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as.mo improvement

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dr. M.S. (Matthijs) Berends
2019-02-26 12:33:26 +01:00
parent f25a4b3679
commit f9ded23023
67 changed files with 391 additions and 342 deletions
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88
R/mo_property.R
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@ -132,7 +132,7 @@
#' mo_taxonomy("E. coli")
mo_fullname <- function(x, language = get_locale(), ...) {
x <- mo_validate(x = x, property = "fullname", ...)
mo_translate(x, language = language)
translate(x, language = language)
}
#' @rdname mo_property
@ -148,46 +148,64 @@ mo_shortname <- function(x, language = get_locale(), ...) {
if (is.null(Lancefield)) {
Lancefield <- FALSE
}
if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df)
res2 <- suppressWarnings(AMR::as.mo(res1, ...))
res2_fullname <- mo_fullname(res2, language = language)
res2_fullname[res2_fullname %like% " \\(CoNS\\)"] <- "CoNS"
res2_fullname[res2_fullname %like% " \\(CoPS\\)"] <- "CoPS"
res2_fullname[res2_fullname %like% " \\(KNS\\)"] <- "KNS"
res2_fullname[res2_fullname %like% " \\(KPS\\)"] <- "KPS"
res2_fullname[res2_fullname %like% " \\(CNS\\)"] <- "CNS"
res2_fullname[res2_fullname %like% " \\(CPS\\)"] <- "CPS"
res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)",
"G\\2S",
res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)]
res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
". ",
suppressWarnings(mo_species(res2_fullname_vector)))
if (sum(res1 == res2, na.rm = TRUE) > 0) {
res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
". ",
suppressWarnings(mo_species(res1[res1 == res2])))
}
res1[res1 != res2] <- res2_fullname
result <- as.character(res1)
} else {
x <- AMR::as.mo(x, ...)
suppressWarnings(
result <- data.frame(mo = x) %>%
left_join(AMR::microorganisms, by = "mo") %>%
mutate(shortname = ifelse(!is.na(genus) & !is.na(species), paste0(substr(genus, 1, 1), ". ", species), NA_character_)) %>%
pull(shortname)
)
shorten <- function(x) {
# easiest: no transformations needed
x <- mo_fullname(x, language = "en")
# shorten for the ones that have a space: shorten first word and write out second word
shorten_these <- x %like% " " & !x %like% "Streptococcus group "
x[shorten_these] <- paste0(substr(x[shorten_these], 1, 1),
". ",
x[shorten_these] %>%
strsplit(" ", fixed = TRUE) %>%
unlist() %>%
.[2])
x
}
mo_translate(result, language = language)
if (isFALSE(Becker) & isFALSE(Lancefield)) {
result <- shorten(x)
} else {
# get result without transformations
res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df)
# and result with transformations
res2 <- suppressWarnings(AMR::as.mo(res1, ...))
if (res1 == res2
& !res1 %like% "^B_STRPT_GR") {
result <- shorten(x)
} else {
res2_fullname <- mo_fullname(res2, language = language)
res2_fullname[res2_fullname %like% " \\(CoNS\\)"] <- "CoNS"
res2_fullname[res2_fullname %like% " \\(CoPS\\)"] <- "CoPS"
res2_fullname[res2_fullname %like% " \\(KNS\\)"] <- "KNS"
res2_fullname[res2_fullname %like% " \\(KPS\\)"] <- "KPS"
res2_fullname[res2_fullname %like% " \\(CNS\\)"] <- "CNS"
res2_fullname[res2_fullname %like% " \\(CPS\\)"] <- "CPS"
res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)",
"G\\2S",
res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)]
res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
". ",
suppressWarnings(mo_species(res2_fullname_vector)))
if (sum(res1 == res2, na.rm = TRUE) > 0) {
res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
". ",
suppressWarnings(mo_species(res1[res1 == res2])))
}
res1[res1 != res2] <- res2_fullname
result <- as.character(res1)
}
}
translate(result, language = language)
}
#' @rdname mo_property
#' @export
mo_subspecies <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "subspecies", ...), language = language)
translate(validate(x = x, property = "subspecies", ...), language = language)
}
#' @rdname mo_property