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(v1.3.0.9029) eucast rules fix, unique()

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dr. M.S. (Matthijs) Berends
2020-09-25 14:44:50 +02:00
parent 1d982a82b4
commit 9667c2994f
32 changed files with 234 additions and 160 deletions
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93
R/mo.R
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@ -204,11 +204,11 @@ as.mo <- function(x,
return(to_class_mo(x))
}
if (tryCatch(all(tolower(x) %in% MO_lookup$fullname_lower, na.rm = TRUE)
if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
& isFALSE(Becker)
& isFALSE(Lancefield), error = function(e) FALSE)) {
# to improve speed, special case for taxonomically correct full names (case-insensitive)
return(MO_lookup[match(tolower(x), MO_lookup$fullname_lower), "mo", drop = TRUE])
return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
}
# start off with replaced language-specific non-ASCII characters with ASCII characters
@ -481,8 +481,8 @@ exec_as.mo <- function(x,
# also, make sure the trailing and leading characters are a-z or 0-9
# in case of non-regex
if (dyslexia_mode == FALSE) {
trimmed <- gsub("^[^a-zA-Z0-9)(]+", "", trimmed)
trimmed <- gsub("[^a-zA-Z0-9)(]+$", "", trimmed)
trimmed <- gsub("^[^a-zA-Z0-9)(]+", "", trimmed, perl = TRUE)
trimmed <- gsub("[^a-zA-Z0-9)(]+$", "", trimmed, perl = TRUE)
}
trimmed
}
@ -497,49 +497,49 @@ exec_as.mo <- function(x,
x_backup[grepl("^(fungus|fungi)$", x)] <- "F_FUNGUS" # will otherwise become the kingdom
# remove spp and species
x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x)
x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x)
x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x) # when ending in SPE instead of SPP and preceded by 2-4 characters
x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x, perl = TRUE)
x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x, perl = TRUE)
x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x, perl = TRUE) # when ending in SPE instead of SPP and preceded by 2-4 characters
x <- strip_whitespace(x, dyslexia_mode)
x_backup_without_spp <- x
x_species <- paste(x, "species")
# translate to English for supported languages of mo_property
x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x)
x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x, perl = TRUE)
# no groups and complexes as ending
x <- gsub("(complex|group)$", "", x)
x <- gsub("((an)?aero+b)[a-z]*", "", x)
x <- gsub("^atyp[a-z]*", "", x)
x <- gsub("(vergroen)[a-z]*", "viridans", x)
x <- gsub("[a-z]*diff?erent[a-z]*", "", x)
x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x)
x <- gsub("(schimmels?|mofo|molde|stampo|moisissure|fungi)[a-z]*", "fungus", x)
x <- gsub("fungus[ph|f]rya", "fungiphrya", x)
x <- gsub("(complex|group)$", "", x, perl = TRUE)
x <- gsub("((an)?aero+b)[a-z]*", "", x, perl = TRUE)
x <- gsub("^atyp[a-z]*", "", x, perl = TRUE)
x <- gsub("(vergroen)[a-z]*", "viridans", x, perl = TRUE)
x <- gsub("[a-z]*diff?erent[a-z]*", "", x, perl = TRUE)
x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x, perl = TRUE)
x <- gsub("(schimmels?|mofo|molde|stampo|moisissure|fungi)[a-z]*", "fungus", x, perl = TRUE)
x <- gsub("fungus[ph|f]rya", "fungiphrya", x, perl = TRUE)
# no contamination
x <- gsub("(contamination|kontamination|mengflora|contaminaci.n|contamina..o)", "", x)
x <- gsub("(contamination|kontamination|mengflora|contaminaci.n|contamina..o)", "", x, perl = TRUE)
# remove non-text in case of "E. coli" except dots and spaces
x <- trimws(gsub("[^.a-zA-Z0-9/ \\-]+", " ", x))
x <- trimws(gsub("[^.a-zA-Z0-9/ \\-]+", " ", x, perl = TRUE))
# but make sure that dots are followed by a space
x <- gsub("[.] ?", ". ", x)
x <- gsub("[.] ?", ". ", x, perl = TRUE)
# replace minus by a space
x <- gsub("-+", " ", x)
x <- gsub("-+", " ", x, perl = TRUE)
# replace hemolytic by haemolytic
x <- gsub("ha?emoly", "haemoly", x)
x <- gsub("ha?emoly", "haemoly", x, perl = TRUE)
# place minus back in streptococci
x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x)
x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x, perl = TRUE)
# remove genus as first word
x <- gsub("^genus ", "", x)
x <- gsub("^genus ", "", x, perl = TRUE)
# remove 'uncertain'-like texts
x <- trimws(gsub("(uncertain|susp[ie]c[a-z]+|verdacht)", "", x))
x <- trimws(gsub("(uncertain|susp[ie]c[a-z]+|verdacht)", "", x, perl = TRUE))
# allow characters that resemble others = dyslexia_mode ----
if (dyslexia_mode == TRUE) {
x <- tolower(x)
x <- gsub("[iy]+", "[iy]+", x)
x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x)
x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x)
x <- gsub("(th|ht|t)+", "(th|ht|t)+", x)
x <- gsub("a+", "a+", x)
x <- gsub("u+", "u+", x)
x <- gsub("[iy]+", "[iy]+", x, perl = TRUE)
x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x, perl = TRUE)
x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x, perl = TRUE)
x <- gsub("(th|ht|t)+", "(th|ht|t)+", x, perl = TRUE)
x <- gsub("a+", "a+", x, perl = TRUE)
x <- gsub("u+", "u+", x, perl = TRUE)
# allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica, -ia and -a (needs perl for the negative backward lookup):
x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
@ -549,11 +549,11 @@ exec_as.mo <- function(x,
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
x <- gsub("(\\[iy\\]\\+a\\+)(?![a-z])",
"([iy]*a+|[iy]+a*)", x, perl = TRUE)
x <- gsub("e+", "e+", x)
x <- gsub("o+", "o+", x)
x <- gsub("(.)\\1+", "\\1+", x)
x <- gsub("e+", "e+", x, perl = TRUE)
x <- gsub("o+", "o+", x, perl = TRUE)
x <- gsub("(.)\\1+", "\\1+", x, perl = TRUE)
# allow multiplication of all other consonants
x <- gsub("([bdgjlnrw]+)", "\\1+", x)
x <- gsub("([bdgjlnrw]+)", "\\1+", x, perl = TRUE)
# allow ending in -en or -us
x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, perl = TRUE)
# if the input is longer than 10 characters, allow any forgotten consonant between all characters, as some might just have forgotten one...
@ -571,12 +571,12 @@ exec_as.mo <- function(x,
x_trimmed <- x
x_trimmed_species <- paste(x_trimmed, "species")
x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed)
x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed, perl = TRUE)
# remove last part from "-" or "/"
x_trimmed_without_group <- gsub("(.*)[-/].*", "\\1", x_trimmed_without_group)
# replace space and dot by regex sign
x_withspaces <- gsub("[ .]+", ".* ", x)
x <- gsub("[ .]+", ".*", x)
x_withspaces <- gsub("[ .]+", ".* ", x, perl = TRUE)
x <- gsub("[ .]+", ".*", x, perl = TRUE)
# add start en stop regex
x <- paste0("^", x, "$")
@ -616,7 +616,7 @@ exec_as.mo <- function(x,
}
# valid fullname ----
found <- lookup(fullname_lower %in% gsub("[^a-zA-Z0-9_. -]", "", tolower(c(x_backup[i], x_backup_without_spp[i]))))
found <- lookup(fullname_lower %in% gsub("[^a-zA-Z0-9_. -]", "", tolower(c(x_backup[i], x_backup_without_spp[i])), perl = TRUE))
# added the gsub() for "(unknown fungus)", since fullname_lower does not contain brackets
if (!is.na(found)) {
x[i] <- found[1L]
@ -670,7 +670,7 @@ exec_as.mo <- function(x,
# very probable: is G. species ----
found <- lookup(g_species %in% gsub("[^a-z0-9/ \\-]+", "",
tolower(c(x_backup[i], x_backup_without_spp[i]))))
tolower(c(x_backup[i], x_backup_without_spp[i])), perl = TRUE))
if (!is.na(found)) {
x[i] <- found[1L]
next
@ -1121,8 +1121,8 @@ exec_as.mo <- function(x,
if (isTRUE(debug)) {
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (4) strip values between brackets\n"))
}
a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup)
a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped))
a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup, perl = TRUE)
a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped, perl = TRUE))
if (isTRUE(debug)) {
message("Running '", a.x_backup_stripped, "'")
}
@ -1612,7 +1612,7 @@ format_uncertainty_as_df <- function(uncertainty_level,
pillar_shaft.mo <- function(x, ...) {
out <- format(x)
# grey out the kingdom (part until first "_")
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)])
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
# and grey out every _
out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
@ -1747,6 +1747,15 @@ c.mo <- function(x, ...) {
as.character(microorganisms.translation$mo_old)))
}
#' @method unique mo
#' @export
#' @noRd
unique.mo <- function(x, incomparables = FALSE, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @rdname as.mo
#' @export
mo_failures <- function() {