P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 01:42:08 +02:00
Code Releases Activity

new EUCAST rules algorithm

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-04-05 18:47:39 +02:00
parent 56d4b4719f
commit fbc9191b13
115 changed files with 1340 additions and 2174 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
R/mo_property.R
View File

@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Property of a microorganism
@ -136,7 +136,7 @@ mo_fullname <- function(x, language = get_locale(), ...) {
}
#' @rdname mo_property
#' @importFrom dplyr %>% left_join mutate pull
#' @importFrom dplyr %>% mutate pull
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
dots <- list(...)
@ -247,7 +247,12 @@ mo_phylum <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_kingdom <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "kingdom", ...), language = language)
kngdm <- mo_validate(x = x, property = "kingdom", ...)
if (language != "en") {
unknowns <- as.mo(x, ...) == "UNKOWN"
kngdm[unknowns] <- mo_translate(kngdm[unknowns], language = language)
}
kngdm
}
#' @rdname mo_property
@ -260,14 +265,14 @@ mo_type <- function(x, language = get_locale(), ...) {
#' @export
mo_gramstain <- function(x, language = get_locale(), ...) {
x.bak <- x
x.mo <- as.mo(x, ...)
x.phylum <- mo_phylum(x.mo)
x.mo <- as.mo(x, language = "en", ...)
x.phylum <- mo_phylum(x.mo, language = "en")
x[x.phylum %in% c("Actinobacteria",
"Chloroflexi",
"Firmicutes",
"Tenericutes")] <- "Gram positive"
x[x != "Gram positive"] <- "Gram negative"
x[mo_kingdom(x.mo) != "Bacteria"] <- NA_character_
x[mo_kingdom(x.mo, language = "en") != "Bacteria"] <- NA_character_
x[x.mo == "B_GRAMP"] <- "Gram positive"
x[x.mo == "B_GRAMN"] <- "Gram negative"