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(v3.0.0.9003) eucast_rules fix, new tidymodels integration

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-06-13 14:03:21 +02:00
parent 3742e9e994
commit 72db2b2562
22 changed files with 760 additions and 107 deletions
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31
R/eucast_rules.R
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@ -442,7 +442,7 @@ eucast_rules <- function(x,
# big speed gain! only analyse unique rows:
pm_distinct(`.rowid`, .keep_all = TRUE) %pm>%
as.data.frame(stringsAsFactors = FALSE)
x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]), info = info)
x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]), info = FALSE)
# rename col_mo to prevent interference with joined columns
colnames(x)[colnames(x) == col_mo] <- ".col_mo"
col_mo <- ".col_mo"
@ -450,8 +450,8 @@ eucast_rules <- function(x,
x <- left_join_microorganisms(x, by = col_mo, suffix = c("_oldcols", ""))
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL, info = FALSE)
x$genus_species <- trimws(paste(x$genus, x$species))
if (isTRUE(info) && NROW(x) > 10000) {
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
if (isTRUE(info) && NROW(x.bak) > 10000) {
message_("OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
}
n_added <- 0
@ -624,31 +624,16 @@ eucast_rules <- function(x,
eucast_rules_df <- eucast_rules_df %pm>%
rbind_AMR(eucast_rules_df_total %pm>%
subset(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
# eucast_rules_df <- subset(
# eucast_rules_df,
# reference.rule_group %unlike% "breakpoint" |
# (reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)
# )
}
if (any(c("all", "expected_phenotypes") %in% rules)) {
eucast_rules_df <- eucast_rules_df %pm>%
rbind_AMR(eucast_rules_df_total %pm>%
subset(reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes))
# eucast_rules_df <- subset(
# eucast_rules_df,
# reference.rule_group %unlike% "expected" |
# (reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes)
# )
}
if (any(c("all", "expert") %in% rules)) {
eucast_rules_df <- eucast_rules_df %pm>%
rbind_AMR(eucast_rules_df_total %pm>%
subset(reference.rule_group %like% "expert" & reference.version == version_expertrules))
# eucast_rules_df <- subset(
# eucast_rules_df,
# reference.rule_group %unlike% "expert" |
# (reference.rule_group %like% "expert" & reference.version == version_expertrules)
# )
}
## filter out AmpC de-repressed cephalosporin-resistant mutants ----
# no need to filter on version number here - the rules contain these version number, so are inherently filtered
@ -671,6 +656,9 @@ eucast_rules <- function(x,
# we only hints on remaining rows in `eucast_rules_df`
screening_abx <- as.character(AMR::antimicrobials$ab[which(AMR::antimicrobials$ab %like% "-S$")])
screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(EUCAST_RULES_DF$and_these_antibiotics[!is.na(EUCAST_RULES_DF$and_these_antibiotics)], ", *")))]
if (isTRUE(info)) {
cat("\n")
}
for (ab_s in screening_abx) {
ab <- gsub("-S$", "", ab_s)
if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
@ -901,7 +889,9 @@ eucast_rules <- function(x,
}
for (i in seq_len(length(custom_rules))) {
rule <- custom_rules[[i]]
rows <- which(eval(parse(text = rule$query), envir = x))
rows <- tryCatch(which(eval(parse(text = rule$query), envir = x)),
error = function(e) stop_(paste0(conditionMessage(e), font_red(" (check available data and compare with the custom rules set)")), call = FALSE)
)
cols <- as.character(rule$result_group)
cols <- c(
cols[cols %in% colnames(x)], # direct column names
@ -915,9 +905,8 @@ eucast_rules <- function(x,
get_antibiotic_names(cols)
)
if (isTRUE(info)) {
# print rule
cat(italicise_taxonomy(
word_wrap(format_custom_query_rule(rule$query, colours = FALSE),
word_wrap(rule_text,
width = getOption("width") - 30,
extra_indent = 6
),