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(v2.1.1.9182) fix AMR selectors for tidymodels, add unit tests

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dr. M.S. (Matthijs) Berends
2025-03-03 12:59:27 +01:00
parent b85890449d
commit 9a9468fa84
16 changed files with 84 additions and 33 deletions
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19
R/aa_helper_functions.R
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@ -989,6 +989,8 @@ ascertain_sir_classes <- function(x, obj_name) {
}
get_current_data <- function(arg_name, call) {
# This function enables AMR selectors (e.g., AMR::carbapenems()) to work seamlessly across different environments, including dplyr, base R, data.table, and tidymodels.
# It identifies and extracts the appropriate data frame from the current execution context.
valid_df <- function(x) {
!is.null(x) && is.data.frame(x)
}
@ -1014,14 +1016,17 @@ get_current_data <- function(arg_name, call) {
}
}
# now go over all underlying environments looking for other dplyr, data.table and base R selection environments
# now go over all underlying environments looking for other dplyr, tidymodels, data.table and base R selection environments
with_generic <- vapply(FUN.VALUE = logical(1), frms, function(e) !is.null(e$`.Generic`))
for (env in frms[which(with_generic)]) {
if (valid_df(env$`.data`)) {
# an element `.data` will be in the environment when using dplyr::select()
return(env$`.data`)
} else if (valid_df(env$training)) {
# an element `training` will be in the environment when using some tidymodels functions such as `prep()`
return(env$training)
} else if (valid_df(env$data)) {
# an element `data` will be in the environment when using older dplyr versions, or tidymodels
# an element `data` will be in the environment when using older dplyr versions, or some tidymodels functions such as `fit()`
return(env$data)
} else if (valid_df(env$xx)) {
# an element `xx` will be in the environment for rows + cols in base R, e.g. `example_isolates[c(1:3), carbapenems()]`
@ -1038,7 +1043,7 @@ get_current_data <- function(arg_name, call) {
for (env in frms[which(with_tbl)]) {
if (!is.null(names(env)) && all(c(".tbl", ".vars", ".cols") %in% names(env), na.rm = TRUE)) {
# an element `.tbl` will be in the environment when using scoped dplyr variants, with or without `dplyr::vars()`
# (e.g. `dplyr::summarise_at()` or `dplyr::mutate_at()`)
# e.g. `dplyr::summarise_at(carbapenems(), ...)` or `dplyr::mutate_at(vars(carbapenems()), ...)`
return(env$`.tbl`)
}
}
@ -1206,7 +1211,13 @@ try_colour <- function(..., before, after, collapse = " ") {
}
}
is_dark <- function() {
if (is.null(AMR_env$is_dark_theme)) {
if (is.null(AMR_env$is_dark_theme) ||
is.null(AMR_env$current_theme) ||
(
!is.null(AMR_env$current_theme) &&
AMR_env$current_theme != tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) "")
)) {
AMR_env$current_theme <- tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) NULL)
AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
}
isTRUE(AMR_env$is_dark_theme)

2
R/disk.R
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@ -121,7 +121,7 @@ as.disk <- function(x, na.rm = FALSE) {
cur_col <- get_current_column()
warning_("in `as.disk()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ",

2
R/mic.R
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@ -250,7 +250,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
cur_col <- get_current_column()
warning_("in `as.mic()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid MICs: ",

2
R/sir.R
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@ -539,7 +539,7 @@ as.sir.default <- function(x,
cur_col <- get_current_column()
warning_("in `as.sir()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid antimicrobial interpretations: ",