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custom mo update

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dr. M.S. (Matthijs) Berends
2022-12-28 14:20:10 +01:00
parent fe09e9252b
commit ba3b237bdf
5 changed files with 66 additions and 52 deletions
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10
R/mo.R
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@ -182,11 +182,11 @@ as.mo <- function(x,
x_lower <- tolower(x)
complexes <- x[trimws2(x_lower) %like_case% "complex$"]
if (length(complexes) > 0) {
warning_("in `as.mo()`: translation of complexes is not supported at the moment - the input text 'complex' was ignored in ", length(complexes), " cases.", call = FALSE)
complexes <- x[trimws2(x_lower) %like_case% " (complex|group)$"]
if (length(complexes) > 0 && identical(remove_from_input, mo_cleaning_regex())) {
warning_("in `as.mo()`: 'complex' and 'group' were ignored from the input in ", length(complexes), " case", ifelse(length(complexes) > 1, "s", ""), ", as they are currently not supported.\nYou can add your own microorganism with `add_custom_microorganisms()`.", call = FALSE)
}
# WHONET: xxx = no growth
x[x_lower %in% c("", "xxx", "na", "nan")] <- NA_character_
@ -536,7 +536,7 @@ mo_cleaning_regex <- function() {
"|",
"([({]|\\[).+([})]|\\])",
"|",
"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|complex)[.]*( |$))"
"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|group|complex)[.]*( |$))"
)
}