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dr. M.S. (Matthijs) Berends 2023-01-19 12:54:53 +01:00
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Package: AMR
Version: 1.8.2.9093
Date: 2023-01-14
Version: 1.8.2.9094
Date: 2023-01-19
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

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# AMR 1.8.2.9093
# AMR 1.8.2.9094
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

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#'
#' 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:
#' **Method 1:** Using the [option `AMR_custom_mo`][AMR-options], which is the preferred method. To use this method:
#'
#' 1. Create a data set in the structure of the [microorganisms] data set (containing at the very least column "genus") 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:
#' 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 be 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:
@ -50,7 +50,7 @@
#'
#' 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:
#' **Method 2:** Loading the microorganism directly from your `.Rprofile` file. An important downside is that this requires the `AMR` package to be installed or else this method will fail. To use this method:
#'
#' 1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`.
#'
@ -58,8 +58,7 @@
#'
#' ```r
#' # Add custom antibiotic drug codes:
#' library(AMR)
#' add_custom_microorganisms(
#' AMR::add_custom_microorganisms(
#' data.frame(genus = "Enterobacter",
#' species = "asburiae/cloacae")
#' )
@ -71,7 +70,6 @@
#' @export
#' @examples
#' \donttest{
#'
#' # a combination of species is not formal taxonomy, so
#' # this will result in only "Enterobacter asburiae":
#' mo_name("Enterobacter asburiae/cloacae")
@ -102,13 +100,15 @@
#'
#' # the function tries to be forgiving:
#' add_custom_microorganisms(
#' data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
#' data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
#' SPECIES = "SPECIES")
#' )
#' mo_name("ESCHERICHIA / KLEBSIELLA")
#' mo_rank("ESCHERICHIA / KLEBSIELLA")
#' mo_name("BACTEROIDES / PARABACTEROIDES")
#' mo_rank("BACTEROIDES / PARABACTEROIDES")
#'
#' # taxonomy still works, although a slashline genus was given as input:
#' mo_family("Escherichia/Klebsiella")
#' mo_family("Bacteroides/Parabacteroides")
#'
#'
#' # for groups and complexes, set them as species or subspecies:
#' add_custom_microorganisms(
@ -208,8 +208,10 @@ add_custom_microorganisms <- function(x) {
x$family[which(x$family == "" & genus_to_check != "")] <- AMR_env$MO_lookup$family[match(genus_to_check[which(x$family == "" & genus_to_check != "")], AMR_env$MO_lookup$genus)]
# fill in other columns that are used in internal algorithms
x$prevalence <- NA_real_
x$prevalence[which(genus_to_check != "")] <- AMR_env$MO_lookup$prevalence[match(genus_to_check[which(genus_to_check != "")], AMR_env$MO_lookup$genus)]
x$prevalence[is.na(x$prevalence)] <- 1.25
x$status <- "accepted"
x$prevalence <- 1
x$ref <- paste("Self-added,", format(Sys.Date(), "%Y"))
x$kingdom_index <- AMR_env$MO_lookup$kingdom_index[match(genus_to_check, AMR_env$MO_lookup$genus)]
# complete missing kingdom index, so mo_matching_score() will not return NA

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@ -777,7 +777,7 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
info <- lapply(x, function(y) {
c(
list(identifier = x),
list(mo = as.character(x)),
mo_taxonomy(y, language = language, keep_synonyms = keep_synonyms),
list(
status = mo_status(y, language = language, keep_synonyms = keep_synonyms),
@ -894,6 +894,8 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
return(set_clean_class(x, new_class = c("mo", "character")))
} else if (property == "snomed") {
return(sort(as.character(eval(parse(text = x)))))
} else if (property == "prevalence") {
return(as.double(x))
} else {
# everything else as character
return(as.character(x))

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# ==================================================================== #
# 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/ #
# ==================================================================== #
#' Options for the AMR package
#'
#' This is an overview of the package-specific [options()] you can set in the `AMR` package.
#' @section Options:
#' * `AMR_custom_ab`: allows to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
#' * `AMR_custom_mo`: allows to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
#' @keywords internal
#' @name AMR-options
# @export
NULL

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/options.R
\name{AMR-options}
\alias{AMR-options}
\title{Options for the AMR package}
\description{
This is an overview of the package-specific \code{\link[=options]{options()}} you can set in the \code{AMR} package.
}
\section{Options}{
\itemize{
\item \code{AMR_custom_ab}: allows to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
\item \code{AMR_custom_mo}: allows to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
}
}
\keyword{internal}

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@ -22,10 +22,10 @@ This function will fill in missing taxonomy for you, if specific taxonomic colum
There are two ways to automate this process:
\strong{Method 1:} Save the microorganisms to a local or remote file (can even be the internet). To use this method:
\strong{Method 1:} Using the , which is the preferred method. To use this method:
\enumerate{
\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least column "genus") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
\item Set the file location to the \code{AMR_custom_mo} \R option: \code{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 \code{.Rprofile} file so that it will loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
\item Set the file location to the \code{AMR_custom_mo} \R option: \code{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 \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
options(AMR_custom_mo = "~/my_custom_mo.rds")
@ -34,14 +34,13 @@ options(AMR_custom_mo = "~/my_custom_mo.rds")
Upon package load, this file will be loaded and run through the \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} function.
}
\strong{Method 2:} Save the microorganism directly to your \code{.Rprofile} file. An important downside is that this requires to load the \code{AMR} package at every start-up. To use this method:
\strong{Method 2:} Loading the microorganism directly from your \code{.Rprofile} file. An important downside is that this requires the \code{AMR} package to be installed or else this method will fail. To use this method:
\enumerate{
\item Edit the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}.
\item Add a text like below and save the file:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
library(AMR)
add_custom_microorganisms(
AMR::add_custom_microorganisms(
data.frame(genus = "Enterobacter",
species = "asburiae/cloacae")
)
@ -52,7 +51,6 @@ Use \code{\link[=clear_custom_microorganisms]{clear_custom_microorganisms()}} to
}
\examples{
\donttest{
# a combination of species is not formal taxonomy, so
# this will result in only "Enterobacter asburiae":
mo_name("Enterobacter asburiae/cloacae")
@ -83,13 +81,15 @@ mo_info("Enterobacter asburiae/cloacae")
# the function tries to be forgiving:
add_custom_microorganisms(
data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
SPECIES = "SPECIES")
)
mo_name("ESCHERICHIA / KLEBSIELLA")
mo_rank("ESCHERICHIA / KLEBSIELLA")
mo_name("BACTEROIDES / PARABACTEROIDES")
mo_rank("BACTEROIDES / PARABACTEROIDES")
# taxonomy still works, although a slashline genus was given as input:
mo_family("Escherichia/Klebsiella")
mo_family("Bacteroides/Parabacteroides")
# for groups and complexes, set them as species or subspecies:
add_custom_microorganisms(

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