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(v0.9.0.9023) EUCAST 2020 guidelines

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dr. M.S. (Matthijs) Berends
2020-02-14 19:54:13 +01:00
parent 5a98e6b777
commit 9b8b02960e
43 changed files with 16588 additions and 14564 deletions
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4
R/guess_ab_col.R
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@ -126,7 +126,7 @@ get_column_abx <- function(x,
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
# or already have the rsi class (as.rsi)
# and that have no more than 50% invalid values
vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[, c("ab", "atc", "name", "abbreviations", "synonyms")])))
vectr_antibiotics <- unique(toupper(unlist(antibiotics[, c("ab", "atc", "name", "abbreviations", "synonyms")])))
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
x_columns <- sapply(colnames(x), function(col, df = x_bak) {
if (toupper(col) %in% vectr_antibiotics |
@ -205,7 +205,7 @@ get_column_abx <- function(x,
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(x)]
missing_txt <- data.frame(missing = missing,
missing_names = AMR::ab_name(missing, tolower = TRUE),
missing_names = ab_name(missing, tolower = TRUE),
stringsAsFactors = FALSE) %>%
mutate(txt = paste0(bold(missing), " (", missing_names, ")")) %>%
arrange(missing_names) %>%