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complexes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-11-17 15:23:29 +01:00
parent f6862a139d
commit 05d536ebb7
7 changed files with 23 additions and 6 deletions
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6
R/mo.R
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@ -180,6 +180,10 @@ as.mo <- function(x,
x <- replace_ignore_pattern(x, ignore_pattern)
x_lower <- tolower(x)
if (any(trimws2(x_lower) %like_case% "complex$", na.rm = TRUE)) {
warning_("in `as.mo()`: translation of complexes is not supported at the moment - the input text 'complex' was ignored.", call = FALSE)
}
# WHONET: xxx = no growth
x[x_lower %in% c("", "xxx", "na", "nan")] <- NA_character_
@ -521,7 +525,7 @@ mo_cleaning_regex <- function() {
"|",
"([({]|\\[).+([})]|\\])",
"|",
"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|e?species)[.]*( |$))"
"(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|complex)[.]*( |$))"
)
}

7
R/rsi.R
View File

@ -285,7 +285,7 @@ as.rsi.default <- function(x, ...) {
x.bak <- x
x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
if (inherits(x.bak, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
# support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
lbls <- attributes(x.bak)$labels
@ -298,6 +298,10 @@ as.rsi.default <- function(x, ...) {
x[x.bak == 2] <- "I"
x[x.bak == 3] <- "R"
}
} else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "I", "R", NA_character_))) {
x[x.bak == "1"] <- "S"
x[x.bak == "2"] <- "I"
x[x.bak == "3"] <- "R"
} else if (!all(is.na(x)) && !identical(levels(x), c("R", "S", "I")) && !all(x %in% c("R", "S", "I", NA))) {
if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
# check if they are actually MICs or disks
@ -312,6 +316,7 @@ as.rsi.default <- function(x, ...) {
x <- trimws2(as.character(unlist(x)))
x[x %in% c(NA, "", "-", "NULL")] <- NA_character_
x.bak <- x
na_before <- length(x[is.na(x)])
# correct for translations