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v1.8.1

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dr. M.S. (Matthijs) Berends 2022-03-24 23:05:04 +01:00
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.Rbuildignore
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^vignettes/SPSS.Rmd$ ^vignettes/SPSS.Rmd$
^vignettes/WHONET.Rmd$ ^vignettes/WHONET.Rmd$
^logo.svg$ ^logo.svg$
^CRAN-SUBMISSION$

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CRAN-SUBMISSION Normal file
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@ -0,0 +1,3 @@
Version: 1.8.1
Date: 2022-03-16 18:22:51 UTC
SHA: 7b0f1596bd65fbb72681a7e3a6a7e4e469a891e8

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DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.0.9010 Version: 1.8.1
Date: 2022-03-15 Date: 2022-03-17
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by
@ -9,7 +9,7 @@ Description: Functions to simplify and standardise antimicrobial resistance (AMR
Authors@R: c( Authors@R: c(
person(given = c("Matthijs", "S."), person(given = c("Matthijs", "S."),
family = "Berends", family = "Berends",
email = "m.s.berends@umcg.nl", email = "m.berends@certe.nl",
role = c("aut", "cre"), role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-7620-1800")), comment = c(ORCID = "0000-0001-7620-1800")),
person(given = c("Christian", "F."), person(given = c("Christian", "F."),

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NEWS.md
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@ -1,5 +1,5 @@
# `AMR` 1.8.0.9010 # `AMR` 1.8.1
## <small>Last updated: 15 March 2022</small>
All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months. All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
@ -276,7 +276,7 @@ All functions in this package are considered to be stable. Updates to the AMR in
filter(is_new_episode(date, episode_days = 60)) filter(is_new_episode(date, episode_days = 60))
``` ```
* Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. * Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
* Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on [EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) from 2020. * Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020.
* Functions `random_mic()`, `random_disk()` and `random_rsi()` for random value generation. The functions `random_mic()` and `random_disk()` take microorganism names and antibiotic names as input to make generation more realistic. * Functions `random_mic()`, `random_disk()` and `random_rsi()` for random value generation. The functions `random_mic()` and `random_disk()` take microorganism names and antibiotic names as input to make generation more realistic.
### Changed ### Changed
@ -1372,7 +1372,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations * Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
* Function `freq` to create **frequency tables**, with additional info in a header * Function `freq` to create **frequency tables**, with additional info in a header
* Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines. * Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
* [Exceptional resistances defined by EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) are also supported instead of countries alone * Exceptional resistances defined by EUCAST are also supported instead of countries alone
* Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively * Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
* New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate` * New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
* New print format for `tibble`s and `data.table`s * New print format for `tibble`s and `data.table`s

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R/aa_globals.R
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@ -36,15 +36,15 @@ EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(version_txt = "v11.0",
EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1", EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
year = 2016, year = 2016,
title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'", title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"), url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"),
"3.2" = list(version_txt = "v3.2", "3.2" = list(version_txt = "v3.2",
year = 2020, year = 2020,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'", title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"), url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"),
"3.3" = list(version_txt = "v3.3", "3.3" = list(version_txt = "v3.3",
year = 2021, year = 2021,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'", title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/")) url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"))
SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)", SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
current_source = "US Edition of SNOMED CT from 1 September 2020", current_source = "US Edition of SNOMED CT from 1 September 2020",

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R/mdro.R
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@ -65,7 +65,7 @@
#' #'
#' * `guideline = "TB"` #' * `guideline = "TB"`
#' #'
#' The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/tb/publications/pmdt_companionhandbook/en/)) #' The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/publications/i/item/9789241548809))
#' #'
#' * `guideline = "MRGN"` #' * `guideline = "MRGN"`
#' #'
@ -343,7 +343,7 @@ mdro <- function(x = NULL,
guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
guideline$author <- "WHO (World Health Organization)" guideline$author <- "WHO (World Health Organization)"
guideline$version <- "WHO/HTM/TB/2014.11, 2014" guideline$version <- "WHO/HTM/TB/2014.11, 2014"
guideline$source_url <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/" guideline$source_url <- "https://www.who.int/publications/i/item/9789241548809"
guideline$type <- "MDR-TB's" guideline$type <- "MDR-TB's"
# support per country: # support per country:

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cran-comments.md
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@ -1 +1,2 @@
* This package has a data folder size of ~1.7 MB, which might return a NOTE on some R CMD CHECKs. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, as it has been in the 16 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible. Extra release for fixing image options, as requested by CRAN team on 17 February 2022 (Kurt Hornik).

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man/antibiotic_class_selectors.Rd
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@ -131,7 +131,7 @@ The \code{\link[=ab_selector]{ab_selector()}} function can be used to internally
The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[=administrable_iv]{administrable_iv()}} functions also rely on the \link{antibiotics} data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the \link{antibiotics} data set. The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[=administrable_iv]{administrable_iv()}} functions also rely on the \link{antibiotics} data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the \link{antibiotics} data set.
The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance. The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
} }
\section{Full list of supported (antibiotic) classes}{ \section{Full list of supported (antibiotic) classes}{

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man/as.rsi.Rd
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@ -74,7 +74,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{conserve_capped_values}{a \link{logical} to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"} \item{conserve_capped_values}{a \link{logical} to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
\item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).} \item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{logical} to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).}
\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{rsi_translation} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.} \item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{rsi_translation} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}

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man/intrinsic_resistant.Rd
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@ -20,7 +20,7 @@ Data set containing defined intrinsic resistance by EUCAST of all bug-drug combi
\details{ \details{
The repository of this \code{AMR} package contains a file comprising this data set with full taxonomic and antibiotic names: \url{https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically. The repository of this \code{AMR} package contains a file comprising this data set with full taxonomic and antibiotic names: \url{https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt}. This file \strong{allows for machine reading EUCAST guidelines about intrinsic resistance}, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
This data set is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). This data set is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).
} }
\section{Reference Data Publicly Available}{ \section{Reference Data Publicly Available}{

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man/mdro.Rd
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@ -105,7 +105,7 @@ The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsi
The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link}) The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
\item \code{guideline = "TB"} \item \code{guideline = "TB"}
The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link}) The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/publications/i/item/9789241548809}{link})
\item \code{guideline = "MRGN"} \item \code{guideline = "MRGN"}
The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6} The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6}

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man/mo_property.Rd
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@ -131,7 +131,7 @@ The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determine
Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}). Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (except when the input is \code{NA} or the MO code is \code{UNKNOWN}).
Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics). Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
All output \link[=translate]{will be translated} where possible. All output \link[=translate]{will be translated} where possible.