P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 16:02:02 +02:00
Code Releases Activity

(v1.3.0.9007) tibble printing

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-08-26 11:33:54 +02:00
parent c8c8bb4e3a
commit 5e45fdcf2a
64 changed files with 266 additions and 77 deletions
Download Patch File Download Diff File Expand all files Collapse all files

7
R/mo_property.R
View File

@ -161,13 +161,18 @@ mo_shortname <- function(x, language = get_locale(), ...) {
}
# get first char of genus and complete species in English
shortnames <- paste0(substr(mo_genus(x.mo, language = NULL), 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
genera <- mo_genus(x.mo, language = NULL)
shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
# exceptions for where no species is known
shortnames[shortnames %like% ".[.] spp[.]"] <- genera[shortnames %like% ".[.] spp[.]"]
# exceptions for Staphylococci
shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
# exceptions for Streptococci: Streptococcus Group A -> GAS
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
# unknown species etc.
shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")")
load_mo_failures_uncertainties_renamed(metadata)
translate_AMR(shortnames, language = language, only_unknown = FALSE)