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revised as.rsi(), fix for mdro()

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dr. M.S. (Matthijs) Berends
2022-11-24 20:29:00 +01:00
parent 05d536ebb7
commit 31fb81c382
10 changed files with 450 additions and 453 deletions
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6
R/mo.R
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@ -181,8 +181,9 @@ as.mo <- function(x,
x_lower <- tolower(x)
if (any(trimws2(x_lower) %like_case% "complex$", na.rm = TRUE)) {
warning_("in `as.mo()`: translation of complexes is not supported at the moment - the input text 'complex' was ignored.", call = FALSE)
complexes <- x[trimws2(x_lower) %like_case% "complex$"]
if (length(complexes) > 0) {
warning_("in `as.mo()`: translation of complexes is not supported at the moment - the input text 'complex' was ignored in ", length(complexes), " cases.", call = FALSE)
}
# WHONET: xxx = no growth
@ -935,6 +936,7 @@ convert_colloquial_input <- function(x) {
out[x %like_case% "^fung(us|i)"] <- "F_FUNGUS"
# Salmonella city names, starting with capital species name - they are all S. enterica
out[x.bak %like_case% "[sS]almonella " & x %like% "paratyphi"] <- "B_SLMNL_ENTR"
out[x.bak %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" & x %unlike% "typhi"] <- "B_SLMNL_ENTR"
out[x %like_case% "salmonella group"] <- "B_SLMNL"