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(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group

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dr. M.S. (Matthijs) Berends
2026-03-09 11:57:36 +01:00
parent cba315c2e7
commit 353eaa3f38
21 changed files with 61 additions and 13 deletions
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16
data-raw/_pre_commit_checks.R
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@@ -369,6 +369,9 @@ pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>%
pull(ab)
pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC"))
pre_commit_lst$AB_AMINOCOUMARINS <- antimicrobials %>%
filter(name %like% "novobiocin|clorobiocin") %>%
pull(ab)
pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>%
filter(group %like% "antifungal") %>%
pull(ab)
@@ -486,6 +489,18 @@ pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%
# this will be used for documentation:
pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
# Check that all AB_* groups with >= 4 members have a corresponding function
for (grp in pre_commit_lst$DEFINED_AB_GROUPS[pre_commit_lst$DEFINED_AB_GROUPS %unlike% "BETALACTAMASE_INHIBITORS|EXCEPT"]) {
if (length(pre_commit_lst[[grp]]) >= 4) {
fn_name <- tolower(gsub("^AB_", "", grp))
if (!fn_name %in% ls(envir = asNamespace("AMR"))) {
stop("Group '", grp, "' has ", length(pre_commit_lst[[grp]]),
" members (", toString(ab_name(pre_commit_lst[[grp]], tolower = T)), ") but no corresponding function '", fn_name, "()' exists in the AMR namespace.",
call. = FALSE)
}
}
}
# Update the antimicrobials$group column
usethis::ui_info("Updating 'group' column in antimicrobials data set from AB_* vectors")
prettify_group_name <- function(name) {
@@ -557,6 +572,7 @@ pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins",
"Beta-lactams",
"Beta-lactamase inhibitors",
"Pleuromutilins",
"Aminocoumarins",
"Other")
if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) {
stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", "))