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AMR/R/zzz.R

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R
Executable File

# ==================================================================== #
# 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/ #
# ==================================================================== #
# set up package environment, used by numerous AMR functions
AMR_env <- new.env(hash = FALSE)
AMR_env$mo_uncertainties <- data.frame(
original_input = character(0),
input = character(0),
fullname = character(0),
mo = character(0),
candidates = character(0),
minimum_matching_score = integer(0),
keep_synonyms = logical(0),
stringsAsFactors = FALSE
)
AMR_env$mo_renamed <- list()
AMR_env$mo_previously_coerced <- data.frame(
x = character(0),
mo = character(0),
stringsAsFactors = FALSE
)
AMR_env$ab_previously_coerced <- data.frame(
x = character(0),
ab = character(0),
stringsAsFactors = FALSE
)
AMR_env$av_previously_coerced <- data.frame(
x = character(0),
av = character(0),
stringsAsFactors = FALSE
)
AMR_env$rsi_interpretation_history <- data.frame(
datetime = Sys.time()[0],
index = integer(0),
ab_input = character(0),
ab_considered = character(0),
mo_input = character(0),
mo_considered = character(0),
guideline = character(0),
ref_table = character(0),
method = character(0),
breakpoint_S = double(0),
breakpoint_R = double(0),
input = double(0),
interpretation = character(0),
stringsAsFactors = FALSE
)
AMR_env$custom_ab_codes <- character(0)
AMR_env$custom_mo_codes <- character(0)
AMR_env$is_dark_theme <- NULL
# determine info icon for messages
utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
is_latex <- tryCatch(import_fn("is_latex_output", "knitr", error_on_fail = FALSE)(),
error = function(e) FALSE
)
if (utf8_supported && !is_latex) {
# \u2139 is a symbol officially named 'information source'
AMR_env$info_icon <- "\u2139"
AMR_env$bullet_icon <- "\u2022"
} else {
AMR_env$info_icon <- "i"
AMR_env$bullet_icon <- "*"
}
.onLoad <- function(lib, pkg) {
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
# without the need to depend on other packages. This was suggested by the
# developers of the vctrs package:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register("pillar::pillar_shaft", "ab")
s3_register("pillar::pillar_shaft", "av")
s3_register("pillar::pillar_shaft", "mo")
s3_register("pillar::pillar_shaft", "rsi")
s3_register("pillar::pillar_shaft", "mic")
s3_register("pillar::pillar_shaft", "disk")
s3_register("pillar::type_sum", "ab")
s3_register("pillar::type_sum", "av")
s3_register("pillar::type_sum", "mo")
s3_register("pillar::type_sum", "rsi")
s3_register("pillar::type_sum", "mic")
s3_register("pillar::type_sum", "disk")
# Support for frequency tables from the cleaner package
s3_register("cleaner::freq", "mo")
s3_register("cleaner::freq", "rsi")
# Support for skim() from the skimr package
if (pkg_is_available("skimr", also_load = FALSE, min_version = "2.0.0")) {
s3_register("skimr::get_skimmers", "mo")
s3_register("skimr::get_skimmers", "rsi")
s3_register("skimr::get_skimmers", "mic")
s3_register("skimr::get_skimmers", "disk")
}
# Support for autoplot() from the ggplot2 package
s3_register("ggplot2::autoplot", "rsi")
s3_register("ggplot2::autoplot", "mic")
s3_register("ggplot2::autoplot", "disk")
s3_register("ggplot2::autoplot", "resistance_predict")
# Support for fortify from the ggplot2 package
s3_register("ggplot2::fortify", "rsi")
s3_register("ggplot2::fortify", "mic")
s3_register("ggplot2::fortify", "disk")
# Support vctrs package for use in e.g. dplyr verbs
# S3: ab_selector
s3_register("vctrs::vec_ptype2", "character.ab_selector")
s3_register("vctrs::vec_ptype2", "ab_selector.character")
s3_register("vctrs::vec_cast", "character.ab_selector")
# S3: ab_selector_any_all
s3_register("vctrs::vec_ptype2", "logical.ab_selector_any_all")
s3_register("vctrs::vec_ptype2", "ab_selector_any_all.logical")
s3_register("vctrs::vec_cast", "logical.ab_selector_any_all")
# S3: ab
s3_register("vctrs::vec_ptype2", "character.ab")
s3_register("vctrs::vec_ptype2", "ab.character")
s3_register("vctrs::vec_cast", "character.ab")
s3_register("vctrs::vec_cast", "ab.character")
# S3: av
s3_register("vctrs::vec_ptype2", "character.av")
s3_register("vctrs::vec_ptype2", "av.character")
s3_register("vctrs::vec_cast", "character.av")
s3_register("vctrs::vec_cast", "av.character")
# S3: mo
s3_register("vctrs::vec_ptype2", "character.mo")
s3_register("vctrs::vec_ptype2", "mo.character")
s3_register("vctrs::vec_cast", "character.mo")
s3_register("vctrs::vec_cast", "mo.character")
# S3: disk
s3_register("vctrs::vec_ptype2", "integer.disk")
s3_register("vctrs::vec_ptype2", "disk.integer")
s3_register("vctrs::vec_cast", "integer.disk")
s3_register("vctrs::vec_cast", "disk.integer")
s3_register("vctrs::vec_cast", "double.disk")
s3_register("vctrs::vec_cast", "disk.double")
s3_register("vctrs::vec_cast", "character.disk")
s3_register("vctrs::vec_cast", "disk.character")
# S3: mic
s3_register("vctrs::vec_cast", "character.mic")
s3_register("vctrs::vec_cast", "double.mic")
s3_register("vctrs::vec_cast", "mic.character")
s3_register("vctrs::vec_cast", "mic.double")
s3_register("vctrs::vec_math", "mic")
# S3: rsi
s3_register("vctrs::vec_ptype2", "character.rsi")
s3_register("vctrs::vec_ptype2", "rsi.character")
s3_register("vctrs::vec_cast", "character.rsi")
s3_register("vctrs::vec_cast", "rsi.character")
# 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)) {
try(invisible(get_mo_source()), silent = TRUE)
}
# be sure to print tibbles as tibbles
if (pkg_is_available("tibble", also_load = FALSE)) {
try(loadNamespace("tibble"), silent = TRUE)
}
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
AMR_env$AB_lookup <- create_AB_lookup()
AMR_env$AV_lookup <- create_AV_lookup()
AMR_env$MO_lookup <- create_MO_lookup()
}
.onAttach <- function(lib, pkg) {
# if custom ab option is available, load it
if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
packageStartupMessage("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'...", appendLF = FALSE)
x <- readRDS2(getOption("AMR_custom_ab"))
tryCatch({
suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
packageStartupMessage("OK.")
}, error = function(e) packageStartupMessage("Failed: ", e$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$message))
}
}
# Helper functions --------------------------------------------------------
create_AB_lookup <- function() {
cbind(AMR::antibiotics, AB_LOOKUP)
}
create_AV_lookup <- function() {
cbind(AMR::antivirals, AV_LOOKUP)
}
create_MO_lookup <- function() {
MO_lookup <- AMR::microorganisms
MO_lookup$kingdom_index <- NA_real_
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
# all the rest
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
if (length(MO_FULLNAME_LOWER) != nrow(MO_lookup)) {
packageStartupMessage("fullname_lower not same size - applied tolower(), update sysdata.rda!")
MO_lookup$fullname_lower <- tolower(MO_lookup$fullname)
} else {
MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
}
MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
MO_lookup$species_first <- tolower(substr(MO_lookup$species, 1, 1)) # tolower for groups (Streptococcus, Salmonella)
MO_lookup$subspecies_first <- tolower(substr(MO_lookup$subspecies, 1, 1)) # tolower for Salmonella serovars
MO_lookup
}
add_intrinsic_resistance_to_AMR_env <- function() {
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
if (is.null(AMR_env$intrinsic_resistant)) {
AMR_env$intrinsic_resistant <- paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab)
}
}