P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 19:01:51 +02:00
Code Releases Activity

unit tests

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-12-20 22:18:50 +01:00
parent f0a2cdbf5e
commit 6f4bb603ec
9 changed files with 57 additions and 69 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
R/mo_property.R
View File

@ -220,7 +220,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
# exceptions for streptococci: Group A Streptococcus -> GAS
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"], perl = TRUE), "S")
shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"] <- paste0("G", gsub("S. Group ([ABCDFGHK])", "\\1", shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"], perl = TRUE), "S")
# unknown species etc.
shortnames[shortnames %like% "unknown"] <- paste0("(", trimws2(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")