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(v2.1.1.9081) HUGE microorganisms update for fungi!

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-09-29 22:17:56 +02:00
parent a558f4c121
commit ac1c40d8bb
119 changed files with 36445 additions and 67400 deletions
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52
data-raw/_pre_commit_checks.R
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@ -158,10 +158,11 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
"group a", "group b", "group c", "group g"
))]
pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
pre_commit_lst$MO_PREVALENT_GENERA <- c(
pre_commit_lst$MO_RELEVANT_GENERA <- c(
"Absidia",
"Acanthamoeba",
"Acremonium",
"Actinomucor",
"Aedes",
"Alternaria",
"Amoeba",
@ -175,20 +176,31 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Aureobasidium",
"Basidiobolus",
"Beauveria",
"Bipolaris",
"Blastobotrys",
"Blastocystis",
"Blastomyces",
"Candida",
"Capillaria",
"Chaetomium",
"Chilomastix",
"Chrysonilia",
"Chrysosporium",
"Cladophialophora",
"Cladosporium",
"Clavispora",
"Coccidioides",
"Cokeromyces",
"Conidiobolus",
"Coniochaeta",
"Contracaecum",
"Cordylobia",
"Cryptococcus",
"Cryptosporidium",
"Cunninghamella",
"Curvularia",
"Cyberlindnera",
"Debaryozyma",
"Demodex",
"Dermatobia",
"Dientamoeba",
@ -197,6 +209,8 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Echinostoma",
"Entamoeba",
"Enterobius",
"Epidermophyton",
"Exidia",
"Exophiala",
"Exserohilum",
"Fasciola",
@ -204,6 +218,7 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Fusarium",
"Geotrichum",
"Giardia",
"Graphium",
"Haloarcula",
"Halobacterium",
"Halococcus",
@ -212,16 +227,19 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Heterophyes",
"Histomonas",
"Histoplasma",
"Hortaea",
"Hymenolepis",
"Hypomyces",
"Hysterothylacium",
"Kloeckera",
"Kluyveromyces",
"Kodamaea",
"Lacazia",
"Leishmania",
"Lichtheimia",
"Lodderomyces",
"Lomentospora",
"Madurella",
"Malassezia",
"Malbranchea",
"Metagonimus",
@ -232,6 +250,7 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Mortierella",
"Mucor",
"Mycocentrospora",
"Nannizzia",
"Necator",
"Nectria",
"Ochroconis",
@ -239,8 +258,12 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Oidiodendron",
"Opisthorchis",
"Paecilomyces",
"Paracoccidioides",
"Pediculus",
"Penicillium",
"Phaeoacremonium",
"Phaeomoniella",
"Phialophora",
"Phlebotomus",
"Phoma",
"Pichia",
@ -252,24 +275,34 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Pseudoscopulariopsis",
"Pseudoterranova",
"Pulex",
"Purpureocillium",
"Quambalaria",
"Rhinocladiella",
"Rhizomucor",
"Rhizopus",
"Rhodotorula",
"Saccharomyces",
"Saksenaea",
"Saprochaete",
"Sarcoptes",
"Scedosporium",
"Schistosoma",
"Schizosaccharomyces",
"Scolecobasidium",
"Scopulariopsis",
"Scytalidium",
"Spirometra",
"Sporobolomyces",
"Sporopachydermia",
"Sporothrix",
"Sporotrichum",
"Stachybotrys",
"Strongyloides",
"Syncephalastrum",
"Syngamus",
"Taenia",
"Talaromyces",
"Teleomorph",
"Toxocara",
"Trichinella",
"Trichobilharzia",
@ -283,8 +316,15 @@ pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Trombicula",
"Trypanosoma",
"Tunga",
"Ulocladium",
"Ustilago",
"Verticillium",
"Wuchereria"
"Wallemia",
"Wangiella",
"Wickerhamomyces",
"Wuchereria",
"Yarrowia",
"Zygosaccharomyces"
)
# antibiotic groups
@ -450,7 +490,6 @@ if (changed_md5(clin_break)) {
write_md5(clin_break)
try(saveRDS(clin_break, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(clinical_breakpoints, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(clin_break, "data-raw/clinical_breakpoints.xpt"), silent = TRUE)
try(haven::write_sav(clin_break, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
try(haven::write_dta(clin_break, "data-raw/clinical_breakpoints.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(clin_break, "data-raw/clinical_breakpoints.xlsx"), silent = TRUE)
@ -466,7 +505,6 @@ if (changed_md5(microorganisms)) {
mo <- microorganisms
mo$snomed <- max_50_snomed
mo <- dplyr::mutate_if(mo, ~ !is.numeric(.), as.character)
try(haven::write_xpt(mo, "data-raw/microorganisms.xpt"), silent = TRUE)
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
mo_all_snomed <- microorganisms %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@ -481,7 +519,6 @@ if (changed_md5(microorganisms.codes)) {
write_md5(microorganisms.codes)
try(saveRDS(microorganisms.codes, "data-raw/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.codes, "data-raw/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(microorganisms.codes, "data-raw/microorganisms.codes.xpt"), silent = TRUE)
try(haven::write_sav(microorganisms.codes, "data-raw/microorganisms.codes.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.codes, "data-raw/microorganisms.codes.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/microorganisms.codes.xlsx"), silent = TRUE)
@ -494,7 +531,6 @@ if (changed_md5(microorganisms.groups)) {
write_md5(microorganisms.groups)
try(saveRDS(microorganisms.groups, "data-raw/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.groups, "data-raw/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(microorganisms.groups, "data-raw/microorganisms.groups.xpt"), silent = TRUE)
try(haven::write_sav(microorganisms.groups, "data-raw/microorganisms.groups.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.groups, "data-raw/microorganisms.groups.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/microorganisms.groups.xlsx"), silent = TRUE)
@ -507,7 +543,6 @@ if (changed_md5(ab)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
write_md5(ab)
try(saveRDS(antibiotics, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
try(haven::write_xpt(ab, "data-raw/antibiotics.xpt"), silent = TRUE)
try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
ab_lists <- antibiotics %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@ -522,7 +557,6 @@ if (changed_md5(av)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
write_md5(av)
try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
try(haven::write_xpt(av, "data-raw/antivirals.xpt"), silent = TRUE)
try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
av_lists <- antivirals %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
@ -543,7 +577,6 @@ if (changed_md5(intrinsicR)) {
write_md5(intrinsicR)
try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(intrinsicR, "data-raw/intrinsic_resistant.xpt"), silent = TRUE)
try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
@ -556,7 +589,6 @@ if (changed_md5(dosage)) {
write_md5(dosage)
try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(dosage, "data-raw/dosage.xpt"), silent = TRUE)
try(haven::write_sav(dosage, "data-raw/dosage.sav"), silent = TRUE)
try(haven::write_dta(dosage, "data-raw/dosage.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)