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(v0.7.0.9001) new pathovars, small fixes

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dr. M.S. (Matthijs) Berends
2019-06-07 22:47:37 +02:00
parent 04c75e8e36
commit f02679fb63
83 changed files with 686 additions and 583 deletions
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24
R/ab.R
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@ -91,6 +91,11 @@ as.ab <- function(x) {
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
next
}
# prevent "bacteria" from coercing to TMP, since Bacterial is a brand name of it
if (identical(tolower(x[i]), "bacteria")) {
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
next
}
# exact AB code
found <- AMR::antibiotics[which(AMR::antibiotics$ab == toupper(x[i])),]$ab
@ -162,23 +167,20 @@ as.ab <- function(x) {
}
x_spelling <- tolower(x[i])
x_spelling <- gsub("[iy]+", "[iy]+", x_spelling)
x_spelling <- gsub("[sz]+", "[sz]+", x_spelling)
x_spelling <- gsub("(c|k|q|qu)+", "(c|k|q|qu)+", x_spelling)
x_spelling <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x_spelling)
x_spelling <- gsub("(ph|f|v)+", "(ph|f|v)+", x_spelling)
x_spelling <- gsub("(th|t)+", "(th|t)+", x_spelling)
x_spelling <- gsub("(x|ks)+", "(x|ks)+", x_spelling)
x_spelling <- gsub("a+", "a+", x_spelling)
x_spelling <- gsub("e+", "e+", x_spelling)
x_spelling <- gsub("o+", "o+", x_spelling)
# allow start with C/S/Z
x_spelling <- gsub("^(\\(c\\|k\\|q\\|qu\\)|\\[sz\\])", "(c|k|q|qu|s|z)", x_spelling)
x_spelling <- gsub("(c|k|q|qu)+[sz]", "(c|k|q|qu|s|x|z)", x_spelling, fixed = TRUE)
# allow any ending of -in/-ine and -im/-ime
x_spelling <- gsub("(\\[iy\\]\\+(n|m)|\\[iy\\]\\+(n|m)e\\+)$", "[iy]+(n|m)e*", x_spelling)
# allow any ending of -ol/-ole
x_spelling <- gsub("(o\\+l|o\\+le\\+)$", "o+le*", x_spelling)
# allow any ending of -on/-one
x_spelling <- gsub("(o\\+n|o\\+ne\\+)$", "o+ne*", x_spelling)
# replace multiple same characters to single one with '+', like "ll" -> "l+"
x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
# try if name starts with it
found <- AMR::antibiotics[which(AMR::antibiotics$name %like% paste0("^", x_spelling)),]$ab
if (length(found) > 0) {
@ -256,3 +258,13 @@ as.data.frame.ab <- function (x, ...) {
pull.ab <- function(.data, ...) {
pull(as.data.frame(.data), ...)
}
#' @exportMethod scale_type.ab
#' @export
#' @noRd
scale_type.ab <- function(x) {
# fix for:
# "Don't know how to automatically pick scale for object of type ab. Defaulting to continuous."
# "Error: Discrete value supplied to continuous scale"
"discrete"
}