We will have to transform some variables to simplify and automate the analysis:
-
-
- Microorganisms should be transformed to our own microorganism IDs (called an
mo) using our Catalogue of Life reference data set, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation withas.mo(). This function also recognises almost all WHONET abbreviations of microorganisms.
+ - Microorganisms should be transformed to our own microorganism codes (called an
mo) using our Catalogue of Life reference data set, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation withas.mo(). This function also recognises almost all WHONET abbreviations of microorganisms. - Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values
"S","I"or"R". That is exactly where theas.rsi()function is for.
diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html
index 5e6b655f..57eac212 100644
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@@ -39,7 +39,7 @@
Data sets for download / own use
-30 May 2021
+01 June 2021
Source:vignettes/datasets.Rmd
datasets.RmdInterpretation from MIC values / disk diameters to R/SI
-A data set with 20,486 rows and 10 columns, containing the following column names:
guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R and uti.
A data set with 21,996 rows and 10 columns, containing the following column names:
guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R and uti.
This data set is in R available as rsi_translation, after you load the AMR package.
It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set here.
+It was last updated on 1 June 2021 06:44:05 UTC. Find more info about the structure of this data set here.
Direct download links:
-
-
- Download as R file (34 kB)
+ - Download as R file (37 kB)
- Download as Excel file (0.7 MB)
- - Download as plain text file (1.7 MB)
+ - Download as plain text file (1.8 MB)
- - Download as SAS file (3.5 MB)
+ - Download as SAS file (3.8 MB)
- - Download as SPSS file (3.8 MB)
+ - Download as SPSS file (2.4 MB)
- - Download as Stata file (3.3 MB) +
- Download as Stata file (3.5 MB)
Source
-This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021).
+This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2020) and EUCAST (2011-2021).
diff --git a/docs/articles/index.html b/docs/articles/index.html index c85570e8..dd469614 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@
Latest released version
-This package is available here on the rOpenSci R-universe platform, as CRAN does not allow frequent updates of large packages (though the AMR package is only 7-9 MB). With CRAN, we apparently cannot update this package frequently enough to implement the latest EUCAST/CLSI guidelines or the latest microbial taxonomy.
Install this package in R by using the command:
+This package is available here on the rOpenSci R-universe platform, as CRAN does not allow frequent updates of large packages (though the AMR package is only 7-9 MB). We are working on splitting this package into two: a new data package containing the microbial taxonomy, and the AMR package that only contains all functions.
In the meanwhile, you have to add our R-universe address to your list of repositories (‘repos’), by running:
-install.packages("AMR", repos = "https://msberends.r-universe.dev")It will be downloaded and installed automatically.
+options(repos = c(getOption("repos"),
+ msberends = "https://msberends.r-universe.dev"))You can now install or update the AMR package in the same way you are used to:
+install.packages("AMR")It will be downloaded and installed automatically. For RStudio, click on the menu Tools > Install Packages… and then type in “AMR” and press Install.
Note: Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.
Latest development version
The latest and unpublished development version can be installed from GitHub using:
-+install.packages("remotes") # if you haven't already remotes::install_github("msberends/AMR")diff --git a/docs/news/index.html b/docs/news/index.html index 455003e5..515f827c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@
NEWS.md
-
- Unreleased
-
- Unreleased AMR 1.7.0.9000
-
+
+
+ Unreleased
+
@@ -280,9 +289,9 @@
-
+ Unreleased AMR 1.7.0.9001
+-Last updated: 30 May 2021 +Last updated: 1 June 2021
+
+
+New
+-
+
- Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using
as.rsi())
+
Changed
-
+
-
+
bug_drug_combinations()now supports grouping using thedplyrpackage - As requested by CRAN administrators: decreased package size by 3 MB in costs of a ~50 times slower loading time of the package (i.e.,
library(AMR))
+
-New
+New- Function
custom_eucast_rules()that brings support for custom AMR rules ineucast_rules()
@@ -363,9 +372,9 @@
-
Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the
@@ -500,9 +509,9 @@eucast_rules()function and inas.rsi()to interpret MIC and disk diffusion values. This is now the default guideline in this package.2021-01-06
-AMR1.5.0+-New
+New-
Functions
@@ -613,9 +622,9 @@get_episode()andis_new_episode()to determine (patient) episodes which are not necessarily based on microorganisms. Theget_episode()function returns the index number of the episode per group, while theis_new_episode()function returns valuesTRUE/FALSEto indicate whether an item in a vector is the start of a new episode. They also supportdplyrs grouping (i.e. usinggroup_by()):2020-10-08
-AMR1.4.0+-New
+NewSupport for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the
eucast_rules()function can now correct for more than 180 different antibiotics and themdro()function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. Theeucast_rules()function consequently gained the argumentsversion_breakpoints(at the moment defaults to v10.0, 2020) andversion_expertrules(at the moment defaults to v3.2, 2020). Theexample_isolatesdata set now also reflects the change from v3.1 to v3.2. Themdro()function now acceptsguideline == "EUCAST3.1"andguideline == "EUCAST3.2".A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html
@@ -716,9 +725,9 @@
Function
ab_from_text()to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it usesas.ab()internally-
@@ -807,7 +816,7 @@
Making this package independent of especially the tidyverse (e.g. packages
dplyrandtidyr) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.Negative effects of this change are:
-
-
- Function
freq()that was borrowed from thecleanerpackage was removed. Usecleaner::freq(), or runlibrary("cleaner")before you usefreq().
+ - Function
freq()that was borrowed from thecleanerpackage was removed. Usecleaner::freq(), or runlibrary("cleaner")before you usefreq(). Printing values of classmoorrsiin a tibble will no longer be in colour and printingrsiin a tibble will show the class<ord>, not<rsi>anymore. This is purely a visual effect.All functions from themo_*family (likemo_name()andmo_gramstain()) are noticeably slower when running on hundreds of thousands of rows.- For developers: classes
moandabnow both also inherit classcharacter, to support any data transformation. This change invalidates code that checks for class length == 1.
@@ -861,9 +870,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- Support for easy principal component analysis for AMR, using the new
pca()function - Plotting biplots for principal component analysis using the new
ggplot_pca()function
@@ -927,9 +936,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- Support for the newest EUCAST Clinical Breakpoint Tables v.10.0, valid from 1 January 2020. This affects translation of MIC and disk zones using
as.rsi()and inferred resistance and susceptibility usingeucast_rules(). - 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://github.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. @@ -1024,9 +1033,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
-
Functions
@@ -1139,13 +1148,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ #> invalid microorganism code, NA generatedsusceptibility()andresistance()as aliases ofproportion_SI()andproportion_R(), respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant. Function
freq()has moved to a new package,clean(CRAN link), since creating frequency tables actually does not fit the scope of this package. Thefreq()function still works, since it is re-exported from thecleanpackage (which will be installed automatically upon updating thisAMRpackage).
+Function
freq()has moved to a new package,clean(CRAN link), since creating frequency tables actually does not fit the scope of this package. Thefreq()function still works, since it is re-exported from thecleanpackage (which will be installed automatically upon updating thisAMRpackage).Renamed data set
septic_patientstoexample_isolates-
Function
@@ -1276,9 +1285,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/bug_drug_combinations()to quickly get adata.framewith the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed withmo_shortname()at default:@@ -233,13 +233,13 @@2019-06-23
-AMR0.7.1+@@ -307,7 +307,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +@@ -314,7 +314,7 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru --New
+New-
Function
@@ -1360,9 +1369,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/rsi_df()to transform adata.frameto a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functionscount_df()andportion_df()to immediately show resistance percentages and number of available isolates:@@ -326,7 +326,7 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru -2019-06-03
-AMR0.7.0+@@ -312,7 +312,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +@@ -288,7 +288,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +-New
+New- Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use
as.rsi()on an MIC value (created withas.mic()), a disk diffusion value (created with the newas.disk()) or on a complete date set containing columns with MIC or disk diffusion values. - Function
mo_name()as alias ofmo_fullname()@@ -1406,7 +1415,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ - The
age()function gained a new argumentexactto determine ages with decimals - Removed deprecated functions
guess_mo(),guess_atc(),EUCAST_rules(),interpretive_reading(),rsi()
- - Frequency tables (
freq()): + - Frequency tables (
freq()):speed improvement for microbial IDs
fixed factor level names for R Markdown
@@ -1416,12 +1425,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- Added ceftazidim intrinsic resistance to Streptococci
- Changed default settings for
-age_groups(), to let groups of fives and tens end with 100+ instead of 120+- Fix for
freq()for when all values areNA+- Fix for
freq()for when all values areNA- Fix for
first_isolate()for when dates are missing- Improved speed of
guess_ab_col()@@ -1475,9 +1484,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/- Contains the complete manual of this package and all of its functions with an explanation of their arguments
- Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more.
-++ freq(mo_genus(mo))-New
+NewBREAKING: removed deprecated functions, arguments and references to ‘bactid’. Use
as.mo()to identify an MO code.- @@ -1670,7 +1679,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- Frequency tables (
freq()function): +- Frequency tables (
freq()function):-
Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
@@ -1680,15 +1689,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # OLD WAY septic_patients %>% mutate(genus = mo_genus(mo)) %>% - freq(genus) + freq(genus) # NEW WAY septic_patients %>% - freq(mo_genus(mo)) + freq(mo_genus(mo)) # Even supports grouping variables: septic_patients %>% group_by(gender) %>% - freq(mo_genus(mo))
Header info is now available as a list, with the
headerfunctionThe argument
headeris now set toTRUEat default, even for markdown@@ -287,7 +287,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +2018-11-30
-AMR0.5.0++ freq(gender)-New
+New- Repository moved to GitLab
- Function
count_allto get all available isolates (that like allportion_*andcount_*functions also supportssummariseandgroup_by), the oldn_rsiis now an alias ofcount_all@@ -1770,7 +1779,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ Using
portion_*functions now throws a warning when total available isolate is below argumentminimumFunctions
as.mo,as.rsi,as.mic,as.atcandfreqwill not set package name as attribute anymore-
-
Frequency tables -
+freq():Frequency tables -
freq():-
Support for grouping variables, test with:
@@ -1778,14 +1787,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/septic_patients %>% group_by(hospital_id) %>% - freq(gender)
-
Support for (un)selecting columns:
Check for
hms::is.hmsRemoved diacritics from all authors (columns
microorganisms$refandmicroorganisms.old$ref) to comply with CRAN policy to only allow ASCII charactersFix for
mo_propertynot working properlyFix for
eucast_ruleswhere some Streptococci would become ceftazidime R in EUCAST rule 4.5Support for named vectors of class
mo, useful fortop_freq()Support for named vectors of class
mo, useful fortop_freq()ggplot_rsiandscale_y_percenthavebreaksargumentAI improvements for
@@ -1843,9 +1852,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/as.mo:@@ -1991,9 +2000,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/2018-10-01
-AMR0.4.0+-New
+NewThe data set
microorganismsnow contains all microbial taxonomic data from ITIS (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data setmicroorganisms.oldcontains all previously known taxonomic names from those kingdoms.- @@ -1970,13 +1979,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ +freq(my_matrix)
For lists, subsetting is possible:
+my_list %>% freq(age) +my_list %>% freq(gender)my_list = list(age = septic_patients$age, gender = septic_patients$gender) -my_list %>% freq(age) -my_list %>% freq(gender)@@ -342,7 +342,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +2018-08-14
-AMR0.3.0+@@ -317,7 +317,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +@@ -285,7 +285,7 @@ --New
+New-
BREAKING:
rsi_dfwas removed in favour of new functionsportion_R,portion_IR,portion_I,portion_SIandportion_Sto selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the oldrsifunction. The old function still works, but is deprecated. @@ -2049,13 +2058,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/- A vignette to explain its usage
- Support for
rsi(antimicrobial resistance) to use as input
- - Support for
tableto use as input:freq(table(x, y))+ - Support for
tableto use as input:freq(table(x, y)) - Support for existing functions
histandplotto use a frequency table as input:hist(freq(df$age)) - Support for
as.vector,as.data.frame,as_tibbleandformat
- - Support for quasiquotation:
freq(mydata, mycolumn)is the same asmydata %>% freq(mycolumn)+ - Support for quasiquotation:
freq(mydata, mycolumn)is the same asmydata %>% freq(mycolumn) - Function
top_freqfunction to return the top/below n items as vector - Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR) @@ -2127,9 +2136,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- Full support for Windows, Linux and macOS
- Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9faffc34..2c224a15 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-05-30T20:01Z +last_built: 2021-06-01T13:31Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index 4e4267a1..c7838cbe 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -82,7 +82,7 @@
@@ -257,7 +257,7 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru -2018-05-03
-AMR0.2.0+@@ -277,7 +277,7 @@ -@@ -431,7 +431,7 @@ The lifecycle of this function is retiredOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +-New
+NewOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Contact Us
@@ -286,7 +286,7 @@Matthijs S. Berends
m.s.berends [at] umcg [dot] nl
University of Groningen -Department of Medical Microbiology +Department of Medical Microbiology and Infection Prevention University Medical Center Groningen
Post Office Box 30001
9700 RB Groningen
diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html index db5d030d..8f8dab31 100644 --- a/docs/reference/WHOCC.html +++ b/docs/reference/WHOCC.html @@ -82,7 +82,7 @@On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
as.ab("meropenem") diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html index a0272c41..3f90b943 100644 --- a/docs/reference/WHONET.html +++ b/docs/reference/WHONET.html @@ -82,7 +82,7 @@
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# mind the bad spelling of amoxicillin in this line, diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index 594f875f..c01a5ac4 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -82,7 +82,7 @@
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/age.html b/docs/reference/age.html index 28e000d6..2912306a 100644 --- a/docs/reference/age.html +++ b/docs/reference/age.html @@ -82,7 +82,7 @@On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index 79d46cb7..43f91e56 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -82,7 +82,7 @@To split ages into groups, use the
age_groups()function.On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index ccb865bb..31475b25 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -83,7 +83,7 @@To determine ages, based on one or more reference dates, use the
age()function.On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# `example_isolates` is a data set available in the AMR package. diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 96e2b60f..a90b28e0 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -82,7 +82,7 @@
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index 9f8944d3..39fd4deb 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -82,7 +82,7 @@ - Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index 1af44927..a379cb4d 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -82,7 +82,7 @@@@ -276,7 +276,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index ef8e44c8..aec8d968 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -82,7 +82,7 @@On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index 95122def..9112e767 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -6,7 +6,7 @@ -Transform Input to a Microorganism ID — as.mo • AMR (for R) +Transform Input to a Microorganism Code — as.mo • AMR (for R) @@ -48,8 +48,8 @@ - - + + @@ -82,7 +82,7 @@@@ -274,7 +274,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +@@ -324,7 +324,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +-Transform Input to a Microorganism ID
+Transform Input to a Microorganism Code
Source:R/mo.Ras.mo.Rd-Use this function to determine a valid microorganism ID (
+mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like"Staphylococcus aureus"), an abbreviated name (such as"S. aureus"), an abbreviation known in the field (such as"MRSA"), or just a genus. See Examples.Use this function to determine a valid microorganism code (
mo). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like"Staphylococcus aureus"), an abbreviated name (such as"S. aureus"), an abbreviation known in the field (such as"MRSA"), or just a genus. See Examples.as.mo( @@ -314,7 +314,7 @@
General Info
-A microorganism ID from this package (class:
mo) is human readable and typically looks like these examples:Code Full name +
A microorganism (MO) code from this package (class:
mo) is human readable and typically looks like these examples:Code Full name --------------- -------------------------------------- B_KLBSL Klebsiella B_KLBSL_PNMN Klebsiella pneumoniae @@ -422,7 +422,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( -On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
@@ -363,8 +363,8 @@microorganisms for the data.frame that is being used to determine ID's.
diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 11c7a8b7..46254753 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -82,7 +82,7 @@Supported Guidelines
-For interpreting MIC values as well as disk diffusion diameters, currently supported guidelines to be used as input for the
-guidelineargument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".Simply using
+"CLSI"or"EUCAST"as input will automatically select the latest version of that guideline. You can set your own data set using thereference_dataargument. Theguidelineargument will then be ignored.For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020).
+Thus, the
guidelineargument must be set to e.g.,"EUCAST 2021"or"CLSI 2020". By simply using"EUCAST"(the default) or"CLSI"as input, the latest version of that guideline will automatically be selected. You can set your own data set using thereference_dataargument. Theguidelineargument will then be ignored.After Interpretation
@@ -374,7 +374,7 @@Machine-Readable Interpretation Guidelines
-The repository of this package contains a machine-readable version of all guidelines. This is a CSV file consisting of 20,486 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This allows for easy implementation of these rules in laboratory information systems (LIS). Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
+The repository of this package contains a machine-readable version of all guidelines. This is a CSV file consisting of 21,996 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This allows for easy implementation of these rules in laboratory information systems (LIS). Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
Other
@@ -395,7 +395,7 @@ A microorganism is categorised as Susceptible, standard dosing regimen, A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. -This AMR package honours this new insight. Use
+susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.This AMR package honours this (new) insight. Use
susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.Stable Lifecycle
@@ -412,7 +412,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index 77b775a8..5529c7fc 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -82,7 +82,7 @@On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# \donttest{ diff --git a/docs/reference/availability.html b/docs/reference/availability.html index 86a3cb3c..1bdae0fd 100644 --- a/docs/reference/availability.html +++ b/docs/reference/availability.html @@ -82,7 +82,7 @@
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
availability(example_isolates) diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index c8184853..d38637c1 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -82,7 +82,7 @@
-
guideline
Name of the guidelinemethod
Either "DISK" or "MIC"site
Body site, e.g. "Oral" or "Respiratory"
@@ -272,7 +272,7 @@
-
2020-04-15
-AMR1.1.0+-New
+New2020-02-17
AMR1.0.0This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
-+--New
+New+--New
+NewThis is important, because a value like
-"testvalue"could never be understood by e.g.mo_name(), although the class would suggest a valid microbial code.+@@ -272,7 +272,7 @@-New
+NewFUN -the function to call on the
mocolumn to transform the microorganism IDs, defaults tomo_shortname()the function to call on the
mocolumn to transform the microorganism codes, defaults tomo_shortname()... @@ -339,7 +339,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# \donttest{ diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index 1d4a4254..4ea117a3 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -82,7 +82,7 @@ @@ -270,7 +270,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( -
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
@@ -262,7 +262,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( -Data set microorganisms for the actual data.
diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html index a1d90273..54c5fd4d 100644 --- a/docs/reference/catalogue_of_life_version.html +++ b/docs/reference/catalogue_of_life_version.html @@ -82,7 +82,7 @@On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/count.html b/docs/reference/count.html index 7425fc39..60c747ee 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( @@ -332,7 +332,7 @@ A microorganism is categorised as Susceptible, standard dosing regimen, A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. -This AMR package honours this new insight. Use
+susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.This AMR package honours this (new) insight. Use
susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.Combination Therapy
@@ -368,7 +368,7 @@ A microorganism is categorised as Susceptible, Increased exposure when -On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/custom_eucast_rules.html b/docs/reference/custom_eucast_rules.html index 14e633e6..ff8e43e1 100644 --- a/docs/reference/custom_eucast_rules.html +++ b/docs/reference/custom_eucast_rules.html @@ -82,7 +82,7 @@ @@ -348,7 +348,7 @@ The lifecycle of this function is maturing< -proportion_*to calculate microbial resistance and susceptibility.On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", diff --git a/docs/reference/dosage.html b/docs/reference/dosage.html index c721108f..6820d47e 100644 --- a/docs/reference/dosage.html +++ b/docs/reference/dosage.html @@ -82,7 +82,7 @@ @@ -271,7 +271,7 @@ -
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
@@ -381,7 +381,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# \donttest{ diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html index 9f33cf80..368f7027 100644 --- a/docs/reference/example_isolates.html +++ b/docs/reference/example_isolates.html @@ -82,7 +82,7 @@ @@ -269,7 +269,7 @@ -
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
@@ -264,7 +264,7 @@ -On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
@@ -448,7 +448,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html index 2e4dcc83..283714bc 100644 --- a/docs/reference/g.test.html +++ b/docs/reference/g.test.html @@ -82,7 +82,7 @@ @@ -342,7 +342,7 @@ The lifecycle of this function is questioni -On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
References
diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html index e5c82cad..d1c0fc02 100644 --- a/docs/reference/get_episode.html +++ b/docs/reference/get_episode.html @@ -82,7 +82,7 @@ @@ -287,7 +287,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index 85ed24b0..fbb5cf46 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -82,7 +82,7 @@ @@ -426,7 +426,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# \donttest{ diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index 5fe7022a..26dab9e7 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -82,7 +82,7 @@ @@ -287,7 +287,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
df <- data.frame(amox = "S", diff --git a/docs/reference/index.html b/docs/reference/index.html index b92204b4..4a3dc0ab 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ @@ -363,7 +363,7 @@
as.mo()is.mo()mo_failures()mo_uncertainties()mo_renamed()Transform Input to a Microorganism ID
Transform Input to a Microorganism Code
diff --git a/docs/reference/intrinsic_resistant.html b/docs/reference/intrinsic_resistant.html index 827b9700..c8e247c3 100644 --- a/docs/reference/intrinsic_resistant.html +++ b/docs/reference/intrinsic_resistant.html @@ -82,7 +82,7 @@ @@ -265,7 +265,7 @@ - On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# \donttest{ diff --git a/docs/reference/italicise_taxonomy.html b/docs/reference/italicise_taxonomy.html index 4c45de27..70977c26 100644 --- a/docs/reference/italicise_taxonomy.html +++ b/docs/reference/italicise_taxonomy.html @@ -82,7 +82,7 @@ @@ -274,7 +274,7 @@ The lifecycle of this function is maturing< -
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
italicise_taxonomy("An overview of Staphylococcus aureus isolates") diff --git a/docs/reference/join.html b/docs/reference/join.html index 8df29b44..09449988 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -82,7 +82,7 @@ @@ -293,7 +293,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
left_join_microorganisms(as.mo("K. pneumoniae")) diff --git a/docs/reference/key_antimicrobials.html b/docs/reference/key_antimicrobials.html index ce2a822c..47093624 100644 --- a/docs/reference/key_antimicrobials.html +++ b/docs/reference/key_antimicrobials.html @@ -82,7 +82,7 @@ @@ -373,7 +373,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html index de26657b..4ac577ad 100644 --- a/docs/reference/kurtosis.html +++ b/docs/reference/kurtosis.html @@ -82,7 +82,7 @@ @@ -281,7 +281,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/like.html b/docs/reference/like.html index 1052957a..e988f856 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -82,7 +82,7 @@ @@ -296,7 +296,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index 761e273b..18b931bc 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -82,7 +82,7 @@ @@ -417,12 +417,12 @@ A microorganism is categorised as Susceptible, standard dosing regimen, A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. -This AMR package honours this new insight. Use
+susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.This AMR package honours this (new) insight. Use
susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.Read more on Our Website!
-On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
mdro(example_isolates, guideline = "EUCAST") diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 2f8491f8..c64e5e0a 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -82,7 +82,7 @@ @@ -268,7 +268,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( -
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 3a664cd1..6cdacdbc 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ @@ -329,7 +329,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( -On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 402e4c33..91316c28 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -82,7 +82,7 @@ @@ -274,7 +274,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( -On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/mo_matching_score.html b/docs/reference/mo_matching_score.html index 5012eb60..e670d871 100644 --- a/docs/reference/mo_matching_score.html +++ b/docs/reference/mo_matching_score.html @@ -82,7 +82,7 @@ @@ -290,7 +290,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Author
Matthijs S. Berends
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index a8b12480..fc7da911 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ @@ -408,7 +408,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( -On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html index 723041cb..5dec67ca 100644 --- a/docs/reference/mo_source.html +++ b/docs/reference/mo_source.html @@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p @@ -342,7 +342,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
@@ -322,7 +322,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# `example_isolates` is a data set available in the AMR package. diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 4f2e1e33..bc692652 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -82,7 +82,7 @@ @@ -380,7 +380,7 @@
Details
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
-For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the
+guidelineargument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the
guidelineargument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".Simply using
"CLSI"or"EUCAST"as input will automatically select the latest version of that guideline.Stable Lifecycle
@@ -393,7 +393,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
some_mic_values <- random_mic(size = 100) diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index 829de574..fc1da429 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be @@ -382,12 +382,12 @@ A microorganism is categorised as Susceptible, standard dosing regimen, A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. -
This AMR package honours this new insight. Use
+susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.This AMR package honours this (new) insight. Use
susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.Read more on Our Website!
-On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/random.html b/docs/reference/random.html index 9e3720da..a457055c 100644 --- a/docs/reference/random.html +++ b/docs/reference/random.html @@ -82,7 +82,7 @@ @@ -291,7 +291,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +count()to count resistant and susceptible isolates.On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
random_mic(100) diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index c4bcd997..8bd39b1e 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -82,7 +82,7 @@ @@ -387,12 +387,12 @@ A microorganism is categorised as Susceptible, standard dosing regimen, A microorganism is categorised as Susceptible, Increased exposure when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. -
This AMR package honours this new insight. Use
+susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.This AMR package honours this (new) insight. Use
susceptibility()(equal toproportion_SI()) to determine antimicrobial susceptibility andcount_susceptible()(equal tocount_SI()) to count susceptible isolates.Read more on Our Website!
-On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
@@ -239,7 +239,7 @@The
diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index 63d73f49..8aa20566 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -49,7 +49,7 @@ - + @@ -82,7 +82,7 @@proportion()functions to calculate resistance-Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021). Use
+as.rsi()to transform MICs or disks measurements to R/SI values.Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use
as.rsi()to transform MICs or disks measurements to R/SI values.rsi_translation@@ -247,7 +247,7 @@Format
-A data.frame with 20,486 observations and 10 variables:
-
+
A data.frame with 21,996 observations and 10 variables:
On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
+On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index ea05ba8b..2b14c272 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu @@ -279,7 +279,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
diff --git a/docs/reference/translate.html b/docs/reference/translate.html index 340ccddc..8cf0d21e 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -82,7 +82,7 @@ @@ -270,7 +270,7 @@ The lifecycle of this function is stableOn our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey! +On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data.
Examples
# The 'language' argument of below functions diff --git a/docs/survey.html b/docs/survey.html index 3e1708ed..8a9aee5a 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ diff --git a/index.md b/index.md index ec1386e2..58143d30 100644 --- a/index.md +++ b/index.md @@ -98,15 +98,22 @@ This package can be used for: #### Latest released version -This package is [available here](https://msberends.r-universe.dev) on the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), as CRAN does not allow frequent updates of large packages (though the `AMR` package is only 7-9 MB). With CRAN, we apparently cannot update this package frequently enough to implement the latest EUCAST/CLSI guidelines or the latest microbial taxonomy. +This package is [available here](https://msberends.r-universe.dev) on the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), as CRAN does not allow frequent updates of large packages (though the `AMR` package is only 7-9 MB). We are working on splitting this package into two: a new data package containing the microbial taxonomy, and the `AMR` package that only contains all functions. -Install this package in R by using the command: +In the meanwhile, you have to add [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'), by running: ```r -install.packages("AMR", repos = "https://msberends.r-universe.dev") +options(repos = c(getOption("repos"), + msberends = "https://msberends.r-universe.dev")) ``` -It will be downloaded and installed automatically. +You can now install or update the `AMR` package in the same way you are used to: + +```r +install.packages("AMR") +``` + +It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press Install. **Note:** Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version. diff --git a/man/AMR-deprecated.Rd b/man/AMR-deprecated.Rd index 140b1de5..14adc638 100644 --- a/man/AMR-deprecated.Rd +++ b/man/AMR-deprecated.Rd @@ -213,7 +213,7 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \keyword{internal} diff --git a/man/AMR.Rd b/man/AMR.Rd index f2b58d1e..7fcbe362 100644 --- a/man/AMR.Rd +++ b/man/AMR.Rd @@ -40,7 +40,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \section{Contact Us}{ @@ -50,7 +50,7 @@ For suggestions, comments or questions, please contact us at: Matthijs S. Berends \cr m.s.berends [at] umcg [dot] nl \cr University of Groningen -Department of Medical Microbiology +Department of Medical Microbiology and Infection Prevention University Medical Center Groningen \cr Post Office Box 30001 \cr 9700 RB Groningen \cr diff --git a/man/WHOCC.Rd b/man/WHOCC.Rd index b09739db..9bbfe7b7 100644 --- a/man/WHOCC.Rd +++ b/man/WHOCC.Rd @@ -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.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/WHONET.Rd b/man/WHONET.Rd index b66d7079..3072cb9c 100644 --- a/man/WHONET.Rd +++ b/man/WHONET.Rd @@ -48,7 +48,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \keyword{datasets} diff --git a/man/ab_from_text.Rd b/man/ab_from_text.Rd index c04bafc2..2f39df62 100644 --- a/man/ab_from_text.Rd +++ b/man/ab_from_text.Rd @@ -67,7 +67,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/ab_property.Rd b/man/ab_property.Rd index 921eb3b6..884e6e0b 100644 --- a/man/ab_property.Rd +++ b/man/ab_property.Rd @@ -100,7 +100,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/age.Rd b/man/age.Rd index ef23a199..766a1ebc 100644 --- a/man/age.Rd +++ b/man/age.Rd @@ -38,7 +38,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/age_groups.Rd b/man/age_groups.Rd index 79670565..1bfec65a 100644 --- a/man/age_groups.Rd +++ b/man/age_groups.Rd @@ -43,7 +43,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index 7257e8c8..eeef6c72 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -84,7 +84,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd index 3b13195a..094b1f42 100644 --- a/man/antibiotics.Rd +++ b/man/antibiotics.Rd @@ -94,7 +94,7 @@ 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.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \seealso{ diff --git a/man/as.ab.Rd b/man/as.ab.Rd index 86930eca..4bd0071f 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -76,7 +76,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/as.disk.Rd b/man/as.disk.Rd index d6192706..4b239a88 100644 --- a/man/as.disk.Rd +++ b/man/as.disk.Rd @@ -34,7 +34,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/as.mic.Rd b/man/as.mic.Rd index 618ce8e1..6f45fe9b 100755 --- a/man/as.mic.Rd +++ b/man/as.mic.Rd @@ -66,7 +66,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/as.mo.Rd b/man/as.mo.Rd index c80f57d7..846fb145 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -7,7 +7,7 @@ \alias{mo_failures} \alias{mo_uncertainties} \alias{mo_renamed} -\title{Transform Input to a Microorganism ID} +\title{Transform Input to a Microorganism Code} \usage{ as.mo( x, @@ -56,12 +56,12 @@ This excludes \emph{Enterococci} at default (who are in group D), use \code{Lanc A \link{character} \link{vector} with additional class \code{\link{mo}} } \description{ -Use this function to determine a valid microorganism ID (\code{\link{mo}}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see \emph{Source}). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (such as \code{"S. aureus"}), an abbreviation known in the field (such as \code{"MRSA"}), or just a genus. See \emph{Examples}. +Use this function to determine a valid microorganism code (\code{\link{mo}}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see \emph{Source}). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (such as \code{"S. aureus"}), an abbreviation known in the field (such as \code{"MRSA"}), or just a genus. See \emph{Examples}. } \details{ \subsection{General Info}{ -A microorganism ID from this package (class: \code{\link{mo}}) is human readable and typically looks like these examples:\preformatted{ Code Full name +A microorganism (MO) code from this package (class: \code{\link{mo}}) is human readable and typically looks like these examples:\preformatted{ Code Full name --------------- -------------------------------------- B_KLBSL Klebsiella B_KLBSL_PNMN Klebsiella pneumoniae @@ -180,7 +180,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index 7edab8cc..49e5974c 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -104,9 +104,9 @@ your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0 \subsection{Supported Guidelines}{ -For interpreting MIC values as well as disk diffusion diameters, currently supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010". +For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). -Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored. +Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2021"} or \code{"CLSI 2020"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored. } \subsection{After Interpretation}{ @@ -116,7 +116,7 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast \subsection{Machine-Readable Interpretation Guidelines}{ -The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 20,486 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. +The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 21,996 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. } \subsection{Other}{ @@ -138,7 +138,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } -This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. +This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } \section{Stable Lifecycle}{ @@ -156,7 +156,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/atc_online.Rd b/man/atc_online.Rd index 02b2c33f..9a233365 100644 --- a/man/atc_online.Rd +++ b/man/atc_online.Rd @@ -76,7 +76,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/availability.Rd b/man/availability.Rd index 166a59a5..8b7f749b 100644 --- a/man/availability.Rd +++ b/man/availability.Rd @@ -30,7 +30,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/bug_drug_combinations.Rd b/man/bug_drug_combinations.Rd index 2dbb72a3..101c6e90 100644 --- a/man/bug_drug_combinations.Rd +++ b/man/bug_drug_combinations.Rd @@ -29,7 +29,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...) \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} -\item{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link[=mo_shortname]{mo_shortname()}}} +\item{FUN}{the function to call on the \code{mo} column to transform the microorganism codes, defaults to \code{\link[=mo_shortname]{mo_shortname()}}} \item{...}{arguments passed on to \code{FUN}} @@ -73,7 +73,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/catalogue_of_life.Rd b/man/catalogue_of_life.Rd index a8126c4c..be81aad9 100644 --- a/man/catalogue_of_life.Rd +++ b/man/catalogue_of_life.Rd @@ -33,7 +33,7 @@ The syntax used to transform the original data to a cleansed \R format, can be f \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/catalogue_of_life_version.Rd b/man/catalogue_of_life_version.Rd index 0d75afcb..cbc141f2 100644 --- a/man/catalogue_of_life_version.Rd +++ b/man/catalogue_of_life_version.Rd @@ -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.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \seealso{ diff --git a/man/count.Rd b/man/count.Rd index 6ad485e7..1a273144 100644 --- a/man/count.Rd +++ b/man/count.Rd @@ -92,7 +92,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } -This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. +This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } \section{Combination Therapy}{ @@ -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.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/custom_eucast_rules.Rd b/man/custom_eucast_rules.Rd index 36a3d305..72574cc0 100644 --- a/man/custom_eucast_rules.Rd +++ b/man/custom_eucast_rules.Rd @@ -102,7 +102,7 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unly \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/dosage.Rd b/man/dosage.Rd index 4411a297..cf5a3d25 100644 --- a/man/dosage.Rd +++ b/man/dosage.Rd @@ -34,7 +34,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \keyword{datasets} diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index eb68b1eb..94b03a40 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -119,7 +119,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/example_isolates.Rd b/man/example_isolates.Rd index 58dda0c5..5171c867 100644 --- a/man/example_isolates.Rd +++ b/man/example_isolates.Rd @@ -32,7 +32,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \keyword{datasets} diff --git a/man/example_isolates_unclean.Rd b/man/example_isolates_unclean.Rd index a9271eb0..ec7c958f 100644 --- a/man/example_isolates_unclean.Rd +++ b/man/example_isolates_unclean.Rd @@ -27,7 +27,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \keyword{datasets} diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index 8168dfa1..e494fb65 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -174,7 +174,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/g.test.Rd b/man/g.test.Rd index 8830475c..bfac5c1d 100644 --- a/man/g.test.Rd +++ b/man/g.test.Rd @@ -105,7 +105,7 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/get_episode.Rd b/man/get_episode.Rd index 466a0325..a3f7b581 100644 --- a/man/get_episode.Rd +++ b/man/get_episode.Rd @@ -42,7 +42,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/ggplot_rsi.Rd b/man/ggplot_rsi.Rd index 629d95e4..b4f6d817 100644 --- a/man/ggplot_rsi.Rd +++ b/man/ggplot_rsi.Rd @@ -150,7 +150,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/guess_ab_col.Rd b/man/guess_ab_col.Rd index 7f2cdd7f..f7c916b5 100644 --- a/man/guess_ab_col.Rd +++ b/man/guess_ab_col.Rd @@ -39,7 +39,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/intrinsic_resistant.Rd b/man/intrinsic_resistant.Rd index 1c8e6582..b02ab533 100644 --- a/man/intrinsic_resistant.Rd +++ b/man/intrinsic_resistant.Rd @@ -29,7 +29,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/italicise_taxonomy.Rd b/man/italicise_taxonomy.Rd index 1917ce39..f4d5bc4e 100644 --- a/man/italicise_taxonomy.Rd +++ b/man/italicise_taxonomy.Rd @@ -32,7 +32,7 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unly \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/join.Rd b/man/join.Rd index bc2deb40..25ca528f 100755 --- a/man/join.Rd +++ b/man/join.Rd @@ -53,7 +53,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/key_antimicrobials.Rd b/man/key_antimicrobials.Rd index 45df3a17..8b640873 100644 --- a/man/key_antimicrobials.Rd +++ b/man/key_antimicrobials.Rd @@ -117,7 +117,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/kurtosis.Rd b/man/kurtosis.Rd index ffd05abb..c4273c6b 100644 --- a/man/kurtosis.Rd +++ b/man/kurtosis.Rd @@ -35,7 +35,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \seealso{ diff --git a/man/like.Rd b/man/like.Rd index 0a7f86ac..64dc5777 100755 --- a/man/like.Rd +++ b/man/like.Rd @@ -55,7 +55,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/mdro.Rd b/man/mdro.Rd index 58f6219c..4e35e9ef 100644 --- a/man/mdro.Rd +++ b/man/mdro.Rd @@ -181,12 +181,12 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } -This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. +This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index 74989282..0745bd7c 100755 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -96,7 +96,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \seealso{ diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index 62f54089..3c16bb0f 100644 --- a/man/microorganisms.codes.Rd +++ b/man/microorganisms.codes.Rd @@ -32,7 +32,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \seealso{ diff --git a/man/microorganisms.old.Rd b/man/microorganisms.old.Rd index 12539293..4218d4c4 100644 --- a/man/microorganisms.old.Rd +++ b/man/microorganisms.old.Rd @@ -39,7 +39,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \seealso{ diff --git a/man/mo_matching_score.Rd b/man/mo_matching_score.Rd index f3bd793b..a66a5f89 100644 --- a/man/mo_matching_score.Rd +++ b/man/mo_matching_score.Rd @@ -50,7 +50,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/mo_property.Rd b/man/mo_property.Rd index dff64267..12d51357 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -193,7 +193,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/mo_source.Rd b/man/mo_source.Rd index 521ac5ce..635eec55 100644 --- a/man/mo_source.Rd +++ b/man/mo_source.Rd @@ -105,6 +105,6 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } diff --git a/man/pca.Rd b/man/pca.Rd index d44c6883..74aef3c0 100644 --- a/man/pca.Rd +++ b/man/pca.Rd @@ -69,7 +69,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/plot.Rd b/man/plot.Rd index 1f70323a..67e10f88 100644 --- a/man/plot.Rd +++ b/man/plot.Rd @@ -119,7 +119,7 @@ Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support f \details{ The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases. -For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010". +For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010". Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline. } @@ -133,7 +133,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/proportion.Rd b/man/proportion.Rd index 8fdec034..552ca7dc 100644 --- a/man/proportion.Rd +++ b/man/proportion.Rd @@ -138,12 +138,12 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } -This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. +This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/random.Rd b/man/random.Rd index 56e0554e..c35c2b72 100644 --- a/man/random.Rd +++ b/man/random.Rd @@ -45,7 +45,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd index 3b334f2d..fbb97bce 100644 --- a/man/resistance_predict.Rd +++ b/man/resistance_predict.Rd @@ -123,12 +123,12 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. } -This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. +This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. } \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/man/rsi_translation.Rd b/man/rsi_translation.Rd index 17e09a66..5a1e205d 100644 --- a/man/rsi_translation.Rd +++ b/man/rsi_translation.Rd @@ -5,7 +5,7 @@ \alias{rsi_translation} \title{Data Set for R/SI Interpretation} \format{ -A \link{data.frame} with 20,486 observations and 10 variables: +A \link{data.frame} with 21,996 observations and 10 variables: \itemize{ \item \code{guideline}\cr Name of the guideline \item \code{method}\cr Either "DISK" or "MIC" @@ -23,7 +23,7 @@ A \link{data.frame} with 20,486 observations and 10 variables: rsi_translation } \description{ -Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values. +Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values. } \details{ The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically. @@ -35,7 +35,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation, \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \seealso{ diff --git a/man/skewness.Rd b/man/skewness.Rd index b8f6e3a8..43b42037 100644 --- a/man/skewness.Rd +++ b/man/skewness.Rd @@ -35,7 +35,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \seealso{ diff --git a/man/translate.Rd b/man/translate.Rd index 7307bd88..134527c6 100644 --- a/man/translate.Rd +++ b/man/translate.Rd @@ -37,7 +37,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp \section{Read more on Our Website!}{ -On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! +On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. } \examples{ diff --git a/vignettes/WHONET.Rmd b/vignettes/WHONET.Rmd index 26ba10e5..6216f620 100644 --- a/vignettes/WHONET.Rmd +++ b/vignettes/WHONET.Rmd @@ -47,7 +47,7 @@ library(cleaner) # to create frequency tables We will have to transform some variables to simplify and automate the analysis: -* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms. +* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms. * Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.rsi()` function is for. ```{r}
- Function
2020-07-31
-AMR1.3.0+-New
+New
-
2021-03-14 AMR 1.6.0
-
+