mirror of
https://github.com/msberends/AMR.git
synced 2024-12-24 18:46:14 +01:00
support new mo codes
This commit is contained in:
parent
e493248ea5
commit
f619fb683b
6
.github/prehooks/pre-commit
vendored
6
.github/prehooks/pre-commit
vendored
@ -13,9 +13,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
.github/workflows/check-current.yaml
vendored
6
.github/workflows/check-current.yaml
vendored
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
.github/workflows/check-old.yaml
vendored
6
.github/workflows/check-old.yaml
vendored
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
.github/workflows/codecovr.yaml
vendored
6
.github/workflows/codecovr.yaml
vendored
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
.github/workflows/lintr.yaml
vendored
6
.github/workflows/lintr.yaml
vendored
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
.github/workflows/website.yaml
vendored
6
.github/workflows/website.yaml
vendored
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 1.8.2.9069
|
||||
Date: 2022-12-21
|
||||
Version: 1.8.2.9070
|
||||
Date: 2022-12-27
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
|
@ -191,6 +191,7 @@ export(ab_synonyms)
|
||||
export(ab_tradenames)
|
||||
export(ab_url)
|
||||
export(add_custom_antimicrobials)
|
||||
export(add_custom_microorganisms)
|
||||
export(administrable_iv)
|
||||
export(administrable_per_os)
|
||||
export(age)
|
||||
@ -238,6 +239,7 @@ export(cephalosporins_3rd)
|
||||
export(cephalosporins_4th)
|
||||
export(cephalosporins_5th)
|
||||
export(clear_custom_antimicrobials)
|
||||
export(clear_custom_microorganisms)
|
||||
export(count_I)
|
||||
export(count_IR)
|
||||
export(count_R)
|
||||
|
2
NEWS.md
2
NEWS.md
@ -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!)*
|
||||
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
@ -1375,6 +1375,13 @@ trimws2 <- function(..., whitespace = "[\u0009\u000A\u000B\u000C\u000D\u0020\u00
|
||||
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 ----
|
||||
|
||||
match <- function(x, table, ...) {
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/ab.R
6
R/ab.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
@ -31,22 +31,41 @@
|
||||
#'
|
||||
#' 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"
|
||||
#' @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
|
||||
#' # Open .Rprofile file
|
||||
#' utils::file.edit("~/.Rprofile")
|
||||
#' ```r
|
||||
#' # Add custom antibiotic drug codes:
|
||||
#' 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")`.
|
||||
#'
|
||||
#' # Add custom antibiotic drug codes:
|
||||
#' library(AMR)
|
||||
#' add_custom_antimicrobials(
|
||||
#' data.frame(ab = "TESTAB",
|
||||
#' name = "Test Antibiotic",
|
||||
#' group = "Test Group")
|
||||
#' )
|
||||
#' ```
|
||||
#' 2. Add a text like below and save the file:
|
||||
#'
|
||||
#' ```r
|
||||
#' # Add custom antibiotic drug codes:
|
||||
#' library(AMR)
|
||||
#' add_custom_antimicrobials(
|
||||
#' data.frame(ab = "TESTAB",
|
||||
#' name = "Test Antibiotic",
|
||||
#' group = "Test Group")
|
||||
#' )
|
||||
#' ```
|
||||
#'
|
||||
#' 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
|
||||
#' @export
|
||||
#' @examples
|
||||
@ -84,7 +103,7 @@
|
||||
#' ab = "COFLU",
|
||||
#' name = "Co-fluampicil",
|
||||
#' atc = "J01CR50",
|
||||
#' group = "Beta-lactams/penicillines"
|
||||
#' group = "Beta-lactams/penicillins"
|
||||
#' )
|
||||
#' )
|
||||
#' ab_atc("Co-fluampicil")
|
||||
@ -109,19 +128,21 @@ add_custom_antimicrobials <- function(x) {
|
||||
any(x$ab %in% AMR_env$AB_lookup$ab),
|
||||
"Antimicrobial drug code(s) ", vector_and(x$ab[x$ab %in% AMR_env$AB_lookup$ab]), " already exist in the internal `antibiotics` data set."
|
||||
)
|
||||
|
||||
# remove any extra class/type, such as grouped tbl, or data.table:
|
||||
x <- as.data.frame(x, stringsAsFactors = FALSE)
|
||||
# keep only columns available in the antibiotics data set
|
||||
x <- x[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %in% colnames(x)], drop = FALSE]
|
||||
x$generalised_name <- generalise_antibiotic_name(x$name)
|
||||
x$generalised_all <- as.list(x$generalised_name)
|
||||
if ("atc" %in% colnames(x)) {
|
||||
x$atc <- as.list(x$atc)
|
||||
}
|
||||
if ("loinc" %in% colnames(x)) {
|
||||
x$loinc <- as.list(x$loinc)
|
||||
for (col in colnames(x)) {
|
||||
if (is.list(AMR_env$AB_lookup[, col, drop = TRUE])) {
|
||||
x[, col] <- as.list(x[, col, drop = TRUE])
|
||||
}
|
||||
}
|
||||
|
||||
AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
|
||||
class(AMR_env$AB_lookup$ab) <- "character"
|
||||
|
||||
|
||||
new_df <- AMR_env$AB_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)
|
||||
@ -134,6 +155,7 @@ add_custom_antimicrobials <- function(x) {
|
||||
new_df[, col] <- x[, col, drop = TRUE]
|
||||
}
|
||||
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$ab) <- c("ab", "character")
|
||||
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.")
|
||||
}
|
||||
@ -141,7 +163,9 @@ add_custom_antimicrobials <- function(x) {
|
||||
#' @rdname add_custom_antimicrobials
|
||||
#' @export
|
||||
clear_custom_antimicrobials <- function() {
|
||||
n <- nrow(AMR_env$AB_lookup)
|
||||
AMR_env$AB_lookup <- create_AB_lookup()
|
||||
n2 <- nrow(AMR_env$AB_lookup)
|
||||
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
212
R/add_custom_microorganisms.R
Normal file
@ -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
6
R/age.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/amr.R
6
R/amr.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/av.R
6
R/av.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/data.R
6
R/data.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/disk.R
6
R/disk.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
@ -204,7 +204,7 @@ eucast_rules <- function(x,
|
||||
expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]]
|
||||
|
||||
# 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")
|
||||
}
|
||||
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/like.R
6
R/like.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/mdro.R
6
R/mdro.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/mic.R
6
R/mic.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
67
R/mo.R
67
R/mo.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
@ -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]])]
|
||||
}
|
||||
# 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$mo])
|
||||
# From full name ----
|
||||
out[is.na(out) & x_lower %in% AMR_env$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$fullname_lower)]
|
||||
# one exception: "Fungi" matches the kingdom, but instead it should return the 'unknown' code for fungi
|
||||
@ -210,7 +210,7 @@ as.mo <- function(x,
|
||||
# From SNOMED ----
|
||||
if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(microorganisms$snomed), na.rm = TRUE)) {
|
||||
# found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331
|
||||
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 ----
|
||||
# such as Salmonella groups, colloquial names, etc.
|
||||
@ -382,20 +382,20 @@ as.mo <- function(x,
|
||||
} # end of loop over all yet unknowns
|
||||
|
||||
# Keep or replace synonyms ----
|
||||
lpsn_matches <- AMR::microorganisms$lpsn_renamed_to[match(out, AMR::microorganisms$mo)]
|
||||
lpsn_matches[!lpsn_matches %in% AMR::microorganisms$lpsn] <- NA
|
||||
lpsn_matches <- AMR_env$MO_lookup$lpsn_renamed_to[match(out, AMR_env$MO_lookup$mo)]
|
||||
lpsn_matches[!lpsn_matches %in% AMR_env$MO_lookup$lpsn] <- NA
|
||||
# GBIF only for non-bacteria, since we use LPSN as primary source for bacteria
|
||||
# (an example is Strep anginosus, renamed according to GBIF, not according to LPSN)
|
||||
gbif_matches <- AMR::microorganisms$gbif_renamed_to[AMR::microorganisms$kingdom != "Bacteria"][match(out, AMR::microorganisms$mo[AMR::microorganisms$kingdom != "Bacteria"])]
|
||||
gbif_matches[!gbif_matches %in% AMR::microorganisms$gbif] <- NA
|
||||
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_env$MO_lookup$gbif] <- NA
|
||||
AMR_env$mo_renamed <- list(
|
||||
old = out[!is.na(gbif_matches) | !is.na(lpsn_matches)],
|
||||
gbif_matches = gbif_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)],
|
||||
lpsn_matches = lpsn_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)]
|
||||
)
|
||||
if (isFALSE(keep_synonyms)) {
|
||||
out[which(!is.na(gbif_matches))] <- AMR::microorganisms$mo[match(gbif_matches[which(!is.na(gbif_matches))], AMR::microorganisms$gbif)]
|
||||
out[which(!is.na(lpsn_matches))] <- AMR::microorganisms$mo[match(lpsn_matches[which(!is.na(lpsn_matches))], AMR::microorganisms$lpsn)]
|
||||
out[which(!is.na(gbif_matches))] <- AMR_env$MO_lookup$mo[match(gbif_matches[which(!is.na(gbif_matches))], AMR_env$MO_lookup$gbif)]
|
||||
out[which(!is.na(lpsn_matches))] <- AMR_env$MO_lookup$mo[match(lpsn_matches[which(!is.na(lpsn_matches))], AMR_env$MO_lookup$lpsn)]
|
||||
if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) {
|
||||
print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)")
|
||||
}
|
||||
@ -416,7 +416,7 @@ as.mo <- function(x,
|
||||
"Staphylococcus",
|
||||
c("caledonicus", "canis", "durrellii", "lloydii", "ratti", "roterodami", "singaporensis", "taiwanensis")
|
||||
)
|
||||
if (any(out %in% AMR::microorganisms$mo[match(post_Becker, AMR::microorganisms$fullname)])) {
|
||||
if (any(out %in% AMR_env$MO_lookup$mo[match(post_Becker, AMR_env$MO_lookup$fullname)])) {
|
||||
if (message_not_thrown_before("as.mo", "becker")) {
|
||||
warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
|
||||
vector_and(font_italic(gsub("Staphylococcus", "S.", post_Becker, fixed = TRUE), collapse = NULL), quotes = FALSE),
|
||||
@ -492,10 +492,10 @@ mo_renamed <- function() {
|
||||
x <- AMR_env$mo_renamed
|
||||
|
||||
x$new <- synonym_mo_to_accepted_mo(x$old)
|
||||
mo_old <- AMR::microorganisms$fullname[match(x$old, AMR::microorganisms$mo)]
|
||||
mo_new <- AMR::microorganisms$fullname[match(x$new, AMR::microorganisms$mo)]
|
||||
ref_old <- AMR::microorganisms$ref[match(x$old, AMR::microorganisms$mo)]
|
||||
ref_new <- AMR::microorganisms$ref[match(x$new, AMR::microorganisms$mo)]
|
||||
mo_old <- AMR_env$MO_lookup$fullname[match(x$old, AMR_env$MO_lookup$mo)]
|
||||
mo_new <- AMR_env$MO_lookup$fullname[match(x$new, AMR_env$MO_lookup$mo)]
|
||||
ref_old <- AMR_env$MO_lookup$ref[match(x$old, AMR_env$MO_lookup$mo)]
|
||||
ref_new <- AMR_env$MO_lookup$ref[match(x$new, AMR_env$MO_lookup$mo)]
|
||||
|
||||
df_renamed <- data.frame(
|
||||
old = mo_old,
|
||||
@ -553,6 +553,9 @@ pillar_shaft.mo <- function(x, ...) {
|
||||
# markup NA and UNKNOWN
|
||||
out[is.na(x)] <- font_na(" NA")
|
||||
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),
|
||||
error = function(e) NULL
|
||||
@ -563,7 +566,7 @@ pillar_shaft.mo <- function(x, ...) {
|
||||
mo_cols <- NULL
|
||||
}
|
||||
|
||||
all_mos <- c(AMR::microorganisms$mo, NA)
|
||||
all_mos <- c(AMR_env$MO_lookup$mo, NA)
|
||||
if (!all(x %in% all_mos) ||
|
||||
(!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% all_mos))) {
|
||||
# markup old mo codes
|
||||
@ -665,7 +668,7 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
|
||||
}
|
||||
x <- as.character(x)
|
||||
names(x) <- x_names
|
||||
if (!all(x %in% c(AMR::microorganisms$mo, NA))) {
|
||||
if (!all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
|
||||
warning_(
|
||||
"Some MO codes are from a previous AMR package version. ",
|
||||
"Please update the MO codes with `as.mo()`.",
|
||||
@ -698,7 +701,7 @@ summary.mo <- function(object, ...) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
as.data.frame.mo <- function(x, ...) {
|
||||
if (!all(x %in% c(AMR::microorganisms$mo, NA))) {
|
||||
if (!all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
|
||||
warning_(
|
||||
"The data contains old MO codes (from a previous AMR package version). ",
|
||||
"Please update your MO codes with `as.mo()`."
|
||||
@ -735,7 +738,7 @@ as.data.frame.mo <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
# must only contain valid MOs
|
||||
return_after_integrity_check(y, "microorganism code", as.character(AMR::microorganisms$mo))
|
||||
return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
|
||||
}
|
||||
#' @method [[<- mo
|
||||
#' @export
|
||||
@ -744,7 +747,7 @@ as.data.frame.mo <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(i)
|
||||
# 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$mo))
|
||||
}
|
||||
#' @method c mo
|
||||
#' @export
|
||||
@ -753,7 +756,7 @@ c.mo <- function(...) {
|
||||
x <- list(...)[[1L]]
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
return_after_integrity_check(y, "microorganism code", as.character(AMR::microorganisms$mo))
|
||||
return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
|
||||
}
|
||||
|
||||
#' @method unique mo
|
||||
@ -859,10 +862,10 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
# 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, "\""), ""),
|
||||
# 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(
|
||||
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, ]$mo), ")."), collapse = NULL)
|
||||
),
|
||||
""
|
||||
),
|
||||
@ -1030,7 +1033,7 @@ parse_and_convert <- function(x) {
|
||||
replace_old_mo_codes <- function(x, property) {
|
||||
# this function transform old MO codes to current codes, such as:
|
||||
# B_ESCH_COL (AMR v0.5.0) -> B_ESCHR_COLI
|
||||
ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !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)) {
|
||||
# get the ones that match
|
||||
affected <- x[ind]
|
||||
@ -1144,17 +1147,17 @@ load_mo_uncertainties <- function(metadata) {
|
||||
}
|
||||
|
||||
synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE) {
|
||||
x_gbif <- AMR::microorganisms$gbif_renamed_to[match(x, AMR::microorganisms$mo)]
|
||||
x_lpsn <- AMR::microorganisms$lpsn_renamed_to[match(x, AMR::microorganisms$mo)]
|
||||
x_gbif[!x_gbif %in% AMR::microorganisms$gbif] <- NA
|
||||
x_lpsn[!x_lpsn %in% AMR::microorganisms$lpsn] <- NA
|
||||
x_gbif <- AMR_env$MO_lookup$gbif_renamed_to[match(x, AMR_env$MO_lookup$mo)]
|
||||
x_lpsn <- AMR_env$MO_lookup$lpsn_renamed_to[match(x, AMR_env$MO_lookup$mo)]
|
||||
x_gbif[!x_gbif %in% AMR_env$MO_lookup$gbif] <- NA
|
||||
x_lpsn[!x_lpsn %in% AMR_env$MO_lookup$lpsn] <- NA
|
||||
|
||||
out <- ifelse(is.na(x_lpsn),
|
||||
AMR::microorganisms$mo[match(x_gbif, AMR::microorganisms$gbif)],
|
||||
AMR::microorganisms$mo[match(x_lpsn, AMR::microorganisms$lpsn)]
|
||||
AMR_env$MO_lookup$mo[match(x_gbif, AMR_env$MO_lookup$gbif)],
|
||||
AMR_env$MO_lookup$mo[match(x_lpsn, AMR_env$MO_lookup$lpsn)]
|
||||
)
|
||||
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
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
@ -676,9 +676,9 @@ mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
|
||||
metadata <- get_mo_uncertainties()
|
||||
|
||||
syns <- lapply(x.mo, function(y) {
|
||||
gbif <- AMR::microorganisms$gbif[match(y, AMR::microorganisms$mo)]
|
||||
lpsn <- AMR::microorganisms$lpsn[match(y, AMR::microorganisms$mo)]
|
||||
out <- AMR::microorganisms[which(AMR::microorganisms$lpsn_renamed_to == lpsn | AMR::microorganisms$gbif_renamed_to == gbif), "fullname", drop = TRUE]
|
||||
gbif <- AMR_env$MO_lookup$gbif[match(y, AMR_env$MO_lookup$mo)]
|
||||
lpsn <- AMR_env$MO_lookup$lpsn[match(y, AMR_env$MO_lookup$mo)]
|
||||
out <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$lpsn_renamed_to == lpsn | AMR_env$MO_lookup$gbif_renamed_to == gbif), "fullname", drop = TRUE]
|
||||
if (length(out) == 0) {
|
||||
NULL
|
||||
} else {
|
||||
@ -760,10 +760,10 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
|
||||
x.mo <- as.mo(x = x, language = language, keep_synonyms = keep_synonyms, ... = ...)
|
||||
metadata <- get_mo_uncertainties()
|
||||
|
||||
x.rank <- AMR::microorganisms$rank[match(x.mo, AMR::microorganisms$mo)]
|
||||
x.name <- AMR::microorganisms$fullname[match(x.mo, AMR::microorganisms$mo)]
|
||||
x.lpsn <- AMR::microorganisms$lpsn[match(x.mo, AMR::microorganisms$mo)]
|
||||
x.gbif <- AMR::microorganisms$gbif[match(x.mo, AMR::microorganisms$mo)]
|
||||
x.rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)]
|
||||
x.name <- AMR_env$MO_lookup$fullname[match(x.mo, AMR_env$MO_lookup$mo)]
|
||||
x.lpsn <- AMR_env$MO_lookup$lpsn[match(x.mo, AMR_env$MO_lookup$mo)]
|
||||
x.gbif <- AMR_env$MO_lookup$gbif[match(x.mo, AMR_env$MO_lookup$mo)]
|
||||
|
||||
u <- character(length(x))
|
||||
u[!is.na(x.gbif)] <- paste0(TAXONOMY_VERSION$GBIF$url, "/species/", x.gbif[!is.na(x.gbif)])
|
||||
@ -792,7 +792,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), k
|
||||
x <- find_mo_col(fn = "mo_property")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR::microorganisms))
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR_env$MO_lookup))
|
||||
language <- validate_language(language)
|
||||
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
|
||||
# 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)
|
||||
)
|
||||
|
||||
@ -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")
|
||||
|
||||
# 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$mo, NA)) && !has_Becker_or_Lancefield) {
|
||||
# do nothing, just don't run the other if-else's
|
||||
@ -833,7 +833,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
|
||||
}
|
||||
|
||||
# get property reeaaally fast using match()
|
||||
x <- AMR::microorganisms[[property]][match(x, AMR::microorganisms$mo)]
|
||||
x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
|
||||
|
||||
if (property == "mo") {
|
||||
return(set_clean_class(x, new_class = c("mo", "character")))
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# Developed at the University of Groningen and the University Medical #
|
||||
# Center Groningen in The Netherlands, in collaboration with many #
|
||||
# colleagues from around the world, see our website. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
@ -149,7 +149,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
|
||||
df <- NULL
|
||||
if (path %like% "[.]rds$") {
|
||||
df <- readRDS(path)
|
||||
df <- readRDS2(path)
|
||||
} else if (path %like% "[.]xlsx?$") {
|
||||
# is Excel file (old or new)
|
||||
stop_ifnot_installed("readxl")
|
||||
@ -248,7 +248,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
|
||||
return(NULL)
|
||||
}
|
||||
if (is.null(AMR_env$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
|
||||
|
6
R/pca.R
6
R/pca.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/plot.R
6
R/plot.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
6
R/rsi.R
6
R/rsi.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
@ -91,7 +91,7 @@
|
||||
#' ab_name("amox/clav")
|
||||
get_AMR_locale <- function() {
|
||||
# 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 = ...)`"))
|
||||
}
|
||||
lang <- ""
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
@ -95,7 +95,7 @@ vec_cast.character.mo <- function(x, to, ...) {
|
||||
as.character(x)
|
||||
}
|
||||
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$mo))
|
||||
}
|
||||
|
||||
# S3: disk
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# Developed at the University of Groningen and the University Medical #
|
||||
# Center Groningen in The Netherlands, in collaboration with many #
|
||||
# colleagues from around the world, see our website. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
|
31
R/zzz.R
31
R/zzz.R
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# Developed at the University of Groningen and the University Medical #
|
||||
# Center Groningen in The Netherlands, in collaboration with many #
|
||||
# colleagues from around the world, see our website. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
@ -72,6 +72,7 @@ AMR_env$rsi_interpretation_history <- data.frame(
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
AMR_env$custom_ab_codes <- character(0)
|
||||
AMR_env$custom_mo_codes <- character(0)
|
||||
AMR_env$is_dark_theme <- NULL
|
||||
|
||||
# determine info icon for messages
|
||||
@ -171,12 +172,11 @@ if (utf8_supported && !is_latex) {
|
||||
|
||||
# if mo source exists, fire it up (see mo_source())
|
||||
if (tryCatch(file.exists(getOption("AMR_mo_source", "~/mo_source.rds")), error = function(e) FALSE)) {
|
||||
invisible(get_mo_source())
|
||||
try(invisible(get_mo_source()), silent = TRUE)
|
||||
}
|
||||
|
||||
# be sure to print tibbles as tibbles
|
||||
if (pkg_is_available("tibble", also_load = FALSE)) {
|
||||
loadNamespace("tibble")
|
||||
try(loadNamespace("tibble"), silent = TRUE)
|
||||
}
|
||||
|
||||
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
||||
@ -184,6 +184,25 @@ if (utf8_supported && !is_latex) {
|
||||
AMR_env$AB_lookup <- create_AB_lookup()
|
||||
AMR_env$AV_lookup <- create_AV_lookup()
|
||||
AMR_env$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 --------------------------------------------------------
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
43
inst/tinytest/test-add_custom_microorganisms.R
Normal file
43
inst/tinytest/test-add_custom_microorganisms.R
Normal file
@ -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")
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
@ -11,9 +11,9 @@
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# 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 #
|
||||
|
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue
Block a user