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(v2.1.1.9142) unit test fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-07 19:03:02 +01:00
parent 8ba2e4ed94
commit cc2bb151ab
11 changed files with 21 additions and 23 deletions
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29
R/eucast_rules.R
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@ -460,16 +460,14 @@ eucast_rules <- function(x,
# >>> Apply Other rules: enzyme inhibitors <<< ------------------------------------------
if (any(c("all", "other") %in% rules)) {
if (isTRUE(info)) {
cat("\n")
cat(paste0("\n", font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
cat(word_wrap(
font_bold(paste0(
"Rules by this AMR package (",
font_red(paste0(
"v", utils::packageDescription("AMR")$Version, ", ",
format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y")
)), "), see `?eucast_rules`\n"
))
paste0("Rules by the ",
font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
" (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
"), see `?eucast_rules`\n")
))
cat("\n\n")
}
ab_enzyme <- subset(AMR::antibiotics, name %like% "/")[, c("ab", "name"), drop = FALSE]
colnames(ab_enzyme) <- c("enzyme_ab", "enzyme_name")
@ -495,8 +493,8 @@ eucast_rules <- function(x,
## Set base to R where base + enzyme inhibitor is R ----
rule_current <- paste0(
ab_enzyme$base_name[i], " ('", font_bold(col_base), "') = R if ",
tolower(ab_enzyme$enzyme_name[i]), " ('", font_bold(col_enzyme), "') = R"
ab_enzyme$base_name[i], " (`", col_base, "`) = R if ",
tolower(ab_enzyme$enzyme_name[i]), " (`", col_enzyme, "`) = R"
)
if (isTRUE(info)) {
cat(word_wrap(rule_current,
@ -536,8 +534,8 @@ eucast_rules <- function(x,
## Set base + enzyme inhibitor to S where base is S ----
rule_current <- paste0(
ab_enzyme$enzyme_name[i], " ('", font_bold(col_enzyme), "') = S if ",
tolower(ab_enzyme$base_name[i]), " ('", font_bold(col_base), "') = S"
ab_enzyme$enzyme_name[i], " (`", col_enzyme, "`) = S if ",
tolower(ab_enzyme$base_name[i]), " (`", col_base, "`) = S"
)
if (isTRUE(info)) {
@ -559,7 +557,8 @@ eucast_rules <- function(x,
original_data = x.bak,
warned = warned,
info = info,
verbose = verbose
verbose = verbose,
overwrite = overwrite
)
n_added <- n_added + run_changes$added
n_changed <- n_changed + run_changes$changed
@ -1037,9 +1036,9 @@ eucast_rules <- function(x,
cat(paste0(font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
if (isFALSE(verbose) && total_n_added + total_n_changed > 0) {
cat("\n", word_wrap("Use ", font_bold("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
cat("\n", word_wrap("Use `eucast_rules(..., verbose = TRUE)` (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
} else if (isTRUE(verbose)) {
cat("\n", word_wrap("Used 'Verbose mode' (", font_bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", font_bold("verbose = FALSE"), " to apply the rules on your data."), "\n\n", sep = "")
cat("\n", word_wrap("Used 'Verbose mode' (`verbose = TRUE`), which returns a data.frame with all specified edits.\nUse `verbose = FALSE` to apply the rules on your data."), "\n\n", sep = "")
}
}