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(v2.1.1.9064) unit tests

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dr. M.S. (Matthijs) Berends
2024-07-16 15:55:58 +02:00
parent 640888f408
commit 7f344836ea
7 changed files with 60 additions and 15 deletions
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19
R/mo.R
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@ -420,17 +420,21 @@ as.mo <- function(x,
# Keep or replace synonyms ----
lpsn_matches <- AMR_env$MO_lookup$lpsn_renamed_to[match(out, AMR_env$MO_lookup$mo)]
lpsn_matches[!lpsn_matches %in% AMR_env$MO_lookup$lpsn] <- NA
# GBIF only for non-bacteria, since we use LPSN as primary source for bacteria
mycobank_matches <- AMR_env$MO_lookup$mycobank_renamed_to[match(out, AMR_env$MO_lookup$mo)]
mycobank_matches[!mycobank_matches %in% AMR_env$MO_lookup$mycobank] <- NA
# GBIF only for non-bacteria and non-fungi, since we use LPSN as primary source for bacteria and MycoBank for fungi
# (an example is Strep anginosus, renamed according to GBIF, not according to LPSN)
gbif_matches <- AMR_env$MO_lookup$gbif_renamed_to[AMR_env$MO_lookup$kingdom != "Bacteria"][match(out, AMR_env$MO_lookup$mo[AMR_env$MO_lookup$kingdom != "Bacteria"])]
gbif_matches <- AMR_env$MO_lookup$gbif_renamed_to[!AMR_env$MO_lookup$kingdom %in% c("Bacteria", "Fungi")][match(out, AMR_env$MO_lookup$mo[!AMR_env$MO_lookup$kingdom %in% c("Bacteria", "Fungi")])]
gbif_matches[!gbif_matches %in% AMR_env$MO_lookup$gbif] <- NA
AMR_env$mo_renamed <- list(
old = out[!is.na(gbif_matches) | !is.na(lpsn_matches)],
gbif_matches = gbif_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)],
lpsn_matches = lpsn_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)]
old = out[!is.na(gbif_matches) | !is.na(lpsn_matches) | !is.na(mycobank_matches)],
gbif_matches = gbif_matches[!is.na(gbif_matches) | !is.na(lpsn_matches) | !is.na(mycobank_matches)],
mycobank_matches = mycobank_matches[!is.na(gbif_matches) | !is.na(lpsn_matches) | !is.na(mycobank_matches)],
lpsn_matches = lpsn_matches[!is.na(gbif_matches) | !is.na(lpsn_matches) | !is.na(mycobank_matches)]
)
if (isFALSE(keep_synonyms)) {
out[which(!is.na(gbif_matches))] <- AMR_env$MO_lookup$mo[match(gbif_matches[which(!is.na(gbif_matches))], AMR_env$MO_lookup$gbif)]
out[which(!is.na(mycobank_matches))] <- AMR_env$MO_lookup$mo[match(mycobank_matches[which(!is.na(mycobank_matches))], AMR_env$MO_lookup$mycobank)]
out[which(!is.na(lpsn_matches))] <- AMR_env$MO_lookup$mo[match(lpsn_matches[which(!is.na(lpsn_matches))], AMR_env$MO_lookup$lpsn)]
if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) {
print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)")
@ -1040,13 +1044,14 @@ convert_colloquial_input <- function(x) {
out[x %like_case% "anaerob[a-z]+ .*gram[ -]?neg.*"] <- "B_ANAER-NEG"
out[x %like_case% "anaerob[a-z]+ .*gram[ -]?pos.*"] <- "B_ANAER-POS"
out[is.na(out) & x %like_case% "anaerob[a-z]+ (micro)?.*organism"] <- "B_ANAER"
out[is.na(out) & x %like_case% "anaerob[a-z]+ bacter"] <- "B_ANAER"
# coryneform bacteria
out[x %like_case% "^coryneform"] <- "B_CORYNF"
# yeasts and fungi
out[x %like_case% "^yeast?"] <- "F_YEAST"
out[x %like_case% "^fung(us|i)"] <- "F_FUNGUS"
out[x %like_case% "(^| )yeast?"] <- "F_YEAST"
out[x %like_case% "(^| )fung(us|i)"] <- "F_FUNGUS"
# trivial names known to the field
out[x %like_case% "meningo[ck]o[ck]"] <- "B_NESSR_MNNG"