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support new mo codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-12-27 15:16:15 +01:00
parent e493248ea5
commit f619fb683b
127 changed files with 859 additions and 443 deletions
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31
R/zzz.R
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@ -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 --------------------------------------------------------