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support new mo codes

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dr. M.S. (Matthijs) Berends 2022-12-27 15:16:15 +01:00
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commit f619fb683b
127 changed files with 859 additions and 443 deletions
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6
.github/prehooks/pre-commit vendored
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

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.github/workflows/check-current.yaml vendored
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

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.github/workflows/check-old.yaml vendored
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

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.github/workflows/codecovr.yaml vendored
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

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.github/workflows/lintr.yaml vendored
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

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.github/workflows/website.yaml vendored
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

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DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.2.9069 Version: 1.8.2.9070
Date: 2022-12-21 Date: 2022-12-27
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

2
NAMESPACE
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@ -191,6 +191,7 @@ export(ab_synonyms)
export(ab_tradenames) export(ab_tradenames)
export(ab_url) export(ab_url)
export(add_custom_antimicrobials) export(add_custom_antimicrobials)
export(add_custom_microorganisms)
export(administrable_iv) export(administrable_iv)
export(administrable_per_os) export(administrable_per_os)
export(age) export(age)
@ -238,6 +239,7 @@ export(cephalosporins_3rd)
export(cephalosporins_4th) export(cephalosporins_4th)
export(cephalosporins_5th) export(cephalosporins_5th)
export(clear_custom_antimicrobials) export(clear_custom_antimicrobials)
export(clear_custom_microorganisms)
export(count_I) export(count_I)
export(count_IR) export(count_IR)
export(count_R) export(count_R)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9069 # AMR 1.8.2.9070
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

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R/aa_globals.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

13
R/aa_helper_functions.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -1375,6 +1375,13 @@ trimws2 <- function(..., whitespace = "[\u0009\u000A\u000B\u000C\u000D\u0020\u00
trimws(..., whitespace = whitespace) trimws(..., whitespace = whitespace)
} }
readRDS2 <- function(file, refhook = NULL) {
# this is readRDS with remote file support
con <- file(file)
on.exit(close(con))
readRDS(con, refhook = refhook)
}
# Faster data.table implementations ---- # Faster data.table implementations ----
match <- function(x, table, ...) { match <- function(x, table, ...) {

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R/aa_helper_pm_functions.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/ab.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/ab_from_text.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/ab_property.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/ab_selectors.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

50
R/add_custom_antimicrobials.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -31,12 +31,30 @@
#' #'
#' With [add_custom_antimicrobials()] you can add your own custom antimicrobial drug codes to the `AMR` package. #' With [add_custom_antimicrobials()] you can add your own custom antimicrobial drug codes to the `AMR` package.
#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name" #' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, although this requires to load the `AMR` package at every start-up: #' @details **Important:** Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited.
#'
#' There are two ways to automate this process:
#'
#' **Method 1:** Save the antimicrobials to a local or remote file (can even be the internet). To use this method:
#'
#' 1. Create a data set in the structure of the [antibiotics] data set (containing at the very least columns "ab" and "name") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_ab.rds"`, or any remote location.
#'
#' 2. Set the file location to the `AMR_custom_ab` \R option: `options(AMR_custom_ab = "~/my_custom_ab.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
#' #'
#' ```r #' ```r
#' # Open .Rprofile file #' # Add custom antibiotic drug codes:
#' utils::file.edit("~/.Rprofile") #' options(AMR_custom_ab = "~/my_custom_ab.rds")
#' ```
#' #'
#' Upon package load, this file will be loaded and run through the [add_custom_antimicrobials()] function.
#'
#' **Method 2:** Save the antimicrobial additions directly to your `.Rprofile` file. An important downside is that this requires to load the `AMR` package at every start-up. To use this method:
#'
#' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`.
#'
#' 2. Add a text like below and save the file:
#'
#' ```r
#' # Add custom antibiotic drug codes: #' # Add custom antibiotic drug codes:
#' library(AMR) #' library(AMR)
#' add_custom_antimicrobials( #' add_custom_antimicrobials(
@ -47,6 +65,7 @@
#' ``` #' ```
#' #'
#' Use [clear_custom_antimicrobials()] to clear the previously added antimicrobials. #' Use [clear_custom_antimicrobials()] to clear the previously added antimicrobials.
#' @seealso [add_custom_microorganisms()] to add custom microorganisms to this package.
#' @rdname add_custom_antimicrobials #' @rdname add_custom_antimicrobials
#' @export #' @export
#' @examples #' @examples
@ -84,7 +103,7 @@
#' ab = "COFLU", #' ab = "COFLU",
#' name = "Co-fluampicil", #' name = "Co-fluampicil",
#' atc = "J01CR50", #' atc = "J01CR50",
#' group = "Beta-lactams/penicillines" #' group = "Beta-lactams/penicillins"
#' ) #' )
#' ) #' )
#' ab_atc("Co-fluampicil") #' ab_atc("Co-fluampicil")
@ -109,16 +128,18 @@ add_custom_antimicrobials <- function(x) {
any(x$ab %in% AMR_env$AB_lookup$ab), any(x$ab %in% AMR_env$AB_lookup$ab),
"Antimicrobial drug code(s) ", vector_and(x$ab[x$ab %in% AMR_env$AB_lookup$ab]), " already exist in the internal `antibiotics` data set." "Antimicrobial drug code(s) ", vector_and(x$ab[x$ab %in% AMR_env$AB_lookup$ab]), " already exist in the internal `antibiotics` data set."
) )
# remove any extra class/type, such as grouped tbl, or data.table:
x <- as.data.frame(x, stringsAsFactors = FALSE)
# keep only columns available in the antibiotics data set
x <- x[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %in% colnames(x)], drop = FALSE] x <- x[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %in% colnames(x)], drop = FALSE]
x$generalised_name <- generalise_antibiotic_name(x$name) x$generalised_name <- generalise_antibiotic_name(x$name)
x$generalised_all <- as.list(x$generalised_name) x$generalised_all <- as.list(x$generalised_name)
if ("atc" %in% colnames(x)) { for (col in colnames(x)) {
x$atc <- as.list(x$atc) if (is.list(AMR_env$AB_lookup[, col, drop = TRUE])) {
x[, col] <- as.list(x[, col, drop = TRUE])
} }
if ("loinc" %in% colnames(x)) {
x$loinc <- as.list(x$loinc)
} }
AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab) AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
class(AMR_env$AB_lookup$ab) <- "character" class(AMR_env$AB_lookup$ab) <- "character"
@ -134,6 +155,7 @@ add_custom_antimicrobials <- function(x) {
new_df[, col] <- x[, col, drop = TRUE] new_df[, col] <- x[, col, drop = TRUE]
} }
AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df)) AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df))
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% new_df$ab), , drop = FALSE]
class(AMR_env$AB_lookup$ab) <- c("ab", "character") class(AMR_env$AB_lookup$ab) <- c("ab", "character")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.") message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.")
} }
@ -141,7 +163,9 @@ add_custom_antimicrobials <- function(x) {
#' @rdname add_custom_antimicrobials #' @rdname add_custom_antimicrobials
#' @export #' @export
clear_custom_antimicrobials <- function() { clear_custom_antimicrobials <- function() {
n <- nrow(AMR_env$AB_lookup)
AMR_env$AB_lookup <- create_AB_lookup() AMR_env$AB_lookup <- create_AB_lookup()
n2 <- nrow(AMR_env$AB_lookup)
AMR_env$custom_ab_codes <- character(0) AMR_env$custom_ab_codes <- character(0)
message_("Custom antimicrobials cleared.") message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `antibiotics` data set.")
} }

212
R/add_custom_microorganisms.R Normal file
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@ -0,0 +1,212 @@
# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Add Custom Microorganisms to This Package
#'
#' With [add_custom_microorganisms()] you can add your own custom antimicrobial drug codes to the `AMR` package.
#' @param x a [data.frame] resembling the [microorganisms] data set, at least containing columns "mo", "genus" and "species"
#' @details This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see *Examples*.
#'
#' **Important:** Due to how \R works, the [add_custom_microorganisms()] function has to be run in every \R session - added microorganisms are not stored between sessions and are thus lost when \R is exited.
#'
#' There are two ways to automate this process:
#'
#' **Method 1:** Save the microorganisms to a local or remote file (can even be the internet). To use this method:
#'
#' 1. Create a data set in the structure of the [microorganisms] data set (containing at the very least columns "ab" and "name") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
#'
#' 2. Set the file location to the `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
#'
#' ```r
#' # Add custom microorganism codes:
#' options(AMR_custom_mo = "~/my_custom_mo.rds")
#' ```
#'
#' Upon package load, this file will be loaded and run through the [add_custom_microorganisms()] function.
#'
#' **Method 2:** Save the microorganism directly to your `.Rprofile` file. An important downside is that this requires to load the `AMR` package at every start-up. To use this method:
#'
#' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`.
#'
#' 2. Add a text like below and save the file:
#'
#' ```r
#' # Add custom antibiotic drug codes:
#' library(AMR)
#' add_custom_microorganisms(
#' data.frame(mo = "ENT_ASB_CLO",
#' genus = "Enterobacter",
#' species = "asburiae/cloacae")
#' )
#' ```
#'
#' Use [clear_custom_microorganisms()] to clear the previously added antimicrobials.
#' @seealso [add_custom_antimicrobials()] to add custom antimicrobials to this package.
#' @rdname add_custom_microorganisms
#' @export
#' @examples
#' \donttest{
#'
#' # a combination of species is not formal taxonomy, so
#' # this will result in only "Enterobacter asburiae":
#' mo_name("Enterobacter asburiae/cloacae")
#'
#' # now add a custom entry - it will be considered by as.mo() and
#' # all mo_*() functions
#' add_custom_microorganisms(
#' data.frame(mo = "ENT_ASB_CLO",
#' genus = "Enterobacter",
#' species = "asburiae/cloacae"
#' )
#' )
#'
#' # "ENT_ASB_CLO" is now a new microorganism:
#' mo_name("Enterobacter asburiae/cloacae")
#' as.mo("ent_asb_clo")
#' mo_name("ent_asb_clo")
#' # all internal algorithms will work as well:
#' mo_name("Ent asburia cloacae")
#'
#' # and even the taxonomy was added based on the genus!
#' mo_family("ent_asb_clo")
#' mo_gramstain("Enterobacter asburiae/cloacae")
#'
#' mo_info("ent_asb_clo")
#' }
add_custom_microorganisms <- function(x) {
meet_criteria(x, allow_class = "data.frame")
required_cols <- c("mo", "genus", "species")
stop_ifnot(
all(required_cols %in% colnames(x)),
paste0("`x` must contain columns ", vector_and(required_cols, sort = FALSE), ".")
)
stop_if(
any(x$mo %in% AMR_env$MO_lookup$mo),
"Microorganism code(s) ", vector_and(x$mo[x$mo %in% AMR_env$MO_lookup$mo]), " already exist in the internal `microorganisms` data set."
)
# remove any extra class/type, such as grouped tbl, or data.table:
x <- as.data.frame(x, stringsAsFactors = FALSE)
# rename 'name' to 'fullname' if it's in the data set
if ("name" %in% colnames(x) && !"fullname" %in% colnames(x)) {
colnames(x)[colnames(x) == "name"] <- "fullname"
}
# keep only columns available in the microorganisms data set
x <- x[, colnames(AMR_env$MO_lookup)[colnames(AMR_env$MO_lookup) %in% colnames(x)], drop = FALSE]
# clean the input ----
if (!"subspecies" %in% colnames(x)) {
x$subspecies <- NA_character_
}
x$genus <- trimws2(x$genus)
x$species <- trimws2(x$species)
x$subspecies <- trimws2(x$subspecies)
x$genus[x$genus == ""] <- NA_character_
x$species[x$species == ""] <- NA_character_
x$subspecies[x$subspecies == ""] <- NA_character_
stop_if(any(x$genus[!is.na(x$genus)] %like% " "),
"the 'genus' column must not contain spaces")
stop_if(any(x$species[!is.na(x$species)] %like% " "),
"the 'species' column must not contain spaces")
stop_if(any(x$subspecies[!is.na(x$subspecies)] %like% " "),
"the 'subspecies' column must not contain spaces")
if ("rank" %in% colnames(x)) {
stop_ifnot(all(x$rank %in% AMR_env$MO_lookup$rank),
"the 'rank' column can only contain these values: ", vector_or(AMR_env$MO_lookup$rank))
} else {
x$rank <- ifelse(!is.na(x$subspecies), "subspecies",
ifelse(!is.na(x$species), "species",
ifelse(!is.na(x$genus), "genus",
stop("in add_custom_microorganisms(): the 'genus' column cannot be empty",
call. = FALSE))))
}
if (!"fullname" %in% colnames(x)) {
x$fullname <- paste(x$genus, x$species, x$subspecies)
x$fullname <- gsub(" NA", "", x$fullname)
}
if (!"kingdom" %in% colnames(x)) x$kingdom <- NA_character_
if (!"phylum" %in% colnames(x)) x$phylum <- NA_character_
if (!"class" %in% colnames(x)) x$class <- NA_character_
if (!"order" %in% colnames(x)) x$order <- NA_character_
if (!"family" %in% colnames(x)) x$family <- NA_character_
for (col in colnames(x)) {
if (is.list(AMR_env$MO_lookup[, col, drop = TRUE])) {
x[, col] <- as.list(x[, col, drop = TRUE])
}
}
# fill in other columns
x$status <- "accepted"
x$prevalence <- 1
x$kingdom <- AMR_env$MO_lookup$kingdom[match(x$genus, AMR_env$MO_lookup$genus)]
x$phylum <- AMR_env$MO_lookup$phylum[match(x$genus, AMR_env$MO_lookup$genus)]
x$class <- AMR_env$MO_lookup$class[match(x$genus, AMR_env$MO_lookup$genus)]
x$order <- AMR_env$MO_lookup$order[match(x$genus, AMR_env$MO_lookup$genus)]
x$family <- AMR_env$MO_lookup$family[match(x$genus, AMR_env$MO_lookup$genus)]
x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(x$genus, AMR_env$MO_lookup$genus)]
x$fullname_lower <- tolower(x$fullname)
x$full_first <- substr(x$fullname_lower, 1, 1)
x$species_first <- tolower(substr(x$species, 1, 1))
x$subspecies_first <- tolower(substr(x$subspecies, 1, 1))
# add to pacakge ----
AMR_env$custom_mo_codes <- c(AMR_env$custom_mo_codes, x$mo)
class(AMR_env$MO_lookup$mo) <- "character"
new_df <- AMR_env$MO_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
rownames(new_df) <- NULL
list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
for (l in which(list_cols)) {
# prevent binding NULLs in lists, replace with NA
new_df[, l] <- as.list(NA_character_)
}
for (col in colnames(x)) {
# assign new values
new_df[, col] <- x[, col, drop = TRUE]
}
AMR_env$MO_lookup <- unique(rbind(AMR_env$MO_lookup, new_df))
AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(!AMR_env$mo_previously_coerced$mo %in% new_df$mo), , drop = FALSE]
class(AMR_env$MO_lookup$mo) <- c("mo", "character")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `microorganisms` data set.")
}
#' @rdname add_custom_microorganisms
#' @export
clear_custom_microorganisms <- function() {
n <- nrow(AMR_env$MO_lookup)
AMR_env$MO_lookup <- create_MO_lookup()
n2 <- nrow(AMR_env$MO_lookup)
AMR_env$custom_mo_codes <- character(0)
AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(AMR_env$mo_previously_coerced$mo %in% AMR_env$MO_lookup$mo), , drop = FALSE]
AMR_env$mo_uncertainties <- AMR_env$mo_uncertainties[0, , drop = FALSE]
message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `microorganisms` data set.")
}

6
R/age.R
View File

@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/amr.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/atc_online.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/av.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/av_from_text.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/av_property.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/availability.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/bug_drug_combinations.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/count.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/custom_eucast_rules.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/data.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/deprecated.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/disk.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/episode.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

8
R/eucast_rules.R
View File

@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -204,7 +204,7 @@ eucast_rules <- function(x,
expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]] expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]]
# support old setting (until AMR v1.3.0) # support old setting (until AMR v1.3.0)
if (missing(rules) && !is.null(getOption("AMR.eucast_rules", default = NULL))) { if (missing(rules) && !is.null(getOption("AMR.eucast_rules"))) {
rules <- getOption("AMR.eucast_rules") rules <- getOption("AMR.eucast_rules")
} }

6
R/first_isolate.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/g.test.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/ggplot_pca.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/ggplot_rsi.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/guess_ab_col.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/italicise_taxonomy.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/join_microorganisms.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/key_antimicrobials.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/kurtosis.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/like.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/mdro.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/mean_amr_distance.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/mic.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

67
R/mo.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -200,7 +200,7 @@ as.mo <- function(x,
out[x %in% reference_df[[1]]] <- reference_df[[2]][match(x[x %in% reference_df[[1]]], reference_df[[1]])] out[x %in% reference_df[[1]]] <- reference_df[[2]][match(x[x %in% reference_df[[1]]], reference_df[[1]])]
} }
# From MO code ---- # From MO code ----
out[is.na(out) & x %in% AMR_env$MO_lookup$mo] <- x[is.na(out) & x %in% AMR_env$MO_lookup$mo] out[is.na(out) & toupper(x) %in% AMR_env$MO_lookup$mo] <- toupper(x[is.na(out) & toupper(x) %in% AMR_env$MO_lookup$mo])
# From full name ---- # From full name ----
out[is.na(out) & x_lower %in% AMR_env$MO_lookup$fullname_lower] <- AMR_env$MO_lookup$mo[match(x_lower[is.na(out) & x_lower %in% AMR_env$MO_lookup$fullname_lower], AMR_env$MO_lookup$fullname_lower)] out[is.na(out) & x_lower %in% AMR_env$MO_lookup$fullname_lower] <- AMR_env$MO_lookup$mo[match(x_lower[is.na(out) & x_lower %in% AMR_env$MO_lookup$fullname_lower], AMR_env$MO_lookup$fullname_lower)]
# one exception: "Fungi" matches the kingdom, but instead it should return the 'unknown' code for fungi # one exception: "Fungi" matches the kingdom, but instead it should return the 'unknown' code for fungi
@ -210,7 +210,7 @@ as.mo <- function(x,
# From SNOMED ---- # From SNOMED ----
if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(microorganisms$snomed), na.rm = TRUE)) { if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(microorganisms$snomed), na.rm = TRUE)) {
# found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331 # found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331
out[is.na(out) & x %in% unlist(AMR::microorganisms$snomed)] <- AMR::microorganisms$mo[rep(seq_along(AMR::microorganisms$snomed), vapply(FUN.VALUE = double(1), AMR::microorganisms$snomed, length))[match(x[is.na(out) & x %in% unlist(AMR::microorganisms$snomed)], unlist(AMR::microorganisms$snomed))]] out[is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed)] <- AMR_env$MO_lookup$mo[rep(seq_along(AMR_env$MO_lookup$snomed), vapply(FUN.VALUE = double(1), AMR_env$MO_lookup$snomed, length))[match(x[is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed)], unlist(AMR_env$MO_lookup$snomed))]]
} }
# From other familiar output ---- # From other familiar output ----
# such as Salmonella groups, colloquial names, etc. # such as Salmonella groups, colloquial names, etc.
@ -382,20 +382,20 @@ as.mo <- function(x,
} # end of loop over all yet unknowns } # end of loop over all yet unknowns
# Keep or replace synonyms ---- # Keep or replace synonyms ----
lpsn_matches <- AMR::microorganisms$lpsn_renamed_to[match(out, AMR::microorganisms$mo)] lpsn_matches <- AMR_env$MO_lookup$lpsn_renamed_to[match(out, AMR_env$MO_lookup$mo)]
lpsn_matches[!lpsn_matches %in% AMR::microorganisms$lpsn] <- NA lpsn_matches[!lpsn_matches %in% AMR_env$MO_lookup$lpsn] <- NA
# GBIF only for non-bacteria, since we use LPSN as primary source for bacteria # GBIF only for non-bacteria, since we use LPSN as primary source for bacteria
# (an example is Strep anginosus, renamed according to GBIF, not according to LPSN) # (an example is Strep anginosus, renamed according to GBIF, not according to LPSN)
gbif_matches <- AMR::microorganisms$gbif_renamed_to[AMR::microorganisms$kingdom != "Bacteria"][match(out, AMR::microorganisms$mo[AMR::microorganisms$kingdom != "Bacteria"])] gbif_matches <- AMR_env$MO_lookup$gbif_renamed_to[AMR_env$MO_lookup$kingdom != "Bacteria"][match(out, AMR_env$MO_lookup$mo[AMR_env$MO_lookup$kingdom != "Bacteria"])]
gbif_matches[!gbif_matches %in% AMR::microorganisms$gbif] <- NA gbif_matches[!gbif_matches %in% AMR_env$MO_lookup$gbif] <- NA
AMR_env$mo_renamed <- list( AMR_env$mo_renamed <- list(
old = out[!is.na(gbif_matches) | !is.na(lpsn_matches)], old = out[!is.na(gbif_matches) | !is.na(lpsn_matches)],
gbif_matches = gbif_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)], gbif_matches = gbif_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)],
lpsn_matches = lpsn_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)] lpsn_matches = lpsn_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)]
) )
if (isFALSE(keep_synonyms)) { if (isFALSE(keep_synonyms)) {
out[which(!is.na(gbif_matches))] <- AMR::microorganisms$mo[match(gbif_matches[which(!is.na(gbif_matches))], AMR::microorganisms$gbif)] out[which(!is.na(gbif_matches))] <- AMR_env$MO_lookup$mo[match(gbif_matches[which(!is.na(gbif_matches))], AMR_env$MO_lookup$gbif)]
out[which(!is.na(lpsn_matches))] <- AMR::microorganisms$mo[match(lpsn_matches[which(!is.na(lpsn_matches))], AMR::microorganisms$lpsn)] out[which(!is.na(lpsn_matches))] <- AMR_env$MO_lookup$mo[match(lpsn_matches[which(!is.na(lpsn_matches))], AMR_env$MO_lookup$lpsn)]
if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) { if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) {
print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)") print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)")
} }
@ -416,7 +416,7 @@ as.mo <- function(x,
"Staphylococcus", "Staphylococcus",
c("caledonicus", "canis", "durrellii", "lloydii", "ratti", "roterodami", "singaporensis", "taiwanensis") c("caledonicus", "canis", "durrellii", "lloydii", "ratti", "roterodami", "singaporensis", "taiwanensis")
) )
if (any(out %in% AMR::microorganisms$mo[match(post_Becker, AMR::microorganisms$fullname)])) { if (any(out %in% AMR_env$MO_lookup$mo[match(post_Becker, AMR_env$MO_lookup$fullname)])) {
if (message_not_thrown_before("as.mo", "becker")) { if (message_not_thrown_before("as.mo", "becker")) {
warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ", warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE), vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE),
@ -492,10 +492,10 @@ mo_renamed <- function() {
x <- AMR_env$mo_renamed x <- AMR_env$mo_renamed
x$new <- synonym_mo_to_accepted_mo(x$old) x$new <- synonym_mo_to_accepted_mo(x$old)
mo_old <- AMR::microorganisms$fullname[match(x$old, AMR::microorganisms$mo)] mo_old <- AMR_env$MO_lookup$fullname[match(x$old, AMR_env$MO_lookup$mo)]
mo_new <- AMR::microorganisms$fullname[match(x$new, AMR::microorganisms$mo)] mo_new <- AMR_env$MO_lookup$fullname[match(x$new, AMR_env$MO_lookup$mo)]
ref_old <- AMR::microorganisms$ref[match(x$old, AMR::microorganisms$mo)] ref_old <- AMR_env$MO_lookup$ref[match(x$old, AMR_env$MO_lookup$mo)]
ref_new <- AMR::microorganisms$ref[match(x$new, AMR::microorganisms$mo)] ref_new <- AMR_env$MO_lookup$ref[match(x$new, AMR_env$MO_lookup$mo)]
df_renamed <- data.frame( df_renamed <- data.frame(
old = mo_old, old = mo_old,
@ -554,6 +554,9 @@ pillar_shaft.mo <- function(x, ...) {
out[is.na(x)] <- font_na(" NA") out[is.na(x)] <- font_na(" NA")
out[x == "UNKNOWN"] <- font_na(" UNKNOWN") out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
# markup manual codes
out[x %in% AMR_env$MO_lookup$mo & !x %in% AMR::microorganisms$mo] <- font_blue(out[x %in% AMR_env$MO_lookup$mo & !x %in% AMR::microorganisms$mo], collapse = NULL)
df <- tryCatch(get_current_data(arg_name = "x", call = 0), df <- tryCatch(get_current_data(arg_name = "x", call = 0),
error = function(e) NULL error = function(e) NULL
) )
@ -563,7 +566,7 @@ pillar_shaft.mo <- function(x, ...) {
mo_cols <- NULL mo_cols <- NULL
} }
all_mos <- c(AMR::microorganisms$mo, NA) all_mos <- c(AMR_env$MO_lookup$mo, NA)
if (!all(x %in% all_mos) || if (!all(x %in% all_mos) ||
(!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% all_mos))) { (!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% all_mos))) {
# markup old mo codes # markup old mo codes
@ -665,7 +668,7 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
} }
x <- as.character(x) x <- as.character(x)
names(x) <- x_names names(x) <- x_names
if (!all(x %in% c(AMR::microorganisms$mo, NA))) { if (!all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
warning_( warning_(
"Some MO codes are from a previous AMR package version. ", "Some MO codes are from a previous AMR package version. ",
"Please update the MO codes with `as.mo()`.", "Please update the MO codes with `as.mo()`.",
@ -698,7 +701,7 @@ summary.mo <- function(object, ...) {
#' @export #' @export
#' @noRd #' @noRd
as.data.frame.mo <- function(x, ...) { as.data.frame.mo <- function(x, ...) {
if (!all(x %in% c(AMR::microorganisms$mo, NA))) { if (!all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
warning_( warning_(
"The data contains old MO codes (from a previous AMR package version). ", "The data contains old MO codes (from a previous AMR package version). ",
"Please update your MO codes with `as.mo()`." "Please update your MO codes with `as.mo()`."
@ -735,7 +738,7 @@ as.data.frame.mo <- function(x, ...) {
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(i) attributes(y) <- attributes(i)
# must only contain valid MOs # must only contain valid MOs
return_after_integrity_check(y, "microorganism code", as.character(AMR::microorganisms$mo)) return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
} }
#' @method [[<- mo #' @method [[<- mo
#' @export #' @export
@ -744,7 +747,7 @@ as.data.frame.mo <- function(x, ...) {
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(i) attributes(y) <- attributes(i)
# must only contain valid MOs # must only contain valid MOs
return_after_integrity_check(y, "microorganism code", as.character(AMR::microorganisms$mo)) return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
} }
#' @method c mo #' @method c mo
#' @export #' @export
@ -753,7 +756,7 @@ c.mo <- function(...) {
x <- list(...)[[1L]] x <- list(...)[[1L]]
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(x) attributes(y) <- attributes(x)
return_after_integrity_check(y, "microorganism code", as.character(AMR::microorganisms$mo)) return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
} }
#' @method unique mo #' @method unique mo
@ -859,10 +862,10 @@ print.mo_uncertainties <- function(x, ...) {
# Add "Based on {input}" text if it differs from the original input # Add "Based on {input}" text if it differs from the original input
ifelse(x[i, ]$original_input != x[i, ]$input, paste0(strrep(" ", nchar(x[i, ]$original_input) + 6), "Based on input \"", x[i, ]$input, "\""), ""), ifelse(x[i, ]$original_input != x[i, ]$input, paste0(strrep(" ", nchar(x[i, ]$original_input) + 6), "Based on input \"", x[i, ]$input, "\""), ""),
# Add note if result was coerced to accepted taxonomic name # Add note if result was coerced to accepted taxonomic name
ifelse(x[i, ]$keep_synonyms == FALSE & x[i, ]$mo %in% AMR::microorganisms$mo[which(AMR::microorganisms$status == "synonym")], ifelse(x[i, ]$keep_synonyms == FALSE & x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
paste0( paste0(
strrep(" ", nchar(x[i, ]$original_input) + 6), strrep(" ", nchar(x[i, ]$original_input) + 6),
font_red(paste0("This old taxonomic name was converted to ", font_italic(AMR::microorganisms$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR::microorganisms$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL) font_red(paste0("This old taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL)
), ),
"" ""
), ),
@ -1030,7 +1033,7 @@ parse_and_convert <- function(x) {
replace_old_mo_codes <- function(x, property) { replace_old_mo_codes <- function(x, property) {
# this function transform old MO codes to current codes, such as: # this function transform old MO codes to current codes, such as:
# B_ESCH_COL (AMR v0.5.0) -> B_ESCHR_COLI # B_ESCH_COL (AMR v0.5.0) -> B_ESCHR_COLI
ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% AMR::microorganisms$mo ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% AMR_env$MO_lookup$mo
if (any(ind, na.rm = TRUE)) { if (any(ind, na.rm = TRUE)) {
# get the ones that match # get the ones that match
affected <- x[ind] affected <- x[ind]
@ -1144,17 +1147,17 @@ load_mo_uncertainties <- function(metadata) {
} }
synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE) { synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE) {
x_gbif <- AMR::microorganisms$gbif_renamed_to[match(x, AMR::microorganisms$mo)] x_gbif <- AMR_env$MO_lookup$gbif_renamed_to[match(x, AMR_env$MO_lookup$mo)]
x_lpsn <- AMR::microorganisms$lpsn_renamed_to[match(x, AMR::microorganisms$mo)] x_lpsn <- AMR_env$MO_lookup$lpsn_renamed_to[match(x, AMR_env$MO_lookup$mo)]
x_gbif[!x_gbif %in% AMR::microorganisms$gbif] <- NA x_gbif[!x_gbif %in% AMR_env$MO_lookup$gbif] <- NA
x_lpsn[!x_lpsn %in% AMR::microorganisms$lpsn] <- NA x_lpsn[!x_lpsn %in% AMR_env$MO_lookup$lpsn] <- NA
out <- ifelse(is.na(x_lpsn), out <- ifelse(is.na(x_lpsn),
AMR::microorganisms$mo[match(x_gbif, AMR::microorganisms$gbif)], AMR_env$MO_lookup$mo[match(x_gbif, AMR_env$MO_lookup$gbif)],
AMR::microorganisms$mo[match(x_lpsn, AMR::microorganisms$lpsn)] AMR_env$MO_lookup$mo[match(x_lpsn, AMR_env$MO_lookup$lpsn)]
) )
if (isTRUE(fill_in_accepted)) { if (isTRUE(fill_in_accepted)) {
x_accepted <- which(AMR::microorganisms$status[match(x, AMR::microorganisms$mo)] == "accepted") x_accepted <- which(AMR_env$MO_lookup$status[match(x, AMR_env$MO_lookup$mo)] == "accepted")
out[x_accepted] <- x[x_accepted] out[x_accepted] <- x[x_accepted]
} }
out out

6
R/mo_matching_score.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

28
R/mo_property.R
View File

@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -676,9 +676,9 @@ mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
metadata <- get_mo_uncertainties() metadata <- get_mo_uncertainties()
syns <- lapply(x.mo, function(y) { syns <- lapply(x.mo, function(y) {
gbif <- AMR::microorganisms$gbif[match(y, AMR::microorganisms$mo)] gbif <- AMR_env$MO_lookup$gbif[match(y, AMR_env$MO_lookup$mo)]
lpsn <- AMR::microorganisms$lpsn[match(y, AMR::microorganisms$mo)] lpsn <- AMR_env$MO_lookup$lpsn[match(y, AMR_env$MO_lookup$mo)]
out <- AMR::microorganisms[which(AMR::microorganisms$lpsn_renamed_to == lpsn | AMR::microorganisms$gbif_renamed_to == gbif), "fullname", drop = TRUE] out <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$lpsn_renamed_to == lpsn | AMR_env$MO_lookup$gbif_renamed_to == gbif), "fullname", drop = TRUE]
if (length(out) == 0) { if (length(out) == 0) {
NULL NULL
} else { } else {
@ -760,10 +760,10 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
x.mo <- as.mo(x = x, language = language, keep_synonyms = keep_synonyms, ... = ...) x.mo <- as.mo(x = x, language = language, keep_synonyms = keep_synonyms, ... = ...)
metadata <- get_mo_uncertainties() metadata <- get_mo_uncertainties()
x.rank <- AMR::microorganisms$rank[match(x.mo, AMR::microorganisms$mo)] x.rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)]
x.name <- AMR::microorganisms$fullname[match(x.mo, AMR::microorganisms$mo)] x.name <- AMR_env$MO_lookup$fullname[match(x.mo, AMR_env$MO_lookup$mo)]
x.lpsn <- AMR::microorganisms$lpsn[match(x.mo, AMR::microorganisms$mo)] x.lpsn <- AMR_env$MO_lookup$lpsn[match(x.mo, AMR_env$MO_lookup$mo)]
x.gbif <- AMR::microorganisms$gbif[match(x.mo, AMR::microorganisms$mo)] x.gbif <- AMR_env$MO_lookup$gbif[match(x.mo, AMR_env$MO_lookup$mo)]
u <- character(length(x)) u <- character(length(x))
u[!is.na(x.gbif)] <- paste0(TAXONOMY_VERSION$GBIF$url, "/species/", x.gbif[!is.na(x.gbif)]) u[!is.na(x.gbif)] <- paste0(TAXONOMY_VERSION$GBIF$url, "/species/", x.gbif[!is.na(x.gbif)])
@ -792,7 +792,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), k
x <- find_mo_col(fn = "mo_property") x <- find_mo_col(fn = "mo_property")
} }
meet_criteria(x, allow_NA = TRUE) meet_criteria(x, allow_NA = TRUE)
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR::microorganisms)) meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR_env$MO_lookup))
language <- validate_language(language) language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
@ -803,7 +803,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
# try to catch an error when inputting an invalid argument # try to catch an error when inputting an invalid argument
# so the 'call.' can be set to FALSE # so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% unlist(AMR::microorganisms[1, property, drop = TRUE]), tryCatch(x[1L] %in% unlist(AMR_env$MO_lookup[1, property, drop = TRUE]),
error = function(e) stop(e$message, call. = FALSE) error = function(e) stop(e$message, call. = FALSE)
) )
@ -819,7 +819,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") || Lancefield %in% c(TRUE, "all") has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") || Lancefield %in% c(TRUE, "all")
# get microorganisms data set, but remove synonyms if keep_synonyms is FALSE # get microorganisms data set, but remove synonyms if keep_synonyms is FALSE
mo_data_check <- AMR::microorganisms[which(AMR::microorganisms$status %in% if (isTRUE(keep_synonyms)) c("synonym", "accepted") else "accepted"), , drop = FALSE] mo_data_check <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$status %in% if (isTRUE(keep_synonyms)) c("synonym", "accepted") else "accepted"), , drop = FALSE]
if (all(x %in% c(mo_data_check$mo, NA)) && !has_Becker_or_Lancefield) { if (all(x %in% c(mo_data_check$mo, NA)) && !has_Becker_or_Lancefield) {
# do nothing, just don't run the other if-else's # do nothing, just don't run the other if-else's
@ -833,7 +833,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
} }
# get property reeaaally fast using match() # get property reeaaally fast using match()
x <- AMR::microorganisms[[property]][match(x, AMR::microorganisms$mo)] x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
if (property == "mo") { if (property == "mo") {
return(set_clean_class(x, new_class = c("mo", "character"))) return(set_clean_class(x, new_class = c("mo", "character")))

10
R/mo_source.R
View File

@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -149,7 +149,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
df <- NULL df <- NULL
if (path %like% "[.]rds$") { if (path %like% "[.]rds$") {
df <- readRDS(path) df <- readRDS2(path)
} else if (path %like% "[.]xlsx?$") { } else if (path %like% "[.]xlsx?$") {
# is Excel file (old or new) # is Excel file (old or new)
stop_ifnot_installed("readxl") stop_ifnot_installed("readxl")
@ -248,7 +248,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
return(NULL) return(NULL)
} }
if (is.null(AMR_env$mo_source)) { if (is.null(AMR_env$mo_source)) {
AMR_env$mo_source <- readRDS(path.expand(destination)) AMR_env$mo_source <- readRDS2(path.expand(destination))
} }
old_time <- attributes(AMR_env$mo_source)$mo_source_timestamp old_time <- attributes(AMR_env$mo_source)$mo_source_timestamp

6
R/pca.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/plot.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/proportion.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/random.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/resistance_predict.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/rsi.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/rsi_calc.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/rsi_df.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
R/skewness.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

8
R/translate.R
View File

@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -91,7 +91,7 @@
#' ab_name("amox/clav") #' ab_name("amox/clav")
get_AMR_locale <- function() { get_AMR_locale <- function() {
# a message for this will be thrown in translate_into_language() if outcome is non-English # a message for this will be thrown in translate_into_language() if outcome is non-English
if (!is.null(getOption("AMR_locale", default = NULL))) { if (!is.null(getOption("AMR_locale"))) {
return(validate_language(getOption("AMR_locale"), extra_txt = "set with `options(AMR_locale = ...)`")) return(validate_language(getOption("AMR_locale"), extra_txt = "set with `options(AMR_locale = ...)`"))
} }
lang <- "" lang <- ""

8
R/vctrs.R
View File

@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -95,7 +95,7 @@ vec_cast.character.mo <- function(x, to, ...) {
as.character(x) as.character(x)
} }
vec_cast.mo.character <- function(x, to, ...) { vec_cast.mo.character <- function(x, to, ...) {
return_after_integrity_check(x, "microorganism code", as.character(AMR::microorganisms$mo)) return_after_integrity_check(x, "microorganism code", as.character(AMR_env$MO_lookup$mo))
} }
# S3: disk # S3: disk

6
R/whocc.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

31
R/zzz.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #
@ -72,6 +72,7 @@ AMR_env$rsi_interpretation_history <- data.frame(
stringsAsFactors = FALSE stringsAsFactors = FALSE
) )
AMR_env$custom_ab_codes <- character(0) AMR_env$custom_ab_codes <- character(0)
AMR_env$custom_mo_codes <- character(0)
AMR_env$is_dark_theme <- NULL AMR_env$is_dark_theme <- NULL
# determine info icon for messages # determine info icon for messages
@ -171,12 +172,11 @@ if (utf8_supported && !is_latex) {
# if mo source exists, fire it up (see mo_source()) # if mo source exists, fire it up (see mo_source())
if (tryCatch(file.exists(getOption("AMR_mo_source", "~/mo_source.rds")), error = function(e) FALSE)) { if (tryCatch(file.exists(getOption("AMR_mo_source", "~/mo_source.rds")), error = function(e) FALSE)) {
invisible(get_mo_source()) try(invisible(get_mo_source()), silent = TRUE)
} }
# be sure to print tibbles as tibbles # be sure to print tibbles as tibbles
if (pkg_is_available("tibble", also_load = FALSE)) { if (pkg_is_available("tibble", also_load = FALSE)) {
loadNamespace("tibble") try(loadNamespace("tibble"), silent = TRUE)
} }
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed # reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
@ -184,6 +184,25 @@ if (utf8_supported && !is_latex) {
AMR_env$AB_lookup <- create_AB_lookup() AMR_env$AB_lookup <- create_AB_lookup()
AMR_env$AV_lookup <- create_AV_lookup() AMR_env$AV_lookup <- create_AV_lookup()
AMR_env$MO_lookup <- create_MO_lookup() AMR_env$MO_lookup <- create_MO_lookup()
# if custom ab option is available, load it
if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
packageStartupMessage("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'...", appendLF = FALSE)
x <- readRDS2(getOption("AMR_custom_ab"))
tryCatch({
suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
packageStartupMessage("OK.")
}, error = function(e) packageStartupMessage("Failed: ", e$message))
}
# if custom mo option is available, load it
if (!is.null(getOption("AMR_custom_mo")) && file.exists(getOption("AMR_custom_mo", default = ""))) {
packageStartupMessage("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'...", appendLF = FALSE)
x <- readRDS2(getOption("AMR_custom_mo"))
tryCatch({
suppressWarnings(suppressMessages(add_custom_microorganisms(x)))
packageStartupMessage("OK.")
}, error = function(e) packageStartupMessage("Failed: ", e$message))
}
} }
# Helper functions -------------------------------------------------------- # Helper functions --------------------------------------------------------

6
_pkgdown.yml
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
codecov.yml
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/_install_deps.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/_language_update.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/_pre_commit_hook.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/loinc.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/poorman_prepend.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/read_EUCAST.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/reproduction_of_antibiotics.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/reproduction_of_antivirals.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/reproduction_of_dosage.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/reproduction_of_example_isolates_unclean.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/reproduction_of_intrinsic_resistant.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/reproduction_of_microorganisms.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/reproduction_of_rsi_translation.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
data-raw/salmonellae.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-_deprecated.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-_misc.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-ab.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-ab_from_text.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-ab_property.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-ab_selectors.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-add_custom_antimicrobials.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

43
inst/tinytest/test-add_custom_microorganisms.R Normal file
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@ -0,0 +1,43 @@
# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_identical(as.mo("Enterobacter asburiae/cloacae"),
as.mo("Enterobacter asburiae"))
suppressMessages(
add_custom_microorganisms(
data.frame(mo = "ENT_ASB_CLO",
genus = "Enterobacter",
species = "asburiae/cloacae")
)
)
expect_identical(as.character(as.mo("ENT_ASB_CLO")), "ENT_ASB_CLO")
expect_identical(mo_name("ENT_ASB_CLO"), "Enterobacter asburiae/cloacae")
expect_identical(mo_gramstain("ENT_ASB_CLO", language = NULL), "Gram-negative")

6
inst/tinytest/test-age.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-atc_online.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-av.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-av_from_text.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-av_property.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-availability.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-bug_drug_combinations.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-count.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-data.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-disk.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-episode.R
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# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-eucast_rules.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

6
inst/tinytest/test-first_isolate.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # doi:10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen, the Netherlands, in # # Developed at the University of Groningen and the University Medical #
# collaboration with non-profit organisations Certe Medical # # Center Groningen in The Netherlands, in collaboration with many #
# Diagnostics & Advice, and University Medical Center Groningen. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the # # it for both personal and commercial purposes under the terms of the #

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