|
||||
<span id="cb26-4"><a href="#cb26-4"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></span>
|
||||
<span id="cb26-5"><a href="#cb26-5"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus)</span>
|
||||
<span id="cb26-6"><a href="#cb26-6"></a><span class="co"># NEW WAY</span></span>
|
||||
<span id="cb26-7"><a href="#cb26-7"></a>septic_patients <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb26-8"><a href="#cb26-8"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</span>
|
||||
<span id="cb26-9"><a href="#cb26-9"></a></span>
|
||||
<span id="cb26-10"><a href="#cb26-10"></a><span class="co"># Even supports grouping variables:</span></span>
|
||||
<span id="cb26-11"><a href="#cb26-11"></a>septic_patients <span class="op">%>%</span></span>
|
||||
<span id="cb26-12"><a href="#cb26-12"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(gender) <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb26-13"><a href="#cb26-13"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb26"><pre class="r"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
|
||||
<span class="co"># OLD WAY</span>
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="kw">genus</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>)) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">genus</span>)
|
||||
<span class="co"># NEW WAY</span>
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>))
|
||||
|
||||
<span class="co"># Even supports grouping variables:</span>
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">gender</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="no">mo</span>))</pre></div>
|
||||
</li>
|
||||
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
||||
<li><p>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
|
||||
@@ -1028,7 +1050,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-050" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.5.0">
|
||||
<a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
|
||||
</h1>
|
||||
<div id="new-7" class="section level4">
|
||||
@@ -1045,9 +1067,9 @@
|
||||
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-6" class="section level4">
|
||||
<div id="changed-7" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-6" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-7" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
|
||||
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
|
||||
@@ -1069,10 +1091,10 @@
|
||||
<li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
|
||||
<li>
|
||||
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
|
||||
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></span>
|
||||
<span id="cb27-2"><a href="#cb27-2"></a><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></span>
|
||||
<span id="cb27-3"><a href="#cb27-3"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></span>
|
||||
<span id="cb27-4"><a href="#cb27-4"></a><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb27"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></li>
|
||||
<li><p>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</p></li>
|
||||
@@ -1084,15 +1106,15 @@
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb28-1"><a href="#cb28-1"></a>septic_patients <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb28-2"><a href="#cb28-2"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb28-3"><a href="#cb28-3"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(gender)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb28"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="no">hospital_id</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">gender</span>)</pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb29-1"><a href="#cb29-1"></a>septic_patients <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb29-2"><a href="#cb29-2"></a><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb29-3"><a href="#cb29-3"></a><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb29"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">hospital_id</span>) <span class="kw">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<span class="no">count</span>, -<span class="no">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span></pre></div>
|
||||
</li>
|
||||
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
|
||||
<li><p>Now prints in markdown at default in non-interactive sessions</p></li>
|
||||
@@ -1147,7 +1169,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-040" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.4.0">
|
||||
<a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
|
||||
</h1>
|
||||
<div id="new-8" class="section level4">
|
||||
@@ -1168,18 +1190,18 @@
|
||||
</li>
|
||||
</ul>
|
||||
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb30-1"><a href="#cb30-1"></a><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</span>
|
||||
<span id="cb30-2"><a href="#cb30-2"></a><span class="co"># [1] "Gram negative"</span></span>
|
||||
<span id="cb30-3"><a href="#cb30-3"></a><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></span>
|
||||
<span id="cb30-4"><a href="#cb30-4"></a><span class="co"># [1] "Gramnegativ"</span></span>
|
||||
<span id="cb30-5"><a href="#cb30-5"></a><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></span>
|
||||
<span id="cb30-6"><a href="#cb30-6"></a><span class="co"># [1] "Gram negativo"</span></span>
|
||||
<span id="cb30-7"><a href="#cb30-7"></a><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></span>
|
||||
<span id="cb30-8"><a href="#cb30-8"></a><span class="co"># [1] "Streptococcus grupo A"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb30"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="co"># [1] "Gram negative"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>) <span class="co"># German</span>
|
||||
<span class="co"># [1] "Gramnegativ"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>) <span class="co"># Spanish</span>
|
||||
<span class="co"># [1] "Gram negativo"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span>
|
||||
<span class="co"># [1] "Streptococcus grupo A"</span></pre></div>
|
||||
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
|
||||
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb31-1"><a href="#cb31-1"></a><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</span>
|
||||
<span id="cb31-2"><a href="#cb31-2"></a><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></span>
|
||||
<span id="cb31-3"><a href="#cb31-3"></a><span class="co"># [1] "Gram negative"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb31"><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
|
||||
<span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
|
||||
<span class="co"># [1] "Gram negative"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates</p>
|
||||
@@ -1190,18 +1212,18 @@
|
||||
<li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %>% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
|
||||
<li>
|
||||
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
|
||||
<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb32-1"><a href="#cb32-1"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</span>
|
||||
<span id="cb32-2"><a href="#cb32-2"></a><span class="co"># [1] B_ESCHR_COL</span></span>
|
||||
<span id="cb32-3"><a href="#cb32-3"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</span>
|
||||
<span id="cb32-4"><a href="#cb32-4"></a><span class="co"># [1] B_STPHY_AUR</span></span>
|
||||
<span id="cb32-5"><a href="#cb32-5"></a><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</span>
|
||||
<span id="cb32-6"><a href="#cb32-6"></a><span class="co"># [1] B_STRPTC_GRA</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb32"><pre class="r"><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="co"># [1] B_ESCHR_COL</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)
|
||||
<span class="co"># [1] B_STPHY_AUR</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)
|
||||
<span class="co"># [1] B_STRPTC_GRA</span></pre></div>
|
||||
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
|
||||
<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb33-1"><a href="#cb33-1"></a>thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</span>
|
||||
<span id="cb33-2"><a href="#cb33-2"></a>microbenchmark<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</span>
|
||||
<span id="cb33-3"><a href="#cb33-3"></a><span class="co"># Unit: seconds</span></span>
|
||||
<span id="cb33-4"><a href="#cb33-4"></a><span class="co"># min median max neval</span></span>
|
||||
<span id="cb33-5"><a href="#cb33-5"></a><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb33"><pre class="r"><span class="no">thousands_of_E_colis</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
|
||||
<span class="kw pkg">microbenchmark</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="no">thousands_of_E_colis</span>), <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"s"</span>)
|
||||
<span class="co"># Unit: seconds</span>
|
||||
<span class="co"># min median max neval</span>
|
||||
<span class="co"># 0.01817717 0.01843957 0.03878077 100</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</p></li>
|
||||
<li>
|
||||
@@ -1222,19 +1244,19 @@
|
||||
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-7" class="section level4">
|
||||
<div id="changed-8" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-7" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-8" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
|
||||
<li>
|
||||
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
|
||||
<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb34-1"><a href="#cb34-1"></a><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</span>
|
||||
<span id="cb34-2"><a href="#cb34-2"></a><span class="co"># [1] "Mupirocin"</span></span>
|
||||
<span id="cb34-3"><a href="#cb34-3"></a><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</span>
|
||||
<span id="cb34-4"><a href="#cb34-4"></a><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></span>
|
||||
<span id="cb34-5"><a href="#cb34-5"></a><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</span>
|
||||
<span id="cb34-6"><a href="#cb34-6"></a><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></span></code></pre></div>
|
||||
<div class="sourceCode" id="cb34"><pre class="r"><span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
|
||||
<span class="co"># [1] "Mupirocin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
|
||||
<span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))
|
||||
<span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></pre></div>
|
||||
</li>
|
||||
<li><p>For <code>first_isolate</code>, rows will be ignored when there’s no species available</p></li>
|
||||
<li><p>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</p></li>
|
||||
@@ -1244,13 +1266,13 @@
|
||||
<li><p>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li>
|
||||
<li>
|
||||
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
|
||||
<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb35-1"><a href="#cb35-1"></a>septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</span>
|
||||
<span id="cb35-2"><a href="#cb35-2"></a><span class="co"># which is the same as:</span></span>
|
||||
<span id="cb35-3"><a href="#cb35-3"></a>septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</span>
|
||||
<span id="cb35-4"><a href="#cb35-4"></a></span>
|
||||
<span id="cb35-5"><a href="#cb35-5"></a>septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl)</span>
|
||||
<span id="cb35-6"><a href="#cb35-6"></a>septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl, gent)</span>
|
||||
<span id="cb35-7"><a href="#cb35-7"></a>septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl, gent, pita)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb35"><pre class="r"><span class="no">septic_patients</span> <span class="kw">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>) <span class="kw">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
|
||||
<span class="co"># which is the same as:</span>
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="no">amox</span>, <span class="no">cipr</span>)
|
||||
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="no">amcl</span>)
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="no">amcl</span>, <span class="no">gent</span>)
|
||||
<span class="no">septic_patients</span> <span class="kw">%>%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(<span class="no">amcl</span>, <span class="no">gent</span>, <span class="no">pita</span>)</pre></div>
|
||||
</li>
|
||||
<li><p>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</p></li>
|
||||
<li><p>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</p></li>
|
||||
@@ -1262,12 +1284,12 @@
|
||||
<li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li>
|
||||
<li>
|
||||
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
||||
<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb36-1"><a href="#cb36-1"></a>my_matrix =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/with.html">with</a></span>(septic_patients, <span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</span>
|
||||
<span id="cb36-2"><a href="#cb36-2"></a><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_matrix)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb36"><pre class="r"><span class="no">my_matrix</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="no">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">age</span>, <span class="no">gender</span>), <span class="kw">ncol</span> <span class="kw">=</span> <span class="fl">2</span>))
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">my_matrix</span>)</pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb37-1"><a href="#cb37-1"></a>my_list =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</span>
|
||||
<span id="cb37-2"><a href="#cb37-2"></a>my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age)</span>
|
||||
<span id="cb37-3"><a href="#cb37-3"></a>my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(gender)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb37"><pre class="r"><span class="no">my_list</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="kw">age</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">age</span>, <span class="kw">gender</span> <span class="kw">=</span> <span class="no">septic_patients</span>$<span class="no">gender</span>)
|
||||
<span class="no">my_list</span> <span class="kw">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">age</span>)
|
||||
<span class="no">my_list</span> <span class="kw">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="no">gender</span>)</pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
@@ -1280,7 +1302,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-030" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.3.0">
|
||||
<a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
|
||||
</h1>
|
||||
<div id="new-9" class="section level4">
|
||||
@@ -1356,9 +1378,9 @@
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-8" class="section level4">
|
||||
<div id="changed-9" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-8" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-9" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
|
||||
<li>More antibiotics added as parameters for EUCAST rules</li>
|
||||
@@ -1417,7 +1439,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-020" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.2.0">
|
||||
<a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
|
||||
</h1>
|
||||
<div id="new-10" class="section level4">
|
||||
@@ -1442,9 +1464,9 @@
|
||||
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-9" class="section level4">
|
||||
<div id="changed-10" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-9" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-10" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
|
||||
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>
|
||||
@@ -1475,7 +1497,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-011" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.1.1">
|
||||
<a href="#amr-011" class="anchor"></a>AMR 0.1.1<small> 2018-03-14 </small>
|
||||
</h1>
|
||||
<ul>
|
||||
@@ -1488,7 +1510,7 @@
|
||||
</ul>
|
||||
</div>
|
||||
<div id="amr-010" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<h1 class="page-header" data-toc-text="0.1.0">
|
||||
<a href="#amr-010" class="anchor"></a>AMR 0.1.0<small> 2018-02-22 </small>
|
||||
</h1>
|
||||
<ul>
|
||||
@@ -1497,27 +1519,10 @@
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-1019004">1.0.1.9004</a></li>
|
||||
<li><a href="#amr-101">1.0.1</a></li>
|
||||
<li><a href="#amr-100">1.0.0</a></li>
|
||||
<li><a href="#amr-090">0.9.0</a></li>
|
||||
<li><a href="#amr-080">0.8.0</a></li>
|
||||
<li><a href="#amr-071">0.7.1</a></li>
|
||||
<li><a href="#amr-070">0.7.0</a></li>
|
||||
<li><a href="#amr-061">0.6.1</a></li>
|
||||
<li><a href="#amr-060">0.6.0</a></li>
|
||||
<li><a href="#amr-050">0.5.0</a></li>
|
||||
<li><a href="#amr-040">0.4.0</a></li>
|
||||
<li><a href="#amr-030">0.3.0</a></li>
|
||||
<li><a href="#amr-020">0.2.0</a></li>
|
||||
<li><a href="#amr-011">0.1.1</a></li>
|
||||
<li><a href="#amr-010">0.1.0</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
@@ -1529,7 +1534,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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</div>
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</footer>
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|
||||
121
docs/pkgdown.css
121
docs/pkgdown.css
@@ -17,6 +17,10 @@ html, body {
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height: 100%;
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}
|
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body {
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position: relative;
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}
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|
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body > .container {
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height: 100%;
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@@ -67,6 +71,10 @@ summary {
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margin-top: calc(-60px + 1em);
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a.anchor {
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@@ -100,29 +108,132 @@ a.anchor {
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.dropdown-submenu.pull-left>.dropdown-menu {
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#sidebar {
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nav[data-toggle='toc'] .nav > .active > a,
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nav[data-toggle='toc'] .nav > .active:hover > a,
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/* Nav: second level (shown on .active) */
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nav[data-toggle='toc'] .nav .nav {
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||||
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||||
padding-bottom: 10px;
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||||
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||||
nav[data-toggle='toc'] .nav .nav > li > a {
|
||||
padding-left: 16px;
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||||
font-size: 1.35rem;
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||||
}
|
||||
|
||||
nav[data-toggle='toc'] .nav .nav > li > a:hover,
|
||||
nav[data-toggle='toc'] .nav .nav > li > a:focus {
|
||||
padding-left: 15px;
|
||||
}
|
||||
|
||||
nav[data-toggle='toc'] .nav .nav > .active > a,
|
||||
nav[data-toggle='toc'] .nav .nav > .active:hover > a,
|
||||
nav[data-toggle='toc'] .nav .nav > .active:focus > a {
|
||||
padding-left: 15px;
|
||||
font-weight: 500;
|
||||
font-size: 1.35rem;
|
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}
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||||
/* orcid ------------------------------------------------------------------- */
|
||||
|
||||
.orcid {
|
||||
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|
||||
font-size: 16px;
|
||||
color: #A6CE39;
|
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/* margins are required by official ORCID trademark and display guidelines */
|
||||
margin-left:4px;
|
||||
margin-right:4px;
|
||||
|
||||
@@ -9,11 +9,6 @@
|
||||
$('body').css('padding-top', $('.navbar').height() + 10);
|
||||
});
|
||||
|
||||
$('body').scrollspy({
|
||||
target: '#sidebar',
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offset: 60
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|
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|
||||
$('[data-toggle="tooltip"]').tooltip();
|
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|
||||
var cur_path = paths(location.pathname);
|
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|
||||
@@ -1,5 +1,5 @@
|
||||
pandoc: 2.7.3
|
||||
pkgdown: 1.4.1
|
||||
pkgdown: 1.5.0
|
||||
pkgdown_sha: ~
|
||||
articles:
|
||||
AMR: AMR.html
|
||||
@@ -10,6 +10,7 @@ articles:
|
||||
WHONET: WHONET.html
|
||||
benchmarks: benchmarks.html
|
||||
resistance_predict: resistance_predict.html
|
||||
last_built: 2020-04-13T19:09Z
|
||||
urls:
|
||||
reference: https://msberends.gitlab.io/AMR/reference
|
||||
article: https://msberends.gitlab.io/AMR/articles
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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||||
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||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Deprecated functions — AMR-deprecated" />
|
||||
<meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -253,7 +259,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#retired-lifecycle">Retired lifecycle</a></li>
|
||||
@@ -270,7 +276,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
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|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="The <code>AMR</code> Package — AMR" />
|
||||
<meta property="og:description" content="Welcome to the AMR package." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
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<meta property="og:image" content="/logo.svg" />
|
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|
||||
|
||||
|
||||
@@ -276,7 +275,7 @@ The Netherlands</p>
|
||||
<a href='https://gitlab.com/msberends/AMR/issues'>https://gitlab.com/msberends/AMR/issues</a></p>
|
||||
|
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</div>
|
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
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<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#details">Details</a></li>
|
||||
@@ -294,7 +293,7 @@ The Netherlands</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -17,16 +17,16 @@
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- Font Awesome icons -->
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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<!-- clipboard.js -->
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC" />
|
||||
<meta property="og:description" content="All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary" />
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<meta property="og:image" content="/logo.svg" />
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@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -248,7 +254,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#whocc">WHOCC</a></li>
|
||||
@@ -266,7 +272,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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</div>
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</footer>
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@@ -17,23 +17,27 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
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<script src="../bootstrap-toc.js"></script>
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<!-- Font Awesome icons -->
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
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<!-- clipboard.js -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
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<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -46,8 +50,7 @@
|
||||
|
||||
<meta property="og:title" content="Data set with 500 isolates - WHONET example — WHONET" />
|
||||
<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our example_isolates data set." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -65,7 +68,7 @@
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-reference-topic">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -79,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -224,7 +227,7 @@
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data set with 500 isolates - WHONET example</h1>
|
||||
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>WHONET.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -263,7 +266,7 @@
|
||||
<li><p><code>Inducible clindamycin resistance</code><br /> Clindamycin can be induced?</p></li>
|
||||
<li><p><code>Comment</code><br /> Other comments</p></li>
|
||||
<li><p><code>Date of data entry</code><br /> Date this data was entered in WHONET</p></li>
|
||||
<li><p><code>AMP_ND10:CIP_EE</code><br /> 27 different antibiotics. You can lookup the abbreviatons in the <a href='antibiotics.html'>antibiotics</a> data set, or use e.g. <code><a href='ab_property.html'>ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href='as.rsi.html'>as.rsi()</a></code>.</p></li>
|
||||
<li><p><code>AMP_ND10:CIP_EE</code><br /> 28 different antibiotics. You can lookup the abbreviations in the <a href='antibiotics.html'>antibiotics</a> data set, or use e.g. <code><a href='ab_property.html'>ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href='as.rsi.html'>as.rsi()</a></code>.</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
@@ -273,13 +276,10 @@
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
</ul>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -290,7 +290,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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</div>
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</footer>
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@@ -17,16 +17,16 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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|
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<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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|
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<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
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|
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<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Property of an antibiotic — ab_property" />
|
||||
<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
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|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -355,7 +361,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
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<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -378,7 +384,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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</div>
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</footer>
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@@ -17,16 +17,16 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- Font Awesome icons -->
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Age in years of individuals — age" />
|
||||
<meta property="og:description" content="Calculates age in years based on a reference date, which is the sytem date at default." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
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<meta name="twitter:card" content="summary" />
|
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<meta property="og:image" content="/logo.svg" />
|
||||
|
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|
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|
||||
@@ -284,7 +283,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<span class='no'>df</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -305,7 +304,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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</div>
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</footer>
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@@ -17,16 +17,16 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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|
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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<!-- clipboard.js -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Split ages into age groups — age_groups" />
|
||||
<meta property="og:description" content="Split ages into age groups defined by the split parameter. This allows for easier demographic (antimicrobial resistance) analysis." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
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<meta name="twitter:card" content="summary" />
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<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -316,7 +315,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
|
||||
}</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -338,7 +337,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
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</footer>
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@@ -6,7 +6,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Data sets with ~550 antimicrobials — antibiotics • AMR (for R)</title>
|
||||
<title>Data sets with 554 antimicrobials — antibiotics • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
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@@ -17,23 +17,27 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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|
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<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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||||
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
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<script src="../bootstrap-toc.js"></script>
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<!-- Font Awesome icons -->
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
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||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
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<!-- clipboard.js -->
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -44,10 +48,9 @@
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="Data sets with ~550 antimicrobials — antibiotics" />
|
||||
<meta property="og:title" content="Data sets with 554 antimicrobials — antibiotics" />
|
||||
<meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_property() functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -65,7 +68,7 @@
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-reference-topic">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -79,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -223,8 +226,8 @@
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data sets with ~550 antimicrobials</h1>
|
||||
|
||||
<h1>Data sets with 554 antimicrobials</h1>
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>antibiotics.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -312,17 +315,10 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
<li><a href="#source">Source</a></li>
|
||||
<li><a href="#details">Details</a></li>
|
||||
<li><a href="#whocc">WHOCC</a></li>
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
</ul>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -333,7 +329,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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</div>
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</footer>
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@@ -17,16 +17,16 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
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|
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<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
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|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Transform to antibiotic ID — as.ab" />
|
||||
<meta property="og:description" content="Use this function to determine the antibiotic code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and synonyms (brand names)." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -304,7 +310,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -328,7 +334,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Class 'disk' — as.disk" />
|
||||
<meta property="og:description" content="This transforms a vector to a new class disk, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -283,7 +289,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='no'>df</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -305,7 +311,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Class 'mic' — as.mic" />
|
||||
<meta property="og:description" content="This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -285,7 +291,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='no'>mic_data</span>)
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>mic_data</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -307,7 +313,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Transform to microorganism ID — as.mo" />
|
||||
<meta property="og:description" content="Use this function to determine a valid microorganism ID (mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like "Staphylococcus aureus"), an abbreviated name (like "S. aureus"), an abbreviation known in the field (like "MRSA"), or just a genus. Please see Examples." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -431,7 +437,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'>as.mo</span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='no'>genus</span>, <span class='no'>species</span>)))
|
||||
}</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -455,7 +461,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Class 'rsi' — as.rsi" />
|
||||
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &lt; I &lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -406,7 +412,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>) <span class='co'># fails, >80% is invalid</span>
|
||||
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.99</span>) <span class='co'># succeeds</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -429,7 +435,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -47,8 +47,7 @@
|
||||
<meta property="og:title" content="Get ATC properties from WHOCC website — atc_online_property" />
|
||||
<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
|
||||
This function requires an internet connection." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -80,7 +79,7 @@ This function requires an internet connection." />
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -116,6 +115,13 @@ This function requires an internet connection." />
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -318,7 +324,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
<span class='co'># [4] "Penicillins with extended spectrum"</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -339,7 +345,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Check availability of columns — availability" />
|
||||
<meta property="og:description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -274,7 +280,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='no'>is.rsi</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>availability</span>()</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -295,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Determine bug-drug combinations — bug_drug_combinations" />
|
||||
<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -341,7 +347,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='st'>"Others"</span>))
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -363,7 +369,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
|
||||
<meta property="og:description" content="This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -289,7 +295,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"C. elegans"</span>)
|
||||
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
|
||||
@@ -309,7 +315,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
|
||||
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -255,7 +261,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class='no'>microorganisms</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>kingdom</span>)
|
||||
<span class='no'>microorganisms</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>kingdom</span>) <span class='kw'>%>%</span> <span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>phylum</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#value">Value</a></li>
|
||||
@@ -276,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -47,8 +47,7 @@
|
||||
<meta property="og:title" content="Count available isolates — count" />
|
||||
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() and support grouped variables, see Examples.
|
||||
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -80,7 +79,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -116,6 +115,13 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -338,9 +344,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
--------------------------------------------------------------------
|
||||
</pre>
|
||||
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> count_S() + count_I() + count_R() = count_all()
|
||||
proportion_S() + proportion_I() + proportion_R() = 1
|
||||
</pre>
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span>() + <span class='fu'>count_I</span>() + <span class='fu'>count_R</span>() <span class='kw'>=</span> <span class='fu'>count_all</span>()
|
||||
<span class='fu'><a href='proportion.html'>proportion_S</a></span>() + <span class='fu'><a href='proportion.html'>proportion_I</a></span>() + <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
|
||||
|
||||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() >= count_all()
|
||||
proportion_S() + proportion_I() + proportion_R() >= 1
|
||||
@@ -390,7 +395,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>CIP</span>),
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
|
||||
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
|
||||
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
|
||||
@@ -414,7 +419,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -438,7 +443,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -47,8 +47,7 @@
|
||||
<meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
|
||||
<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
|
||||
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -80,7 +79,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -116,6 +115,13 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -437,7 +443,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<span class='no'>c</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -460,7 +466,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Data set with 2,000 example isolates — example_isolates" />
|
||||
<meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read the tutorial on our website." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -257,7 +256,7 @@
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
@@ -274,7 +273,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Data set with unclean data — example_isolates_unclean" />
|
||||
<meta property="og:description" content="A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -252,7 +251,7 @@
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
@@ -269,7 +268,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Extended functions — extended-functions" />
|
||||
<meta property="og:description" content="These functions are extensions of functions in other packages." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -244,7 +250,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
|
||||
@@ -261,7 +267,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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||||
</div>
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||||
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||||
</footer>
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|
||||
@@ -17,16 +17,16 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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||||
|
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<!-- jquery -->
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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||||
<!-- Bootstrap -->
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||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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|
||||
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Filter isolates on result in antibiotic class — filter_ab_class" />
|
||||
<meta property="og:description" content="Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -317,7 +323,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -336,7 +342,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Determine first (weighted) isolates — first_isolate" />
|
||||
<meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -352,19 +358,17 @@
|
||||
<p><strong>WHY THIS IS SO IMPORTANT</strong> <br />
|
||||
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode <a href='https://www.ncbi.nlm.nih.gov/pubmed/17304462'>(ref)</a>. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all <em>S. aureus</em> isolates would be overestimated, because you included this MRSA more than once. It would be <a href='https://en.wikipedia.org/wiki/Selection_bias'>selection bias</a>.</p>
|
||||
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p>
|
||||
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates. The function <code>filter_first_isolate()</code> is essentially equal to:</p><pre> x %>%
|
||||
mutate(only_firsts = first_isolate(x, ...)) %>%
|
||||
filter(only_firsts == TRUE) %>%
|
||||
select(-only_firsts)
|
||||
</pre>
|
||||
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates. The function <code>filter_first_isolate()</code> is essentially equal to:</p><pre> <span class='no'>x</span> <span class='kw'>%&gt;%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>only_firsts</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>, <span class='no'>...</span>)) <span class='kw'>%&gt;%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>only_firsts</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>only_firsts</span>)</pre>
|
||||
|
||||
<p>The function <code>filter_first_weighted_isolate()</code> is essentially equal to:</p><pre> x %>%
|
||||
mutate(keyab = key_antibiotics(.)) %>%
|
||||
mutate(only_weighted_firsts = first_isolate(x,
|
||||
col_keyantibiotics = "keyab", ...)) %>%
|
||||
filter(only_weighted_firsts == TRUE) %>%
|
||||
select(-only_weighted_firsts)
|
||||
</pre>
|
||||
<p>The function <code>filter_first_weighted_isolate()</code> is essentially equal to:</p><pre> <span class='no'>x</span> <span class='kw'>%&gt;%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>only_weighted_firsts</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>,
|
||||
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>"keyab"</span>, <span class='no'>...</span>)) <span class='kw'>%&gt;%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>only_weighted_firsts</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%&gt;%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(-<span class='no'>only_weighted_firsts</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
|
||||
|
||||
@@ -445,7 +449,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='no'>x</span>$<span class='no'>first_blood_isolate</span> <span class='kw'><-</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>, <span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>"Blood"</span>)
|
||||
}</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -469,7 +473,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="<em>G</em>-test for Count Data — g.test" />
|
||||
<meta property="og:description" content="g.test() performs chi-squared contingency table tests and goodness-of-fit tests, just like chisq.test() but is more reliable (1). A G-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a G-test of goodness-of-fit), or to see whether the proportions of one variable are different for different values of the other variable (called a G-test of independence)." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -309,8 +315,7 @@
|
||||
<p>Unlike the exact test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
|
||||
<p>The <em>G</em>-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a <em>G</em>-statistic is:</p>
|
||||
<p>\(G = 2 * sum(x * log(x / E))\)</p>
|
||||
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre>p <- stats::pchisq(G, df, lower.tail = FALSE)
|
||||
</pre>
|
||||
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre><span class='no'>p</span> <span class='kw'>&</span><span class='no'>lt</span>;- <span class='kw pkg'>stats</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span>(<span class='no'>G</span>, <span class='no'>df</span>, <span class='kw'>lower.tail</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
|
||||
<p>where <code>df</code> are the degrees of freedom.</p>
|
||||
<p>If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use <em>G</em>-tests for each category, of course.</p>
|
||||
@@ -370,7 +375,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
<span class='co'># There is a significant difference from a 1:1 ratio.</span>
|
||||
<span class='co'># Meaning: there are significantly more left-billed birds.</span></pre>
|
||||
</div>
|
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<h2>Contents</h2>
|
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<ul class="nav nav-pills nav-stacked">
|
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<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -394,7 +399,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -17,23 +17,27 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
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<!-- headroom.js -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<!-- pkgdown -->
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<link href="../pkgdown.css" rel="stylesheet">
|
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@@ -45,9 +49,8 @@
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="PCA biplot with <code>ggplot2</code> — ggplot_pca" />
|
||||
<meta property="og:description" content="This function is to produce a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:description" content="Produces a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -65,7 +68,7 @@
|
||||
|
||||
</head>
|
||||
|
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<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-reference-topic">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -79,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -224,12 +227,12 @@
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>PCA biplot with <code>ggplot2</code></h1>
|
||||
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ggplot_pca.R'><code>R/ggplot_pca.R</code></a></small>
|
||||
<div class="hidden name"><code>ggplot_pca.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>This function is to produce a <code>ggplot2</code> variant of a so-called <a href='https://en.wikipedia.org/wiki/Biplot'>biplot</a> for PCA (principal component analysis), but is more flexible and more appealing than the base <span style="R">R</span> <code><a href='https://rdrr.io/r/stats/biplot.html'>biplot()</a></code> function.</p>
|
||||
<p>Produces a <code>ggplot2</code> variant of a so-called <a href='https://en.wikipedia.org/wiki/Biplot'>biplot</a> for PCA (principal component analysis), but is more flexible and more appealing than the base <span style="R">R</span> <code><a href='https://rdrr.io/r/stats/biplot.html'>biplot()</a></code> function.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ggplot_pca</span>(
|
||||
@@ -393,16 +396,10 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<span class='co'># new </span>
|
||||
<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
<li><a href="#source">Source</a></li>
|
||||
<li><a href="#details">Details</a></li>
|
||||
<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
|
||||
<li><a href="#examples">Examples</a></li>
|
||||
</ul>
|
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||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -413,7 +410,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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</footer>
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@@ -17,16 +17,16 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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<!-- clipboard.js -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
|
||||
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot2 functions." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
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<meta property="og:image" content="/logo.svg" />
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@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -500,7 +506,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (EARS-Net code)"</span>)
|
||||
}</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -520,7 +526,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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@@ -17,16 +17,16 @@
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- Font Awesome icons -->
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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<!-- clipboard.js -->
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Guess antibiotic column — guess_ab_col" />
|
||||
<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary" />
|
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<meta property="og:image" content="/logo.svg" />
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|
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|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -291,7 +297,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"ampicillin"</span>)
|
||||
<span class='co'># [1] "AMP_ED20"</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -312,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,23 +17,27 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -45,8 +49,7 @@
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="Function reference" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -64,7 +67,7 @@
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-reference-index">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -78,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -240,6 +243,11 @@
|
||||
<p class="section-desc"><p>Functions for cleaning and optimising your data, to be able to add variables later on (like taxonomic properties) or to fix and extend antibiotic interpretations by applying <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a>.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
|
||||
|
||||
</tbody><tbody>
|
||||
|
||||
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
@@ -302,6 +310,11 @@
|
||||
<p class="section-desc"><p>Functions to add new data to your existing data, such as the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
|
||||
|
||||
</tbody><tbody>
|
||||
|
||||
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
@@ -370,6 +383,11 @@
|
||||
<p class="section-desc"><p>Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, or make plots.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
|
||||
|
||||
</tbody><tbody>
|
||||
|
||||
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
@@ -450,18 +468,23 @@
|
||||
<p class="section-desc"><p>Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
|
||||
|
||||
</tbody><tbody>
|
||||
|
||||
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with ~70,000 microorganisms</p></td>
|
||||
<td><p>Data set with 69,447 microorganisms</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data sets with ~550 antimicrobials</p></td>
|
||||
<td><p>Data sets with 554 antimicrobials</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@@ -506,6 +529,11 @@
|
||||
<p class="section-desc"><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
|
||||
|
||||
</tbody><tbody>
|
||||
|
||||
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
@@ -544,6 +572,11 @@
|
||||
<p class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
|
||||
|
||||
</tbody><tbody>
|
||||
|
||||
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
@@ -576,6 +609,11 @@
|
||||
<p class="section-desc"><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
|
||||
|
||||
</tbody><tbody>
|
||||
|
||||
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
@@ -587,17 +625,10 @@
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#section-cleaning-your-data">Cleaning your data</a></li>
|
||||
<li><a href="#section-enhancing-your-data">Enhancing your data</a></li>
|
||||
<li><a href="#section-analysing-your-data">Analysing your data</a></li>
|
||||
<li><a href="#section-included-data-sets">Included data sets</a></li>
|
||||
<li><a href="#section-background-information">Background information</a></li>
|
||||
<li><a href="#section-other-functions">Other functions</a></li>
|
||||
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
|
||||
</ul>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -608,7 +639,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Join a table with <a href='microorganisms.html'>microorganisms</a> — join" />
|
||||
<meta property="og:description" content="Join the data set microorganisms easily to an existing table or character vector." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -254,13 +260,13 @@
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>other parameters to pass on to <code><a href='https://dplyr.tidyverse.org/reference/join.html'>dplyr::join()</a></code></p></td>
|
||||
<td><p>other parameters to pass on to <code><a href='https://dplyr.tidyverse.org/reference/mutate-joins.html'>dplyr::join()</a></code></p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p><strong>Note:</strong> As opposed to the <code><a href='https://dplyr.tidyverse.org/reference/join.html'>dplyr::join()</a></code> functions of <code>dplyr</code>, <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='https://dplyr.tidyverse.org/reference/join.html'>dplyr::join()</a></code> for more information.</p>
|
||||
<p><strong>Note:</strong> As opposed to the <code><a href='https://dplyr.tidyverse.org/reference/mutate-joins.html'>dplyr::join()</a></code> functions of <code>dplyr</code>, <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix. See <code><a href='https://dplyr.tidyverse.org/reference/mutate-joins.html'>dplyr::join()</a></code> for more information.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
@@ -291,7 +297,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='no'>df_joined</span> <span class='kw'><-</span> <span class='fu'>left_join_microorganisms</span>(<span class='no'>df</span>, <span class='st'>"bacteria"</span>)
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span>(<span class='no'>df_joined</span>)</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -311,7 +317,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Key antibiotics for first <em>weighted</em> isolates — key_antibiotics" />
|
||||
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -403,7 +409,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -425,7 +431,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Kurtosis of the sample — kurtosis" />
|
||||
<meta property="og:description" content="Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -265,7 +271,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
<div class='dont-index'><p><code><a href='skewness.html'>skewness()</a></code></p></div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -284,7 +290,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -48,8 +48,7 @@
|
||||
<meta property="og:description" content="Our functions are categorised using the lifecycle circle of the tidyverse as found on www.tidyverse.org/lifecycle.
|
||||
|
||||
This page contains a section for every lifecycle (with text borrowed from the aforementioned tidyverse website), so they can be used in the manual pages of our functions." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -283,7 +282,7 @@ The lifecycle of this function is <strong>dormant</strong>. A dormant function i
|
||||
The lifecycle of this function is <strong>questioning</strong>. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our <code>AMR</code> package at all.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#experimental-lifecycle">Experimental lifecycle</a></li>
|
||||
@@ -305,7 +304,7 @@ The lifecycle of this function is <strong>questioning</strong>. We are no longer
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Pattern Matching — like" />
|
||||
<meta property="og:description" content="Convenient wrapper around base::grep() to match a pattern: a %like% b. It always returns a logical vector and is always case-insensitive (use a %like_case% b for case-sensitive matching). Also, pattern (b) can be as long as x (a) to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -294,7 +300,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>))</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -317,7 +323,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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</div>
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</footer>
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@@ -17,16 +17,16 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- Font Awesome icons -->
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||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
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<!-- clipboard.js -->
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Determine multidrug-resistant organisms (MDRO) — mdro" />
|
||||
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
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<meta name="twitter:card" content="summary" />
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<meta property="og:image" content="/logo.svg" />
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@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -443,7 +449,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>))
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -467,7 +473,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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</div>
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</footer>
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@@ -17,23 +17,27 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
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<link rel="stylesheet" href="../bootstrap-toc.css">
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<script src="../bootstrap-toc.js"></script>
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<!-- Font Awesome icons -->
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
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<!-- clipboard.js -->
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
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<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -46,8 +50,7 @@
|
||||
|
||||
<meta property="og:title" content="Translation table for common microorganism codes — microorganisms.codes" />
|
||||
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
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<meta name="twitter:card" content="summary" />
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
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|
||||
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||||
|
||||
@@ -65,7 +68,7 @@
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-reference-topic">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -79,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -224,7 +227,7 @@
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Translation table for common microorganism codes</h1>
|
||||
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -237,7 +240,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,450 observations and 2 variables:</p><ul>
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,585 observations and 2 variables:</p><ul>
|
||||
<li><p><code>code</code><br /> Commonly used code of a microorganism</p></li>
|
||||
<li><p><code>mo</code><br /> ID of the microorganism in the <a href='microorganisms.html'>microorganisms</a> data set</p></li>
|
||||
</ul>
|
||||
@@ -259,15 +262,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
</ul>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -278,7 +276,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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</div>
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</footer>
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@@ -6,7 +6,7 @@
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||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Data set with ~70,000 microorganisms — microorganisms • AMR (for R)</title>
|
||||
<title>Data set with 69,447 microorganisms — microorganisms • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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@@ -17,23 +17,27 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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|
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
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<link rel="stylesheet" href="../bootstrap-toc.css">
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<script src="../bootstrap-toc.js"></script>
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<!-- Font Awesome icons -->
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
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<!-- clipboard.js -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
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<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
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@@ -44,10 +48,9 @@
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<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="Data set with ~70,000 microorganisms — microorganisms" />
|
||||
<meta property="og:title" content="Data set with 69,447 microorganisms — microorganisms" />
|
||||
<meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo()." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary" />
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
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@@ -65,7 +68,7 @@
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|
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</head>
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|
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<body>
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<body data-spy="scroll" data-target="#toc">
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||||
<div class="container template-reference-topic">
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||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -79,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -223,8 +226,8 @@
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data set with ~70,000 microorganisms</h1>
|
||||
|
||||
<h1>Data set with 69,447 microorganisms</h1>
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>microorganisms.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -262,7 +265,7 @@
|
||||
<li><p>3 entries of <em>Trichomonas</em> (<em>Trichomonas vaginalis</em>, and its family and genus)</p></li>
|
||||
<li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
|
||||
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
|
||||
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not in the Catalogue of Life</p></li>
|
||||
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
|
||||
<li><p>12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
|
||||
</ul>
|
||||
<h3>Direct download</h3>
|
||||
@@ -296,18 +299,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code>, <code><a href='mo_property.html'>mo_property()</a></code>, <a href='microorganisms.codes.html'>microorganisms.codes</a></p></div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
<li><a href="#source">Source</a></li>
|
||||
<li><a href="#details">Details</a></li>
|
||||
<li><a href="#about-the-records-from-dsmz-see-source-">About the records from DSMZ (see source)</a></li>
|
||||
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
</ul>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -318,7 +313,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,23 +17,27 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -46,8 +50,7 @@
|
||||
|
||||
<meta property="og:title" content="Data set with previously accepted taxonomic names — microorganisms.old" />
|
||||
<meta property="og:description" content="A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by as.mo()." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -65,7 +68,7 @@
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-reference-topic">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -79,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -224,7 +227,7 @@
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data set with previously accepted taxonomic names</h1>
|
||||
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>microorganisms.old.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -237,7 +240,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 24,246 observations and 5 variables:</p><ul>
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 24,253 observations and 5 variables:</p><ul>
|
||||
<li><p><code>col_id</code><br /> Catalogue of Life ID that was originally given</p></li>
|
||||
<li><p><code>col_id_new</code><br /> New Catalogue of Life ID that responds to an entry in the <a href='microorganisms.html'>microorganisms</a> data set</p></li>
|
||||
<li><p><code>fullname</code><br /> Old full taxonomic name of the microorganism</p></li>
|
||||
@@ -265,16 +268,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <code><a href='mo_property.html'>mo_property()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
<li><a href="#source">Source</a></li>
|
||||
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
</ul>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -285,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Property of a microorganism — mo_property" />
|
||||
<meta property="og:description" content="Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -430,7 +436,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class='fu'>mo_info</span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -453,7 +459,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -47,8 +47,7 @@
|
||||
<meta property="og:title" content="Use predefined reference data set — mo_source" />
|
||||
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
|
||||
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -80,7 +79,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -116,6 +115,13 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -256,9 +262,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
4 | | |
|
||||
</pre>
|
||||
|
||||
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre>set_mo_source("home/me/ourcodes.xlsx")
|
||||
# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
|
||||
</pre>
|
||||
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre><span class='fu'>set_mo_source</span>(<span class='st'>"home/me/ourcodes.xlsx"</span>)
|
||||
<span class='co'># Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.</span></pre>
|
||||
|
||||
<p>It has now created a file <code>"~/.mo_source.rds"</code> with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.</p>
|
||||
<p>And now we can use it in our functions:</p><pre>as.mo("lab_mo_ecoli")
|
||||
@@ -289,9 +294,8 @@ mo_genus("lab_Staph_aureus")
|
||||
[1] "Staphylococcus"
|
||||
</pre>
|
||||
|
||||
<p>To remove the reference data file completely, just use <code>""</code> or <code>NULL</code> as input for <code>[set_mo_source()]</code>:</p><pre>set_mo_source(NULL)
|
||||
# Removed mo_source file '~/.mo_source.rds'.
|
||||
</pre>
|
||||
<p>To remove the reference data file completely, just use <code>""</code> or <code>NULL</code> as input for <code>[set_mo_source()]</code>:</p><pre><span class='fu'>set_mo_source</span>(<span class='kw'>NULL</span>)
|
||||
<span class='co'># Removed mo_source file '~/.mo_source.rds'.</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
@@ -308,7 +312,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -327,7 +331,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Symbol of a p-value — p_symbol" />
|
||||
<meta property="og:description" content="Return the symbol related to the p-value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above p = 1 will return NA." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -256,7 +262,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -275,7 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Principal Component Analysis (for AMR) — pca" />
|
||||
<meta property="og:description" content="Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -328,7 +327,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_result</span>)
|
||||
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='no'>pca_result</span>) <span class='co'># a new and convenient plot function</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -348,7 +347,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -47,8 +47,7 @@
|
||||
<meta property="og:title" content="Calculate microbial resistance — proportion" />
|
||||
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in summarise()][dplyr::summarise()] and also support grouped variables, please see Examples.
|
||||
resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -80,7 +79,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -116,6 +115,13 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -336,9 +342,8 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
--------------------------------------------------------------------
|
||||
</pre>
|
||||
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> count_S() + count_I() + count_R() = count_all()
|
||||
proportion_S() + proportion_I() + proportion_R() = 1
|
||||
</pre>
|
||||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'><a href='count.html'>count_S</a></span>() + <span class='fu'><a href='count.html'>count_I</a></span>() + <span class='fu'><a href='count.html'>count_R</a></span>() <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>()
|
||||
<span class='fu'>proportion_S</span>() + <span class='fu'>proportion_I</span>() + <span class='fu'>proportion_R</span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
|
||||
|
||||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() >= count_all()
|
||||
proportion_S() + proportion_I() + proportion_R() >= 1
|
||||
@@ -401,7 +406,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class='kw'>SI</span> <span class='kw'>=</span> <span class='fu'>susceptibility</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
|
||||
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
|
||||
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
|
||||
@@ -457,7 +462,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>))
|
||||
}</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -482,7 +487,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
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|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
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|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Read data from 4D database — read.4D" />
|
||||
<meta property="og:description" content="This function is only useful for the MMB department of the UMCG. Use this function to import data by just defining the file parameter. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with as.mo() and transform all antimicrobial columns with as.rsi()." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -394,7 +400,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -413,7 +419,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
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</div>
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|
||||
</footer>
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|
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@@ -17,16 +17,16 @@
|
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
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|
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<!-- jquery -->
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
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|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -51,8 +51,7 @@ below to see their documentation.
|
||||
cleanerfreq
|
||||
|
||||
" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -84,7 +83,7 @@ below to see their documentation.
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -120,6 +119,13 @@ below to see their documentation.
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -239,7 +245,7 @@ below to see their documentation.</p>
|
||||
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
</ul>
|
||||
@@ -254,7 +260,7 @@ below to see their documentation.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -17,16 +17,16 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Predict antimicrobial resistance — resistance_predict" />
|
||||
<meta property="og:description" content="Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns se_min and se_max. See Examples for a real live example." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -427,7 +433,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
|
||||
}</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -450,7 +456,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
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|
||||
</footer>
|
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|
||||
@@ -17,23 +17,27 @@
|
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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||||
<!-- Bootstrap -->
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||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
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|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
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||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -46,8 +50,7 @@
|
||||
|
||||
<meta property="og:title" content="Data set for R/SI interpretation — rsi_translation" />
|
||||
<meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -65,7 +68,7 @@
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-reference-topic">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
@@ -79,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -224,7 +227,7 @@
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data set for R/SI interpretation</h1>
|
||||
|
||||
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>rsi_translation.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -237,7 +240,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 13,975 observations and 9 variables:</p><ul>
|
||||
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 15,745 observations and 10 variables:</p><ul>
|
||||
<li><p><code>guideline</code><br /> Name of the guideline</p></li>
|
||||
<li><p><code>method</code><br /> Either "MIC" or "DISK"</p></li>
|
||||
<li><p><code>site</code><br /> Body site, e.g. "Oral" or "Respiratory"</p></li>
|
||||
@@ -247,6 +250,7 @@
|
||||
<li><p><code>disk_dose</code><br /> Dose of the used disk diffusion method</p></li>
|
||||
<li><p><code>breakpoint_S</code><br /> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
|
||||
<li><p><code>breakpoint_R</code><br /> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
|
||||
<li><p><code>uti</code><br /> A logical value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
@@ -259,14 +263,10 @@
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#format">Format</a></li>
|
||||
<li><a href="#details">Details</a></li>
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
</ul>
|
||||
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@@ -277,7 +277,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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</div>
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|
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</footer>
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|
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@@ -17,16 +17,16 @@
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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|
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<!-- jquery -->
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -47,8 +47,7 @@
|
||||
<meta property="og:title" content="Skewness of the sample — skewness" />
|
||||
<meta property="og:description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
|
||||
When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
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<meta name="twitter:card" content="summary" />
|
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<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -80,7 +79,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -116,6 +115,13 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -267,7 +273,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
<div class='dont-index'><p><code><a href='kurtosis.html'>kurtosis()</a></code></p></div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
@@ -286,7 +292,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
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|
||||
@@ -17,16 +17,16 @@
|
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
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<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/v4-shims.min.css" integrity="sha256-A6jcAdwFD48VMjlI3GDxUd+eCQa7/KWy6G9oe/ovaPA=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
@@ -46,8 +46,7 @@
|
||||
|
||||
<meta property="og:title" content="Translate strings from AMR package — translate" />
|
||||
<meta property="og:description" content="For language-dependent output of AMR functions, like mo_name(), mo_type() and ab_name()." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
<meta property="og:image" content="/logo.svg" />
|
||||
|
||||
|
||||
|
||||
@@ -79,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -115,6 +114,13 @@
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fa fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fa fa-skull-crossbones"></span>
|
||||
@@ -277,7 +283,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"pt"</span>)
|
||||
<span class='co'>#> "Staphylococcus coagulase negativo (CoNS)"</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#details">Details</a></li>
|
||||
@@ -296,7 +302,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -32,7 +32,7 @@ A \code{\link{data.frame}} with 500 observations and 53 variables:
|
||||
\item \verb{Inducible clindamycin resistance}\cr Clindamycin can be induced?
|
||||
\item \code{Comment}\cr Other comments
|
||||
\item \verb{Date of data entry}\cr Date this data was entered in WHONET
|
||||
\item \code{AMP_ND10:CIP_EE}\cr 27 different antibiotics. You can lookup the abbreviatons in the \link{antibiotics} data set, or use e.g. \code{\link[=ab_name]{ab_name("AMP")}} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link[=as.rsi]{as.rsi()}}.
|
||||
\item \code{AMP_ND10:CIP_EE}\cr 28 different antibiotics. You can lookup the abbreviations in the \link{antibiotics} data set, or use e.g. \code{\link[=ab_name]{ab_name("AMP")}} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link[=as.rsi]{as.rsi()}}.
|
||||
}
|
||||
}
|
||||
\usage{
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
\name{antibiotics}
|
||||
\alias{antibiotics}
|
||||
\alias{antivirals}
|
||||
\title{Data sets with ~550 antimicrobials}
|
||||
\title{Data sets with 554 antimicrobials}
|
||||
\format{
|
||||
\subsection{For the \link{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 14 variables:}{
|
||||
\itemize{
|
||||
|
||||
@@ -99,7 +99,7 @@ ggplot_pca(
|
||||
\item{...}{Parameters passed on to functions}
|
||||
}
|
||||
\description{
|
||||
This function is to produce a \code{ggplot2} variant of a so-called \href{https://en.wikipedia.org/wiki/Biplot}{biplot} for PCA (principal component analysis), but is more flexible and more appealing than the base \R \code{\link[=biplot]{biplot()}} function.
|
||||
Produces a \code{ggplot2} variant of a so-called \href{https://en.wikipedia.org/wiki/Biplot}{biplot} for PCA (principal component analysis), but is more flexible and more appealing than the base \R \code{\link[=biplot]{biplot()}} function.
|
||||
}
|
||||
\details{
|
||||
The colours for labels and points can be changed by adding another scale layer for colour, like \code{\link[=scale_colour_viridis_d]{scale_colour_viridis_d()}} or \code{\link[=scale_colour_brewer]{scale_colour_brewer()}}.
|
||||
|
||||
@@ -3,7 +3,7 @@
|
||||
\docType{data}
|
||||
\name{microorganisms}
|
||||
\alias{microorganisms}
|
||||
\title{Data set with ~70,000 microorganisms}
|
||||
\title{Data set with 69,447 microorganisms}
|
||||
\format{
|
||||
A \code{\link{data.frame}} with 69,447 observations and 17 variables:
|
||||
\itemize{
|
||||
@@ -38,7 +38,7 @@ Manually added were:
|
||||
\item 3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)
|
||||
\item 1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
|
||||
\item 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
|
||||
\item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not in the Catalogue of Life
|
||||
\item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
|
||||
\item 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
|
||||
}
|
||||
\subsection{Direct download}{
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
\alias{microorganisms.codes}
|
||||
\title{Translation table for common microorganism codes}
|
||||
\format{
|
||||
A \code{\link{data.frame}} with 5,450 observations and 2 variables:
|
||||
A \code{\link{data.frame}} with 5,585 observations and 2 variables:
|
||||
\itemize{
|
||||
\item \code{code}\cr Commonly used code of a microorganism
|
||||
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
\alias{microorganisms.old}
|
||||
\title{Data set with previously accepted taxonomic names}
|
||||
\format{
|
||||
A \code{\link{data.frame}} with 24,246 observations and 5 variables:
|
||||
A \code{\link{data.frame}} with 24,253 observations and 5 variables:
|
||||
\itemize{
|
||||
\item \code{col_id}\cr Catalogue of Life ID that was originally given
|
||||
\item \code{col_id_new}\cr New Catalogue of Life ID that responds to an entry in the \link{microorganisms} data set
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
\alias{rsi_translation}
|
||||
\title{Data set for R/SI interpretation}
|
||||
\format{
|
||||
A \code{\link{data.frame}} with 13,975 observations and 9 variables:
|
||||
A \code{\link{data.frame}} with 15,745 observations and 10 variables:
|
||||
\itemize{
|
||||
\item \code{guideline}\cr Name of the guideline
|
||||
\item \code{method}\cr Either "MIC" or "DISK"
|
||||
@@ -16,6 +16,7 @@ A \code{\link{data.frame}} with 13,975 observations and 9 variables:
|
||||
\item \code{disk_dose}\cr Dose of the used disk diffusion method
|
||||
\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
|
||||
\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
|
||||
\item \code{uti}\cr A logical value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
|
||||
}
|
||||
}
|
||||
\usage{
|
||||
|
||||
@@ -77,7 +77,7 @@ Good news. The first two components explain a total of `r cleaner::percentage(su
|
||||
biplot(pca_result)
|
||||
```
|
||||
|
||||
But we can't see the explanation of the points. Perhaps this works better with the new `ggplot_pca()` function, that automatically adds the right labels and even groups:
|
||||
But we can't see the explanation of the points. Perhaps this works better with our new `ggplot_pca()` function, that automatically adds the right labels and even groups:
|
||||
|
||||
```{r}
|
||||
ggplot_pca(pca_result)
|
||||
@@ -86,6 +86,7 @@ ggplot_pca(pca_result)
|
||||
You can also print an ellipse per group, and edit the appearance:
|
||||
|
||||
```{r}
|
||||
|
||||
ggplot_pca(pca_result, ellipse = TRUE) +
|
||||
ggplot2::labs(title = "An AMR/PCA biplot!")
|
||||
```
|
||||
|
||||
Reference in New Issue
Block a user