mirror of https://github.com/msberends/AMR.git
(v0.9.0.9026) update documentation
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Package: AMR
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Version: 0.9.0.9025
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Date: 2020-02-16
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Version: 0.9.0.9026
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Date: 2020-02-17
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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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@ -28,9 +28,7 @@ Authors@R: c(
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person(role = "ctb",
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family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"),
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person(role = "ctb",
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family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"),
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person(role = "fnd",
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given = "Stichting Certe Medische Diagnostiek en Advies", email = "medischedataanalyse@certe.nl"))
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family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"))
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Description: Functions to simplify the analysis and prediction of Antimicrobial
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Resistance (AMR) and to work with microbial and antimicrobial properties by
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using evidence-based methods, like those defined by Leclercq et al. (2013)
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8
NEWS.md
8
NEWS.md
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@ -1,9 +1,9 @@
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# AMR 0.9.0.9025
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## <small>Last updated: 16-Feb-2020</small>
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# AMR 0.9.0.9026
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## <small>Last updated: 17-Feb-2020</small>
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### New
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* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](http://www.eucast.org/clinical_breakpoints/), valid from 2020-01-01 (use `as.rsi()` to transform MICs and disk zones)
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* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows for machine reading these 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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* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](http://www.eucast.org/clinical_breakpoints/), valid from 1 January 2020. This affects translation of MIC and disk zones using `as.rsi()` and inferred resistance and susceptibility using `eucast_rules()`.
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* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://gitlab.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R).
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* Support for LOINC and SNOMED codes
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* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
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```r
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8
R/amr.R
8
R/amr.R
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@ -38,15 +38,17 @@
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#' - Getting properties for any microorganism (like Gram stain, species, genus or family)
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#' - Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)
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#' - Plotting antimicrobial resistance
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#' - Applying EUCAST expert rules
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#' - Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
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#' - Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
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#' - Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
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#' @section Read more on our website!:
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#' On our website <https://msberends.gitlab.io/AMR> you can find [a tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html).
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#' On our website <https://msberends.gitlab.io/AMR> you can find [a comprehensive tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html).
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#' @section Contact us:
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#' For suggestions, comments or questions, please contact us at:
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#'
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#' Matthijs S. Berends \cr
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#' m.s.berends at umcg dot nl \cr
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#' m.s.berends \[at\] umcg \[dot\] nl \cr
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#' Department of Medical Microbiology, University of Groningen \cr
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#' University Medical Center Groningen \cr
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#' Post Office Box 30001 \cr
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4
R/data.R
4
R/data.R
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@ -205,8 +205,8 @@ catalogue_of_life <- list(
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#' - `ab`\cr Antibiotic ID, see [as.ab()]
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#' - `ref_tbl`\cr Info about where the guideline rule can be found
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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 millimeters that leads to "S"
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#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimeters that leads to "R"
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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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#' @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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25
R/disk.R
25
R/disk.R
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@ -21,7 +21,7 @@
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#' Class 'disk'
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#'
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#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 50.
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#' 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.
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#' @inheritSection lifecycle Stable lifecycle
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#' @rdname as.disk
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#' @param x vector
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#' @seealso [as.rsi()]
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' # interpret disk values
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#' as.rsi(x = 12,
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#' mo = as.mo("S. pneumoniae"),
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#' ab = "AMX",
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#' # transform existing disk zones to the `disk` class
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#' df <- data.frame(microorganism = "E. coli",
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#' AMP = 20,
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#' CIP = 14,
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#' GEN = 18,
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#' TOB = 16)
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#' df <- df %>% mutate_at(vars(AMP:TOB, as.disk))
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#' df
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#'
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#' # interpret disk values, see ?as.rsi
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#' as.rsi(x = as.disk(18),
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#' mo = "Strep pneu", # `mo` will be coerced with as.mo()
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#' ab = "ampicillin", # and `ab` with as.ab()
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#' guideline = "EUCAST")
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#' as.rsi(x = 12,
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#' mo = as.mo("S. pneumoniae"),
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#' ab = "AMX",
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#' guideline = "CLSI")
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#'
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#' as.rsi(df)
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as.disk <- function(x, na.rm = FALSE) {
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if (is.disk(x)) {
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x
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# ==================================================================== #
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# global variables
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EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019"
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EUCAST_VERSION_BREAKPOINTS <- "10.0, 2020"
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EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' Apply EUCAST rules
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cat(bold(
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case_when(
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rule_group_current %like% "breakpoint" ~
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paste0("\nEUCAST Clinical Breakpoints (v", EUCAST_VERSION_BREAKPOINTS, ")\n"),
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paste0("\nEUCAST Clinical Breakpoints (",
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red(paste0("v", EUCAST_VERSION_BREAKPOINTS)), ")\n"),
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rule_group_current %like% "expert" ~
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paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v", EUCAST_VERSION_EXPERT_RULES, ")\n"),
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paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (",
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red(paste0("v", EUCAST_VERSION_EXPERT_RULES)), ")\n"),
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TRUE ~
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"\nOther rules by this AMR package\n"
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)
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@ -21,7 +21,7 @@
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#' Calculate microbial resistance
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#'
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#' @description 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 [dplyr::summarise()] and support grouped variables, please see *Examples*.
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#' @description 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*.
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#'
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#' [resistance()] should be used to calculate resistance, [susceptibility()] should be used to calculate susceptibility.\cr
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#' @inheritSection lifecycle Stable lifecycle
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#'
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#' **Remember that you should filter your table to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set.
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#'
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#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the [AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can infuence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` parameter).*
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#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the `count()`][AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can influence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` parameter).*
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#'
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#' The function [proportion_df()] takes any variable from `data` that has an [`rsi`] class (created with [as.rsi()]) and calculates the proportions R, I and S. The function [rsi_df()] works exactly like [proportion_df()], but adds the number of isolates.
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#' @section Combination therapy:
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#' When using more than one variable for `...` (= combination therapy)), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how [susceptibility()] works to calculate the %SI:
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#' When using more than one variable for `...` (= combination therapy)), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how [susceptibility()] works to calculate the %SI:
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#'
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#' ```
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#' --------------------------------------------------------------------
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16
R/rsi.R
16
R/rsi.R
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#' 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 < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning.
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#' @inheritSection lifecycle Stable lifecycle
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#' @rdname as.rsi
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#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimeters)
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#' @param mo a microorganism code, generated with [as.mo()]
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#' @param ab an antimicrobial code, generated with [as.ab()]
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#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
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#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
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#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
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#' @inheritParams first_isolate
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#' @param guideline defaults to the latest included EUCAST guideline, run `unique(rsi_translation$guideline)` for all options
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#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
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#'
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#' # a whole data set, even with combined MIC values and disk zones
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#' df <- data.frame(microorganism = "E. coli",
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#' AMP = as.mic(12),
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#' GEN = as.disk(18))
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#' AMP = as.mic(8),
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#' CIP = as.mic(0.256),
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#' GEN = as.disk(18),
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#' TOB = as.disk(16))
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#' as.rsi(df)
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#'
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#'
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@ -239,12 +241,12 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
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if (guideline_coerced != guideline) {
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message(blue(paste0("Note: Using guideline ", bold(guideline_coerced), " as input for `guideline`.")))
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}
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new_rsi <- rep(NA_character_, length(x))
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trans <- rsi_translation %>%
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filter(guideline == guideline_coerced & method == method_param) %>%
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mutate(lookup = paste(mo, ab))
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lookup_mo <- paste(mo, ab)
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lookup_genus <- paste(mo_genus, ab)
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lookup_family <- paste(mo_family, ab)
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
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@ -186,7 +186,3 @@ template:
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params:
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noindex: false
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bootswatch: "flatly"
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docsearch:
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# using algolia.com
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api_key: "f737050abfd4d726c63938e18f8c496e"
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index_name: "amr"
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# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
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# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
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# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
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# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J (2005, PMID 16217180).
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# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
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# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
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# -------------------------------------------------------------------------------------------------------------------------------
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if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group
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@ -37,7 +37,6 @@ genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints
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genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints
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genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints
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genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints
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genus_species is Enterococcus faecium AMP R all_betalactams R Enterococcus Breakpoints
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genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints
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genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints
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genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints
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@ -47,7 +46,8 @@ genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S LVX, MFX S Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S MFX S Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S LVX I Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints
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@ -56,7 +56,8 @@ genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Strept
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genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints
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@ -122,6 +123,11 @@ genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints
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genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints
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genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints
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genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints
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genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints
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genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints
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genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints
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genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints
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genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints
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order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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@ -146,7 +152,7 @@ genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, AT
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genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
|
||||
genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
|
||||
fullname like ^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
|
||||
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
|
||||
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
|
||||
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
|
||||
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
|
||||
|
|
|
|||
|
Can't render this file because it contains an unexpected character in line 6 and column 96.
|
|
|
@ -31,7 +31,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
|||
header = TRUE,
|
||||
strip.white = TRUE,
|
||||
na = c(NA, "", NULL))
|
||||
# take the order of the reference.rule_group column in the orginal data file
|
||||
# take the order of the reference.rule_group column in the original data file
|
||||
eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group,
|
||||
levels = unique(eucast_rules_file$reference.rule_group),
|
||||
ordered = TRUE)
|
||||
|
|
|
|||
|
|
@ -24,6 +24,8 @@ library(dplyr)
|
|||
library(cleaner)
|
||||
library(AMR)
|
||||
|
||||
# USE THIS FUNCTION TO READ THE EUCAST EXCEL FILE THAT CONTAINS THE BREAKPOINT TABLES
|
||||
|
||||
read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx") {
|
||||
|
||||
message("Getting sheet ", sheet)
|
||||
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|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
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@ -210,12 +204,6 @@
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|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
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@ -251,23 +239,6 @@ Content not found. Please use links in the navbar.
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inputSelector: 'input#search-input.form-control',
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@ -40,12 +40,6 @@
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="extra.css" rel="stylesheet">
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@ -84,7 +78,7 @@
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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">0.9.0.9025</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
|
||||
</span>
|
||||
</div>
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||||
|
||||
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|
@ -210,12 +204,6 @@
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</li>
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</ul>
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div><!--/.container -->
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@ -488,7 +476,7 @@ END OF TERMS AND CONDITIONS
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<footer>
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<div class="copyright">
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
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<div class="pkgdown">
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|
@ -499,23 +487,6 @@ END OF TERMS AND CONDITIONS
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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@ -16,9 +16,7 @@
|
|||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
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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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<!-- 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="../pkgdown.js"></script><!-- docsearch --><script src="../docsearch.js"></script><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous">
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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">0.9.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
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</span>
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</div>
|
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|
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@ -166,13 +164,7 @@
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</a>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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<!--/.nav-collapse -->
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<!--/.container -->
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|
|
@ -187,7 +179,7 @@
|
|||
<h1>How to apply EUCAST rules</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">26 January 2020</h4>
|
||||
<h4 class="date">17 February 2020</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>EUCAST.Rmd</code></div>
|
||||
|
|
@ -203,25 +195,169 @@
|
|||
<blockquote>
|
||||
<p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
|
||||
</blockquote>
|
||||
<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 9.0, 2019). Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
|
||||
<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 10.0, 2020). Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
|
||||
</div>
|
||||
<div id="examples" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#examples" class="anchor"></a>Examples</h2>
|
||||
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
|
||||
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solves this:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">oops <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>, </a>
|
||||
<a class="sourceLine" id="cb1-2" data-line-number="2"> <span class="st">"Escherichia"</span>),</a>
|
||||
<a class="sourceLine" id="cb1-3" data-line-number="3"> <span class="dt">ampicillin =</span> <span class="st">"S"</span>)</a>
|
||||
<a class="sourceLine" id="cb1-4" data-line-number="4">oops</a>
|
||||
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co"># mo ampicillin</span></a>
|
||||
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co"># 1 Klebsiella S</span></a>
|
||||
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co"># 2 Escherichia S</span></a>
|
||||
<a class="sourceLine" id="cb1-8" data-line-number="8"></a>
|
||||
<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(oops, <span class="dt">info =</span> <span class="ot">FALSE</span>)</a>
|
||||
<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="co"># mo ampicillin</span></a>
|
||||
<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co"># 1 Klebsiella R</span></a>
|
||||
<a class="sourceLine" id="cb1-12" data-line-number="12"><span class="co"># 2 Escherichia S</span></a></code></pre></div>
|
||||
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
|
||||
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be used with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>oops <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>, </span>
|
||||
<span id="cb1-2"><a href="#cb1-2"></a> <span class="st">"Escherichia"</span>),</span>
|
||||
<span id="cb1-3"><a href="#cb1-3"></a> <span class="dt">ampicillin =</span> <span class="st">"S"</span>)</span>
|
||||
<span id="cb1-4"><a href="#cb1-4"></a>oops</span>
|
||||
<span id="cb1-5"><a href="#cb1-5"></a><span class="co"># mo ampicillin</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># 1 Klebsiella S</span></span>
|
||||
<span id="cb1-7"><a href="#cb1-7"></a><span class="co"># 2 Escherichia S</span></span>
|
||||
<span id="cb1-8"><a href="#cb1-8"></a></span>
|
||||
<span id="cb1-9"><a href="#cb1-9"></a><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(oops, <span class="dt">info =</span> <span class="ot">FALSE</span>)</span>
|
||||
<span id="cb1-10"><a href="#cb1-10"></a><span class="co"># mo ampicillin</span></span>
|
||||
<span id="cb1-11"><a href="#cb1-11"></a><span class="co"># 1 Klebsiella R</span></span>
|
||||
<span id="cb1-12"><a href="#cb1-12"></a><span class="co"># 2 Escherichia S</span></span></code></pre></div>
|
||||
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em> and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></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">mo =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,</span>
|
||||
<span id="cb2-2"><a href="#cb2-2"></a> <span class="st">"Enterococcus faecalis"</span>,</span>
|
||||
<span id="cb2-3"><a href="#cb2-3"></a> <span class="st">"Escherichia coli"</span>,</span>
|
||||
<span id="cb2-4"><a href="#cb2-4"></a> <span class="st">"Klebsiella pneumoniae"</span>,</span>
|
||||
<span id="cb2-5"><a href="#cb2-5"></a> <span class="st">"Pseudomonas aeruginosa"</span>),</span>
|
||||
<span id="cb2-6"><a href="#cb2-6"></a> <span class="dt">VAN =</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span></span>
|
||||
<span id="cb2-7"><a href="#cb2-7"></a> <span class="dt">AMX =</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span></span>
|
||||
<span id="cb2-8"><a href="#cb2-8"></a> <span class="dt">COL =</span> <span class="st">"-"</span>, <span class="co"># Colistin</span></span>
|
||||
<span id="cb2-9"><a href="#cb2-9"></a> <span class="dt">CAZ =</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10"></a> <span class="dt">CXM =</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span></span>
|
||||
<span id="cb2-11"><a href="#cb2-11"></a> <span class="dt">PEN =</span> <span class="st">"S"</span>, <span class="co"># Penicillin G</span></span>
|
||||
<span id="cb2-12"><a href="#cb2-12"></a> <span class="dt">FOX =</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span>
|
||||
<span id="cb2-13"><a href="#cb2-13"></a> <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>data</span></code></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left">mo</th>
|
||||
<th align="center">VAN</th>
|
||||
<th align="center">AMX</th>
|
||||
<th align="center">COL</th>
|
||||
<th align="center">CAZ</th>
|
||||
<th align="center">CXM</th>
|
||||
<th align="center">PEN</th>
|
||||
<th align="center">FOX</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Enterococcus faecalis</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Pseudomonas aeruginosa</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<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="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">info =</span> <span class="ot">FALSE</span>)</span></code></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="left">mo</th>
|
||||
<th align="center">VAN</th>
|
||||
<th align="center">AMX</th>
|
||||
<th align="center">COL</th>
|
||||
<th align="center">CAZ</th>
|
||||
<th align="center">CXM</th>
|
||||
<th align="center">PEN</th>
|
||||
<th align="center">FOX</th>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">S</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>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Enterococcus faecalis</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Pseudomonas aeruginosa</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">-</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
|
@ -253,20 +389,7 @@
|
|||
</div>
|
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|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script><script>
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docsearch({
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
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indexName: 'amr',
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inputSelector: 'input#search-input.form-control',
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transformData: function(hits) {
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return hits.map(function (hit) {
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hit.url = updateHitURL(hit);
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return hit;
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</script>
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</body>
|
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|
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|
||||
</body>
|
||||
</html>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
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|
||||
<!-- docsearch -->
|
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<script src="../docsearch.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../docsearch.css" rel="stylesheet">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
||||
<link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script>
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@ -84,7 +78,7 @@
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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">0.9.0.9025</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
|
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</span>
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</div>
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|
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@ -210,12 +204,6 @@
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</li>
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</ul>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div><!--/.nav-collapse -->
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</div><!--/.container -->
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@ -250,7 +238,7 @@
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<footer>
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<div class="copyright">
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
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</div>
|
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<div class="pkgdown">
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@ -261,23 +249,6 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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docsearch({
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
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inputSelector: 'input#search-input.form-control',
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transformData: function(hits) {
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return hits.map(function (hit) {
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hit.url = updateHitURL(hit);
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return hit;
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</script>
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</body>
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|
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@ -40,12 +40,6 @@
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<script src="pkgdown.js"></script>
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<!-- docsearch -->
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<script src="docsearch.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="docsearch.css" rel="stylesheet">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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<link href="extra.css" rel="stylesheet">
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<script src="extra.js"></script>
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@ -84,7 +78,7 @@
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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">0.9.0.9025</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
|
||||
</span>
|
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</div>
|
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|
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|
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@ -210,12 +204,6 @@
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</li>
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</ul>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<div class="form-group">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div><!--/.nav-collapse -->
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</div><!--/.container -->
|
||||
</div><!--/.navbar -->
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|
|
@ -302,10 +290,6 @@
|
|||
<p><strong>Dennis Souverein</strong>. Contributor.
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||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Stichting Certe Medische Diagnostiek en Advies</strong>. Funder.
|
||||
</p>
|
||||
</li>
|
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</ul>
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@ -316,7 +300,7 @@
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<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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</div>
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<div class="pkgdown">
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@ -327,23 +311,6 @@
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</div>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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inputSelector: 'input#search-input.form-control',
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</body>
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|
|
@ -191,6 +191,9 @@ thead ~ tbody {
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/* only when it has a header */
|
||||
border-bottom: 2px solid black;
|
||||
}
|
||||
th {
|
||||
text-align: inherit;
|
||||
}
|
||||
table a:not(.btn), .table a:not(.btn) {
|
||||
text-decoration: inherit;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -66,10 +66,8 @@ $( document ).ready(function() {
|
|||
// edit footer
|
||||
$('footer').html(
|
||||
'<div>' +
|
||||
'<p>' + $('footer .copyright p').html().replace(
|
||||
"Developed by",
|
||||
'<code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a>.<br>Authors:') + '</p>' +
|
||||
'<a href="https://www.rug.nl"><img src="https://gitlab.com/msberends/AMR/raw/master/docs/logo_rug.png" class="footer_logo"></a>' +
|
||||
'<p><code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' +
|
||||
'<a href="https://www.rug.nl"><img src="https://gitlab.com/msberends/AMR/raw/master/docs/logo_rug.png" class="footer_logo"></a>' +
|
||||
'</div>');
|
||||
// all links should open in new tab/window
|
||||
$('footer').html($('footer').html().replace(/href/g, 'target="_blank" href'));
|
||||
|
|
|
|||
|
|
@ -16,9 +16,7 @@
|
|||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
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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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<!-- 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="pkgdown.js"></script><!-- docsearch --><script src="docsearch.js"></script><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous">
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<link href="docsearch.css" rel="stylesheet">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script><link href="extra.css" rel="stylesheet">
|
||||
<script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
|
||||
<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
|
||||
Resistance (AMR) and to work with microbial and antimicrobial properties by
|
||||
|
|
@ -45,7 +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">0.9.0.9025</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -170,13 +168,7 @@
|
|||
</a>
|
||||
</li>
|
||||
</ul>
|
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<div class="form-group">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div>
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</form>
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</div>
|
||||
<!--/.nav-collapse -->
|
||||
</div>
|
||||
<!--/.container -->
|
||||
|
|
@ -423,7 +415,6 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
|||
<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>
|
||||
<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>
|
||||
<li>Stichting Certe Medische Diagnostiek en Advies <br><small class="roles"> Funder </small> </li>
|
||||
<li><a href="authors.html">All authors...</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
|
|
@ -433,7 +424,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
|||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
|
@ -444,20 +435,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script><script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
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}
|
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|
||||
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|
||||
</body>
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
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|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
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|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
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|
|
@ -84,7 +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">0.9.0.9025</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -210,12 +204,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
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</div>
|
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</form>
|
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|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -231,20 +219,20 @@
|
|||
|
||||
</div>
|
||||
|
||||
<div id="amr-0909025" class="section level1">
|
||||
<div id="amr-0909026" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0909025" class="anchor"></a>AMR 0.9.0.9025<small> Unreleased </small>
|
||||
<a href="#amr-0909026" class="anchor"></a>AMR 0.9.0.9026<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-16-feb-2020" class="section level2">
|
||||
<div id="last-updated-17-feb-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-16-feb-2020" class="anchor"></a><small>Last updated: 16-Feb-2020</small>
|
||||
<a href="#last-updated-17-feb-2020" class="anchor"></a><small>Last updated: 17-Feb-2020</small>
|
||||
</h2>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>Support for the newest <a href="http://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 2020-01-01 (use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to transform MICs and disk zones)</li>
|
||||
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</li>
|
||||
<li>Support for the newest <a href="http://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
|
||||
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
|
||||
<li>Support for LOINC and SNOMED codes
|
||||
<ul>
|
||||
<li>
|
||||
|
|
@ -1462,7 +1450,7 @@
|
|||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-0909025">0.9.0.9025</a></li>
|
||||
<li><a href="#amr-0909026">0.9.0.9026</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>
|
||||
|
|
@ -1484,7 +1472,7 @@
|
|||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
|
@ -1495,23 +1483,6 @@
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
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<script>
|
||||
docsearch({
|
||||
|
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|
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
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indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
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|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
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|
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|
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<!-- docsearch -->
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<script src="../docsearch.js"></script>
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../docsearch.css" rel="stylesheet">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
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|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
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|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
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<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div>
|
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</form>
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|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -262,7 +250,7 @@ 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 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>
|
||||
<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">
|
||||
|
|
@ -289,23 +277,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
|
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</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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<script>
|
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docsearch({
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inputSelector: 'input#search-input.form-control',
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transformData: function(hits) {
|
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return hits.map(function (hit) {
|
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hit.url = updateHitURL(hit);
|
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return hit;
|
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});
|
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}
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|
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</script>
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|
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|
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|
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</body>
|
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|
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@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
|
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<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -254,21 +242,23 @@
|
|||
<li><p>Getting properties for any microorganism (like Gram stain, species, genus or family)</p></li>
|
||||
<li><p>Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)</p></li>
|
||||
<li><p>Plotting antimicrobial resistance</p></li>
|
||||
<li><p>Applying EUCAST expert rules</p></li>
|
||||
<li><p>Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code</p></li>
|
||||
<li><p>Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code</p></li>
|
||||
<li><p>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</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>
|
||||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact us</h2>
|
||||
|
||||
|
||||
|
||||
<p>For suggestions, comments or questions, please contact us at:</p>
|
||||
<p>Matthijs S. Berends <br />
|
||||
m.s.berends at umcg dot nl <br />
|
||||
m.s.berends [at] umcg [dot] nl <br />
|
||||
Department of Medical Microbiology, University of Groningen <br />
|
||||
University Medical Center Groningen <br />
|
||||
Post Office Box 30001 <br />
|
||||
|
|
@ -303,23 +293,6 @@ The Netherlands</p>
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -252,7 +240,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"meropenem"</span>)
|
||||
|
|
@ -285,23 +273,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -274,7 +262,7 @@
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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">
|
||||
|
|
@ -301,23 +289,6 @@
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9014</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -324,7 +312,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>
|
||||
|
|
@ -397,23 +385,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
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|
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
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indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -274,7 +262,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>
|
||||
|
|
@ -317,23 +305,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
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<div class="form-group">
|
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
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</div>
|
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</form>
|
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|
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</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -283,7 +271,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>
|
||||
|
|
@ -350,23 +338,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
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|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -308,7 +296,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
|
|
@ -342,23 +330,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -287,7 +275,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a> for the dataframe that is being used to determine ATCs.</p></div>
|
||||
|
|
@ -336,7 +324,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
|||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
|
@ -347,23 +335,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
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<script>
|
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docsearch({
|
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|
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|
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|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
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}
|
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|
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</script>
|
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|
||||
|
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|
||||
</body>
|
||||
|
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|
|||
|
|
@ -40,18 +40,12 @@
|
|||
<script src="../pkgdown.js"></script>
|
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|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
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|
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<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<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 millimeters between 6 and 50." />
|
||||
<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." />
|
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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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@ -85,7 +79,7 @@
|
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</button>
|
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<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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
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</ul>
|
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|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
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<div class="form-group">
|
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
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</div>
|
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</form>
|
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|
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</div><!--/.nav-collapse -->
|
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</div><!--/.container -->
|
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</div><!--/.navbar -->
|
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|
|
@ -234,7 +222,7 @@
|
|||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>This transforms a vector to a new class <code>disk</code>, which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 50.</p>
|
||||
<p>This transforms a vector to a new class <code>disk</code>, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.disk</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
|
@ -271,21 +259,28 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># interpret disk values</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>12</span>,
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<pre class="examples"><span class='co'># transform existing disk zones to the `disk` class</span>
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
|
||||
<span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fl'>20</span>,
|
||||
<span class='kw'>CIP</span> <span class='kw'>=</span> <span class='fl'>14</span>,
|
||||
<span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fl'>18</span>,
|
||||
<span class='kw'>TOB</span> <span class='kw'>=</span> <span class='fl'>16</span>)
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='no'>df</span> <span class='kw'>%>%</span> <span class='fu'>mutate_at</span>(<span class='fu'>vars</span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>, <span class='no'>as.disk</span>))
|
||||
<span class='no'>df</span>
|
||||
|
||||
<span class='co'># interpret disk values, see ?as.rsi</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.disk</span>(<span class='fl'>18</span>),
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>12</span>,
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"CLSI"</span>)</pre>
|
||||
|
||||
<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">
|
||||
<h2>Contents</h2>
|
||||
|
|
@ -316,23 +311,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -271,7 +259,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
|
||||
|
|
@ -326,23 +314,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -380,7 +368,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a> for the <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that is being used to determine ID's.</p>
|
||||
|
|
@ -474,23 +462,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -257,7 +245,7 @@
|
|||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>vector of values (for class <code><a href='as.mic.html'>mic</a></code>: an MIC value in mg/L, for class <code><a href='as.disk.html'>disk</a></code>: a disk diffusion radius in millimeters)</p></td>
|
||||
<td><p>vector of values (for class <code><a href='as.mic.html'>mic</a></code>: an MIC value in mg/L, for class <code><a href='as.disk.html'>disk</a></code>: a disk diffusion radius in millimetres)</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
|
|
@ -265,11 +253,11 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<th>mo</th>
|
||||
<td><p>a microorganism code, generated with <code><a href='as.mo.html'>as.mo()</a></code></p></td>
|
||||
<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>ab</th>
|
||||
<td><p>an antimicrobial code, generated with <code><a href='as.ab.html'>as.ab()</a></code></p></td>
|
||||
<td><p>any (vector of) text that can be coerced to a valid antimicrobial code with <code><a href='as.ab.html'>as.ab()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>guideline</th>
|
||||
|
|
@ -319,7 +307,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code></p></div>
|
||||
|
|
@ -340,8 +328,10 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
<span class='co'># a whole data set, even with combined MIC values and disk zones</span>
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
|
||||
<span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>12</span>),
|
||||
<span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>))
|
||||
<span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>8</span>),
|
||||
<span class='kw'>CIP</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>0.256</span>),
|
||||
<span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
|
||||
<span class='kw'>TOB</span> <span class='kw'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>16</span>))
|
||||
<span class='fu'>as.rsi</span>(<span class='no'>df</span>)
|
||||
|
||||
|
||||
|
|
@ -391,7 +381,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
|
@ -402,23 +392,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -86,7 +80,7 @@ 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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -212,12 +206,6 @@ This function requires an internet connection." />
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -314,7 +302,7 @@ 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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
|
|
@ -358,23 +346,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -269,7 +257,7 @@ 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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'>availability</span>(<span class='no'>example_isolates</span>)
|
||||
|
|
@ -314,23 +302,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -335,7 +323,7 @@ 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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
|
|
@ -382,23 +370,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -265,7 +253,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />
|
||||
|
|
@ -328,23 +316,6 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -257,7 +245,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
|
|
@ -295,23 +283,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
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<script>
|
||||
docsearch({
|
||||
|
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|
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../docsearch.css" rel="stylesheet">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -212,12 +206,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
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<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
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</div>
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</form>
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|
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</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -332,7 +320,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
|
||||
|
||||
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how <code><a href='proportion.html'>susceptibility()</a></code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
|
||||
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href='proportion.html'>susceptibility()</a></code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
|
||||
only_all_tested = FALSE only_all_tested = TRUE
|
||||
----------------------- -----------------------
|
||||
Drug A Drug B include as include as include as include as
|
||||
|
|
@ -363,7 +351,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='proportion.html'>proportion_*</a></code> to calculate microbial resistance and susceptibility.</p></div>
|
||||
|
|
@ -446,7 +434,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
<footer>
|
||||
<div class="copyright">
|
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
|
@ -457,23 +445,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
</div>
|
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|
||||
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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docsearch({
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
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</body>
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@ -40,12 +40,6 @@
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<script src="../pkgdown.js"></script>
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<!-- docsearch -->
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<script src="../docsearch.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script>
|
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|
|
@ -86,7 +80,7 @@ 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">0.9.0.9014</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -212,12 +206,6 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
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</li>
|
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</ul>
|
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div>
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</form>
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</div><!--/.nav-collapse -->
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||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -405,7 +393,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
|
|
@ -479,23 +467,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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<script>
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docsearch({
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</body>
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@ -40,12 +40,6 @@
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<script src="../pkgdown.js"></script>
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<script src="../docsearch.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
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<link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script>
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@ -85,7 +79,7 @@
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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">0.9.0.9018</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
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|
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@ -211,12 +205,6 @@
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</li>
|
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</ul>
|
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div><!--/.container -->
|
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</div><!--/.navbar -->
|
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|
|
@ -258,7 +246,7 @@
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
|
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</div>
|
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
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@ -285,23 +273,6 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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<script>
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docsearch({
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inputSelector: 'input#search-input.form-control',
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transformData: function(hits) {
|
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return hits.map(function (hit) {
|
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hit.url = updateHitURL(hit);
|
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return hit;
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});
|
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|
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</script>
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|
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|
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|
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</body>
|
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|
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|
|
@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
|
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|
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<!-- docsearch -->
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<script src="../docsearch.js"></script>
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
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|
||||
<link href="../extra.css" rel="stylesheet">
|
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<script src="../extra.js"></script>
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|
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@ -85,7 +79,7 @@
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</button>
|
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<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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
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@ -211,12 +205,6 @@
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</li>
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</ul>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div><!--/.container -->
|
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</div><!--/.navbar -->
|
||||
|
|
@ -253,7 +241,7 @@ 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 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>
|
||||
<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">
|
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|
|
@ -280,23 +268,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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</div>
|
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|
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|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
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<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
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</div>
|
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</form>
|
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|
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</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -393,7 +381,7 @@ To conduct an analysis of antimicrobial resistance, you should only include the
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='key_antibiotics.html'>key_antibiotics()</a></code></p></div>
|
||||
|
|
@ -480,23 +468,6 @@ To conduct an analysis of antimicrobial resistance, you should only include the
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../docsearch.css" rel="stylesheet">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
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|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
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<div class="form-group">
|
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
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</div>
|
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</form>
|
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|
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</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -337,7 +325,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
|
||||
|
||||
|
||||
|
|
@ -413,23 +401,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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<script>
|
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docsearch({
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|
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|
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
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indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
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||||
return hit;
|
||||
});
|
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}
|
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});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
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|
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|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../docsearch.css" rel="stylesheet">
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
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<script src="../extra.js"></script>
|
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|
|
@ -85,7 +79,7 @@
|
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</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
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</ul>
|
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|
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
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<div class="form-group">
|
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div>
|
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</form>
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|
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</div><!--/.nav-collapse -->
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</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -411,7 +399,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
|
|
@ -539,23 +527,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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<script>
|
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docsearch({
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
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inputSelector: 'input#search-input.form-control',
|
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transformData: function(hits) {
|
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return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
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}
|
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});
|
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</script>
|
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|
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|
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|
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</body>
|
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|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
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|
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|
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<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../docsearch.css" rel="stylesheet">
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
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|
||||
<link href="../extra.css" rel="stylesheet">
|
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<script src="../extra.js"></script>
|
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|
|
@ -85,7 +79,7 @@
|
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</button>
|
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<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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
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|
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|
|
@ -211,12 +205,6 @@
|
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</li>
|
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</ul>
|
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|
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
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|
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</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -272,7 +260,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='no'>df</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"S"</span>,
|
||||
|
|
@ -331,23 +319,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
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<script>
|
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docsearch({
|
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|
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|
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
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|
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inputSelector: 'input#search-input.form-control',
|
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transformData: function(hits) {
|
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return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
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return hit;
|
||||
});
|
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}
|
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});
|
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</script>
|
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|
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|
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|
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</body>
|
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|
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|
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|
|
@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
|
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|
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|
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<!-- docsearch -->
|
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<script src="../docsearch.js"></script>
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
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<link href="../extra.css" rel="stylesheet">
|
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<script src="../extra.js"></script>
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@ -84,7 +78,7 @@
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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">0.9.0.9025</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
|
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</span>
|
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</div>
|
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@ -210,12 +204,6 @@
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@ -591,7 +579,7 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
|
@ -602,23 +590,6 @@
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -284,7 +272,7 @@ 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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='fu'>left_join_microorganisms</span>(<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"K. pneumoniae"</span>))
|
||||
|
|
@ -330,23 +318,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -380,7 +368,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>
|
||||
|
|
@ -444,23 +432,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -271,7 +259,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='skewness.html'>skewness()</a></code></p></div>
|
||||
|
|
@ -303,23 +291,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
|||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -280,7 +268,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='https://rdrr.io/r/base/grep.html'>base::grep()</a></code></p></div>
|
||||
|
|
@ -325,7 +313,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
|
@ -336,23 +324,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
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<!-- docsearch -->
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|
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<link href="../extra.css" rel="stylesheet">
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@ -211,12 +205,6 @@
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@ -439,7 +427,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
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|
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|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
|
|
@ -475,7 +463,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
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|
@ -486,23 +474,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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@ -40,12 +40,6 @@
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@ -85,7 +79,7 @@
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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">0.9.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
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</span>
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</div>
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@ -211,12 +205,6 @@
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</li>
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</ul>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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</div><!--/.container -->
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</div><!--/.navbar -->
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|
|
@ -257,7 +245,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
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|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
|
|
@ -289,23 +277,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
</div>
|
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|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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</body>
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@ -40,12 +40,6 @@
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<script src="../pkgdown.js"></script>
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<!-- docsearch -->
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<script src="../docsearch.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../extra.css" rel="stylesheet">
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@ -85,7 +79,7 @@
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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">0.9.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
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</div>
|
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@ -211,12 +205,6 @@
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</li>
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</ul>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div><!--/.container -->
|
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</div><!--/.navbar -->
|
||||
|
|
@ -294,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<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>
|
||||
|
|
@ -329,23 +317,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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return hits.map(function (hit) {
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</body>
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|
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@ -40,12 +40,6 @@
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<script src="../pkgdown.js"></script>
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|
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|
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<!-- docsearch -->
|
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<script src="../docsearch.js"></script>
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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<link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script>
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@ -85,7 +79,7 @@
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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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
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</div>
|
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|
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@ -211,12 +205,6 @@
|
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</li>
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</ul>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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|
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</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -263,7 +251,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<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>
|
||||
|
|
@ -296,23 +284,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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<script>
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|
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|
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|
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|
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</body>
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|
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|
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@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
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|
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|
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<!-- docsearch -->
|
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<script src="../docsearch.js"></script>
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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<link href="../extra.css" rel="stylesheet">
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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">0.9.0.9018</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
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</div>
|
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@ -211,12 +205,6 @@
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</li>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div><!--/.container -->
|
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</div><!--/.navbar -->
|
||||
|
|
@ -352,7 +340,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
|
|
@ -472,23 +460,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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|
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|
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|
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|
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|
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|
||||
|
||||
|
||||
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|
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|
|||
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@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
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@ -86,7 +80,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
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@ -212,12 +206,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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|
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</div><!--/.navbar -->
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@ -317,7 +305,7 @@ 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 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>
|
||||
<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">
|
||||
|
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@ -346,23 +334,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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|
|
@ -40,12 +40,6 @@
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|
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<link href="../extra.css" rel="stylesheet">
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@ -85,7 +79,7 @@
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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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
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|
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@ -211,12 +205,6 @@
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||||
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|
||||
|
|
@ -265,7 +253,7 @@ 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 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>
|
||||
<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">
|
||||
|
|
@ -294,23 +282,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
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|||
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|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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|
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|
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|
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|
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|
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|
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</body>
|
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|
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|
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@ -40,18 +40,12 @@
|
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<script src="../pkgdown.js"></script>
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|
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<!-- docsearch -->
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<script src="../docsearch.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<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 dplyr::summarise() and support grouped variables, please see Examples.
|
||||
<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" />
|
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<meta name="twitter:card" content="summary" />
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@ -212,12 +206,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
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|
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|
|
@ -235,7 +223,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
|||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>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 <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>dplyr::summarise()</a></code> and support grouped variables, please see <em>Examples</em>.</p>
|
||||
<p>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 <code>summarise()</code>][dplyr::summarise()] and also support grouped variables, please see <em>Examples</em>.</p>
|
||||
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
|
||||
</div>
|
||||
|
||||
|
|
@ -324,13 +312,13 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
|||
|
||||
<p>The function <code>resistance()</code> is equal to the function <code>proportion_R()</code>. The function <code>susceptibility()</code> is equal to the function <code>proportion_SI()</code>.</p>
|
||||
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href='first_isolate.html'>first_isolate()</a></code> to determine them in your data set.</p>
|
||||
<p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href='count.html'>AMR::count()</a></code> functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code>count_susceptible() / count_all()</code>. <em>Low counts can infuence the outcome - the <code>proportion</code> functions may camouflage this, since they only return the proportion (albeit being dependent on the <code>minimum</code> parameter).</em></p>
|
||||
<p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href='count.html'>count()</a></code>][AMR::count()] functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code>count_susceptible() / count_all()</code>. <em>Low counts can influence the outcome - the <code>proportion</code> functions may camouflage this, since they only return the proportion (albeit being dependent on the <code>minimum</code> parameter).</em></p>
|
||||
<p>The function <code>proportion_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and calculates the proportions R, I and S. The function <code>rsi_df()</code> works exactly like <code>proportion_df()</code>, but adds the number of isolates.</p>
|
||||
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
|
||||
|
||||
|
||||
|
||||
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how <code>susceptibility()</code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
|
||||
<p>When using more than one variable for <code>...</code> (= combination therapy)), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code>susceptibility()</code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
|
||||
only_all_tested = FALSE only_all_tested = TRUE
|
||||
----------------------- -----------------------
|
||||
Drug A Drug B include as include as include as include as
|
||||
|
|
@ -382,7 +370,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='count.html'>AMR::count()</a></code> to count resistant and susceptible isolates.</p></div>
|
||||
|
|
@ -490,7 +478,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
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|
||||
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|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
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</div>
|
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|
||||
<div class="pkgdown">
|
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|
|
@ -501,23 +489,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
|
@ -85,7 +79,7 @@
|
|||
</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">0.9.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
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|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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|
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</div><!--/.navbar -->
|
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|
|
@ -403,7 +391,7 @@ 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 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>
|
||||
<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">
|
||||
|
|
@ -432,23 +420,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>dormant</
|
|||
</div>
|
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|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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<script>
|
||||
docsearch({
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||||
|
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||||
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transformData: function(hits) {
|
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|
||||
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|
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|
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|
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|
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|
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|
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</body>
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|
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|
|
@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
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|
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<!-- docsearch -->
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<script src="../docsearch.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
||||
<link href="../extra.css" rel="stylesheet">
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||||
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@ -211,12 +205,6 @@
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</ul>
|
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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|
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|
||||
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|
||||
|
|
@ -383,7 +371,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p>The <code><a href='proportion.html'>proportion()</a></code> functions to calculate resistance</p>
|
||||
|
|
@ -458,7 +446,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
|
@ -469,23 +457,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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</div>
|
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|
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|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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@ -40,12 +40,6 @@
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<script src="../pkgdown.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../extra.css" rel="stylesheet">
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@ -211,12 +205,6 @@
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -250,8 +238,8 @@
|
|||
<li><p><code>ab</code><br /> Antibiotic ID, see <code><a href='as.ab.html'>as.ab()</a></code></p></li>
|
||||
<li><p><code>ref_tbl</code><br /> Info about where the guideline rule can be found</p></li>
|
||||
<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 millimeters that leads to "S"</p></li>
|
||||
<li><p><code>breakpoint_R</code><br /> Highest MIC value or lowest number of millimeters that leads to "R"</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>
|
||||
</ul>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
|
|
@ -260,7 +248,7 @@
|
|||
|
||||
|
||||
|
||||
<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 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>
|
||||
<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">
|
||||
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|
@ -277,7 +265,7 @@
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|
||||
<footer>
|
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<div class="copyright">
|
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, Stichting Certe Medische Diagnostiek en Advies.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
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|
||||
|
||||
<div class="pkgdown">
|
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|
|
@ -288,23 +276,6 @@
|
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|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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transformData: function(hits) {
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return hits.map(function (hit) {
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return hit;
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@ -40,12 +40,6 @@
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<script src="../pkgdown.js"></script>
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<!-- docsearch -->
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<script src="../docsearch.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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<link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script>
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@ -86,7 +80,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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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">0.9.0.9013</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
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|
|
@ -212,12 +206,6 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
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</li>
|
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</ul>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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</div><!--/.container -->
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</div><!--/.navbar -->
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|
|
@ -273,7 +261,7 @@ 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 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>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='kurtosis.html'>kurtosis()</a></code></p></div>
|
||||
|
|
@ -305,23 +293,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
|||
</div>
|
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|
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|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
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<script>
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inputSelector: 'input#search-input.form-control',
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transformData: function(hits) {
|
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return hits.map(function (hit) {
|
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hit.url = updateHitURL(hit);
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return hit;
|
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});
|
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}
|
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});
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</script>
|
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|
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|
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|
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</body>
|
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|
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|
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@ -40,12 +40,6 @@
|
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<script src="../pkgdown.js"></script>
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9025</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -211,12 +205,6 @@
|
|||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
||||
</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
|
@ -258,7 +246,7 @@ 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 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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># The 'language' parameter of below functions</span>
|
||||
|
|
@ -315,23 +303,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A reti
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\keyword{internal}
|
||||
|
|
|
|||
|
|
@ -23,12 +23,14 @@ This package can be used for:
|
|||
\item Getting properties for any microorganism (like Gram stain, species, genus or family)
|
||||
\item Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)
|
||||
\item Plotting antimicrobial resistance
|
||||
\item Applying EUCAST expert rules
|
||||
\item Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
|
||||
\item Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
|
||||
\item Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
|
||||
}
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\section{Contact us}{
|
||||
|
|
@ -36,7 +38,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
|
|||
For suggestions, comments or questions, please contact us at:
|
||||
|
||||
Matthijs S. Berends \cr
|
||||
m.s.berends at umcg dot nl \cr
|
||||
m.s.berends [at] umcg [dot] nl \cr
|
||||
Department of Medical Microbiology, University of Groningen \cr
|
||||
University Medical Center Groningen \cr
|
||||
Post Office Box 30001 \cr
|
||||
|
|
|
|||
|
|
@ -20,7 +20,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ This example data set has the exact same structure as an export file from WHONET
|
|||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\keyword{datasets}
|
||||
|
|
|
|||
|
|
@ -86,7 +86,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -43,7 +43,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -79,7 +79,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
|
|
|||
|
|
@ -55,7 +55,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -19,7 +19,7 @@ is.disk(x)
|
|||
An \code{\link{integer}} with additional new class \code{\link{disk}}
|
||||
}
|
||||
\description{
|
||||
This transforms a vector to a new class \code{\link{disk}}, which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 50.
|
||||
This transforms a vector to a new class \code{\link{disk}}, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50.
|
||||
}
|
||||
\details{
|
||||
Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It supports guidelines from EUCAST and CLSI.
|
||||
|
|
@ -34,19 +34,26 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
# interpret disk values
|
||||
as.rsi(x = 12,
|
||||
mo = as.mo("S. pneumoniae"),
|
||||
ab = "AMX",
|
||||
# transform existing disk zones to the `disk` class
|
||||
df <- data.frame(microorganism = "E. coli",
|
||||
AMP = 20,
|
||||
CIP = 14,
|
||||
GEN = 18,
|
||||
TOB = 16)
|
||||
df <- df \%>\% mutate_at(vars(AMP:TOB, as.disk))
|
||||
df
|
||||
|
||||
# interpret disk values, see ?as.rsi
|
||||
as.rsi(x = as.disk(18),
|
||||
mo = "Strep pneu", # `mo` will be coerced with as.mo()
|
||||
ab = "ampicillin", # and `ab` with as.ab()
|
||||
guideline = "EUCAST")
|
||||
as.rsi(x = 12,
|
||||
mo = as.mo("S. pneumoniae"),
|
||||
ab = "AMX",
|
||||
guideline = "CLSI")
|
||||
|
||||
as.rsi(df)
|
||||
}
|
||||
\seealso{
|
||||
\code{\link[=as.rsi]{as.rsi()}}
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -148,7 +148,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -23,13 +23,13 @@ is.rsi(x)
|
|||
is.rsi.eligible(x, threshold = 0.05)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{vector of values (for class \code{\link{mic}}: an MIC value in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimeters)}
|
||||
\item{x}{vector of values (for class \code{\link{mic}}: an MIC value in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
|
||||
|
||||
\item{...}{parameters passed on to methods}
|
||||
|
||||
\item{mo}{a microorganism code, generated with \code{\link[=as.mo]{as.mo()}}}
|
||||
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
|
||||
|
||||
\item{ab}{an antimicrobial code, generated with \code{\link[=as.ab]{as.ab()}}}
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
|
||||
|
||||
\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(rsi_translation$guideline)} for all options}
|
||||
|
||||
|
|
@ -77,7 +77,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
@ -96,8 +96,10 @@ as.rsi(x = as.disk(18),
|
|||
|
||||
# a whole data set, even with combined MIC values and disk zones
|
||||
df <- data.frame(microorganism = "E. coli",
|
||||
AMP = as.mic(12),
|
||||
GEN = as.disk(18))
|
||||
AMP = as.mic(8),
|
||||
CIP = as.mic(0.256),
|
||||
GEN = as.disk(18),
|
||||
TOB = as.disk(16))
|
||||
as.rsi(df)
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -75,7 +75,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ The syntax used to transform the original data to a cleansed R format, can be fo
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -97,7 +97,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
|
|||
|
||||
\section{Combination therapy}{
|
||||
|
||||
When using more than one variable for \code{...} (= combination therapy)), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
|
||||
When using more than one variable for \code{...} (= combination therapy)), use \code{only_all_tested} to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how \code{\link[=susceptibility]{susceptibility()}} works to calculate the \%SI:\preformatted{--------------------------------------------------------------------
|
||||
only_all_tested = FALSE only_all_tested = TRUE
|
||||
----------------------- -----------------------
|
||||
Drug A Drug B include as include as include as include as
|
||||
|
|
@ -128,7 +128,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -161,7 +161,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The u
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@ A data set containing 2,000 microbial isolates with their full antibiograms. The
|
|||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\keyword{datasets}
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\keyword{internal}
|
||||
|
|
|
|||
|
|
@ -127,7 +127,7 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -105,7 +105,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -143,7 +143,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The u
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The u
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -127,7 +127,7 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We
|
|||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue