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.R
View File

@ -385,7 +385,7 @@ as.mo <- function(x,
lpsn_matches <- AMR::microorganisms$lpsn_renamed_to[match(out, AMR::microorganisms$mo)]
lpsn_matches[!lpsn_matches %in% AMR::microorganisms$lpsn] <- NA
# GBIF only for non-bacteria, since we use LPSN as primary source for bacteria
# (example is Strep anginosus, renamed according to GBIF, not according to LPSN)
# (an example is Strep anginosus, renamed according to GBIF, not according to LPSN)
gbif_matches <- AMR::microorganisms$gbif_renamed_to[AMR::microorganisms$kingdom != "Bacteria"][match(out, AMR::microorganisms$mo[AMR::microorganisms$kingdom != "Bacteria"])]
gbif_matches[!gbif_matches %in% AMR::microorganisms$gbif] <- NA
AMR_env$mo_renamed <- list(