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last unit tests fix?

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-04 21:33:04 +02:00
parent 37f6db5ccd
commit aa06aad4ea
22 changed files with 275 additions and 256 deletions
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4
data-raw/_pre_commit_hook.R
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@ -104,7 +104,7 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
MO_staph[which(MO_staph$species %in% c(
"coagulase-negative", "argensis", "arlettae",
"auricularis", "borealis", "caeli", "capitis", "caprae",
"carnosus", "casei", "chromogenes", "cohnii", "condimenti",
"carnosus", "casei", "caseolyticus", "chromogenes", "cohnii", "condimenti",
"croceilyticus",
"debuckii", "devriesei", "edaphicus", "epidermidis",
"equorum", "felis", "fleurettii", "gallinarum",
@ -118,7 +118,7 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
"vitulinus", "vitulus", "warneri", "xylosus",
"caledonicus", "canis",
"durrellii", "lloydii",
"ratti", "taiwanensis"
"ratti", "taiwanensis", "veratri", "urealyticus"
) |
# old, now renamed to S. schleiferi (but still as synonym in our data of course):
(MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),

7
data-raw/reproduction_of_microorganisms.R
View File

@ -1005,7 +1005,7 @@ taxonomy <- taxonomy %>%
# Remove unwanted taxonomic entries from Protoza/Fungi --------------------
# this must be done after the microbial ID generation, since it will otherwise generate a lot of different IDs
taxonomy <- taxonomy %>%
taxonomy <- taxonomy %>%
filter(
# Protozoa:
!(phylum %in% c("Choanozoa", "Mycetozoa") & prevalence == 3),
@ -1016,7 +1016,8 @@ taxonomy <- taxonomy %>%
# Animalia:
!genus %in% c("Lucilia", "Lumbricus"),
!(genus %in% c("Aedes", "Anopheles") & rank %in% c("species", "subspecies")), # only genus of the many hundreds of mosquitoes species
kingdom != "Plantae") # this kingdom only contained Curvularia and Hymenolepis, which have coincidental twin names with Fungi
kingdom != "Plantae"
) # this kingdom only contained Curvularia and Hymenolepis, which have coincidental twin names with Fungi
message("\nCongratulations! The new taxonomic table will contain ", format(nrow(taxonomy), big.mark = ","), " rows.\n")
@ -1071,7 +1072,7 @@ taxonomy$lpsn_renamed_to[which(taxonomy$fullname == "Moraxella catarrhalis")]
taxonomy$status[which(taxonomy$fullname == "Moraxella catarrhalis")] <- "accepted"
taxonomy$lpsn_renamed_to[which(taxonomy$fullname == "Moraxella catarrhalis")] <- NA_character_
taxonomy <- taxonomy %>%
taxonomy <- taxonomy %>%
AMR:::dataset_UTF8_to_ASCII()