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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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10
R/custom_microorganisms.R
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@ -37,7 +37,7 @@
#'
#' There are two ways to automate this process:
#'
#' **Method 1:** Using the [option `AMR_custom_mo`][AMR-options], which is the preferred method. 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.
#'
@ -124,6 +124,8 @@ add_custom_microorganisms <- function(x) {
meet_criteria(x, allow_class = "data.frame")
stop_ifnot("genus" %in% tolower(colnames(x)), paste0("`x` must contain column 'genus'."))
add_MO_lookup_to_AMR_env()
# remove any extra class/type, such as grouped tbl, or data.table:
x <- as.data.frame(x, stringsAsFactors = FALSE)
colnames(x) <- tolower(colnames(x))
@ -269,7 +271,11 @@ add_custom_microorganisms <- function(x) {
#' @export
clear_custom_microorganisms <- function() {
n <- nrow(AMR_env$MO_lookup)
AMR_env$MO_lookup <- create_MO_lookup()
# reset
AMR_env$MO_lookup <- NULL
add_MO_lookup_to_AMR_env()
n2 <- nrow(AMR_env$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]