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(v0.7.1.9080) new LIS codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-09-22 17:19:59 +02:00
parent 57b0bd92a0
commit 66d405ff57
24 changed files with 239 additions and 222 deletions
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12
data-raw/internals.R
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@ -49,14 +49,14 @@ rm(translations_file)
rm(microorganisms.translation)
# Clean mo history ----
mo_history_file <- file.path(file.path(system.file(package = "AMR"), "mo_history"), "mo_history.csv")
usethis::ui_done(paste0("Resetting {usethis::ui_value('", mo_history_file, "')}"))
usethis::ui_done(paste0("Resetting {usethis::ui_value('mo_history.csv')}"))
tryCatch(
write.csv(x = data.frame(x = character(0),
mo = character(0),
uncertainty_level = integer(0),
package_v = character(0),
package_version = character(0),
stringsAsFactors = FALSE),
file = mo_history_file),
warning = function(w) invisible(),
error = function(e) TRUE)
row.names = FALSE,
file = "inst/mo_history/mo_history.csv"),
warning = function(w) cat("Warning:", w$message, "\n"),
error = function(e) cat("Error:", e$message, "\n"))

27
data-raw/reproduction_of_microorganisms.R
View File

@ -94,7 +94,7 @@ rm(ref_taxonomy)
mo_found_in_NL <- c("Absidia", "Acremonium", "Actinotignum", "Aedes", "Alternaria", "Anaerosalibacter", "Ancylostoma",
"Angiostrongylus", "Anisakis", "Anopheles", "Apophysomyces", "Arachnia", "Ascaris", "Aspergillus",
"Aureobacterium", "Aureobasidium", "Bacteroides", "Balantidum", "Basidiobolus", "Beauveria",
"Bilophilia", "Branhamella", "Brochontrix", "Brugia", "Calymmatobacterium", "Candida", "Capillaria",
"Bilophilia", "Blastocystis", "Branhamella", "Brochontrix", "Brugia", "Calymmatobacterium", "Candida", "Capillaria",
"Capnocytophaga", "Catabacter", "Cdc", "Chaetomium", "Chilomastix", "Chryseobacterium",
"Chryseomonas", "Chrysonilia", "Cladophialophora", "Cladosporium", "Clonorchis", "Conidiobolus",
"Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex", "Dermatobia", "Dicrocoelium",
@ -113,7 +113,7 @@ mo_found_in_NL <- c("Absidia", "Acremonium", "Actinotignum", "Aedes", "Alternari
"Rhodotorula", "Salinococcus", "Sanguibacteroides", "Sarcophagidae", "Sarcoptes", "Schistosoma",
"Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra", "Sporobolomyces", "Stachybotrys",
"Stenotrophomononas", "Stomatococcus", "Strongyloides", "Syncephalastraceae", "Syngamus", "Taenia",
"Ternidens", "Torulopsis", "Toxocara", "Treponema", "Trichinella", "Trichobilharzia", "Trichoderma",
"Ternidens", "Torulopsis", "Toxocara", "Toxoplasma", "Treponema", "Trichinella", "Trichobilharzia", "Trichoderma",
"Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium",
"Trombicula", "Trypanosoma", "Tunga", "Ureaplasma", "Wuchereria")
@ -219,6 +219,8 @@ MOs.old <- MOs %>%
distinct(fullname, .keep_all = TRUE) %>%
arrange(col_id)
MO.bak <- MOs
MOs <- MOs %>%
filter(is.na(col_id_new) | source == "DSMZ") %>%
transmute(col_id,
@ -594,6 +596,17 @@ MOs <- MOs %>%
ref = NA_character_,
species_id = "",
source = "manually added"),
# Blastocystis hominis does not exist (it means 'got a Bastocystis from humans', PMID 15634993)
# but let's be nice to the clinical people in microbiology
MOs %>%
filter(fullname == "Blastocystis") %>%
mutate(mo = paste0(mo, "_HMNS"),
fullname = paste(fullname, "hominis"),
species = "hominis",
col_id = NA,
source = "manually added",
ref = NA_character_,
species_id = ""),
# Trichomonas vaginalis is missing, same order as Dientamoeba
MOs %>%
filter(fullname == "Dientamoeba") %>%
@ -636,6 +649,7 @@ MOs <- MOs %>%
ungroup() %>%
filter(fullname != "")
# add prevalence to old taxonomic names
MOs.old <- MOs.old %>%
left_join(MOs %>% select(col_id, prevalence), by = c("col_id_new" = "col_id"))
@ -645,7 +659,8 @@ sum(duplicated(MOs$fullname))
colnames(MOs)
# here we welcome the new ones:
MOs %>% arrange(genus, species, subspecies) %>% filter(!fullname %in% AMR::microorganisms$fullname) %>% View()
MOs %>% arrange(fullname) %>% filter(!fullname %in% AMR::microorganisms$fullname) %>% View()
MOs.old %>% arrange(fullname) %>% filter(!fullname %in% AMR::microorganisms.old$fullname) %>% View()
# and the ones we lost:
AMR::microorganisms %>% filter(!fullname %in% MOs$fullname) %>% View()
# and these IDs have changed:
@ -659,9 +674,11 @@ old_new %>%
View()
# and these codes are now missing (which will throw a unit test error):
AMR::microorganisms.codes %>% filter(!mo %in% MOs$mo)
AMR::rsi_translation %>% filter(!mo %in% MOs$mo)
AMR::microorganisms.translation %>% filter(!mo_new %in% MOs$mo)
# this is how to fix it
microorganisms.codes <- AMR::microorganisms.codes %>%
left_join(MOs %>%
left_join(MOs %>%
mutate(kingdom_fullname = paste(kingdom, fullname)) %>%
left_join(AMR::microorganisms %>%
mutate(kingdom_fullname = paste(kingdom, fullname)) %>%
@ -673,7 +690,7 @@ microorganisms.codes <- AMR::microorganisms.codes %>%
microorganisms.codes %>% filter(!mo %in% MOs$mo)
# arrange
MOs <- MOs %>% arrange(genus, species, subspecies)
MOs <- MOs %>% arrange(fullname)
MOs.old <- MOs.old %>% arrange(fullname)
microorganisms.codes <- microorganisms.codes %>% arrange(code)