mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 23:21:56 +02:00
New mo algorithm, prepare for 2.0
This commit is contained in:
Dr. Matthijs Berends
committed by
GitHub
GitHub
parent
63fe160322
commit
cd2acc4a29
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
@ -28,7 +32,7 @@ install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "
|
||||
install.packages(getwd(), repos = NULL, type = "source")
|
||||
|
||||
pkg_suggests <- gsub(
|
||||
"[^a-zA-Z0-9]+", "",
|
||||
"[^a-zA-Z0-9.]+", "",
|
||||
unlist(strsplit(unlist(packageDescription("AMR",
|
||||
fields = c("Suggests", "Enhances", "LinkingTo")
|
||||
)),
|
||||
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
@ -100,7 +104,7 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
MO_staph[which(MO_staph$species %in% c(
|
||||
"coagulase-negative", "argensis", "arlettae",
|
||||
"auricularis", "borealis", "caeli", "capitis", "caprae",
|
||||
"carnosus", "casei", "chromogenes", "cohnii", "condimenti",
|
||||
"carnosus", "casei", "caseolyticus", "chromogenes", "cohnii", "condimenti",
|
||||
"croceilyticus",
|
||||
"debuckii", "devriesei", "edaphicus", "epidermidis",
|
||||
"equorum", "felis", "fleurettii", "gallinarum",
|
||||
@ -113,8 +117,10 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
"ureilyticus",
|
||||
"vitulinus", "vitulus", "warneri", "xylosus",
|
||||
"caledonicus", "canis",
|
||||
"durrellii", "lloydii"
|
||||
"durrellii", "lloydii",
|
||||
"ratti", "taiwanensis", "veratri", "urealyticus"
|
||||
) |
|
||||
# old, now renamed to S. schleiferi (but still as synonym in our data of course):
|
||||
(MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
|
||||
"mo",
|
||||
drop = TRUE
|
||||
@ -128,8 +134,10 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schweitzeri", "simiae",
|
||||
"roterodami"
|
||||
"roterodami",
|
||||
"singaporensis"
|
||||
) |
|
||||
# old, now renamed to S. coagulans (but still as synonym in our data of course):
|
||||
(MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
|
||||
"mo",
|
||||
drop = TRUE
|
||||
@ -151,31 +159,35 @@ create_MO_fullname_lower <- function() {
|
||||
}
|
||||
MO_CONS <- create_species_cons_cops("CoNS")
|
||||
MO_COPS <- create_species_cons_cops("CoPS")
|
||||
MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
|
||||
MO_STREP_ABCG <- MO_lookup$mo[which(MO_lookup$genus == "Streptococcus" &
|
||||
MO_lookup$species %in% c(
|
||||
"pyogenes", "agalactiae", "dysgalactiae", "equi", "anginosus", "sanguinis", "salivarius",
|
||||
"group A", "group B", "group C", "group D", "group F", "group G", "group H", "group K", "group L"
|
||||
))]
|
||||
MO_FULLNAME_LOWER <- create_MO_fullname_lower()
|
||||
MO_PREVALENT_GENERA <- c(
|
||||
"Absidia", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes", "Alloprevotella",
|
||||
"Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus", "Anisakis", "Anopheles",
|
||||
"Absidia", "Acanthamoeba", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes", "Alloprevotella",
|
||||
"Alternaria", "Amoeba", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus", "Anisakis", "Anopheles",
|
||||
"Apophysomyces", "Arachnia", "Aspergillus", "Aureobasidium", "Bacteroides", "Basidiobolus",
|
||||
"Beauveria", "Bergeyella", "Blastocystis", "Blastomyces", "Borrelia", "Brachyspira", "Branhamella",
|
||||
"Butyricimonas", "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cetobacterium", "Chaetomium",
|
||||
"Chlamydia", "Chlamydophila", "Chryseobacterium", "Chrysonilia", "Cladophialophora", "Cladosporium",
|
||||
"Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus", "Demodex",
|
||||
"Dermatobia", "Diphyllobothrium", "Dirofilaria", "Dysgonomonas", "Echinostoma", "Elizabethkingia",
|
||||
"Empedobacter", "Enterobius", "Exophiala", "Exserohilum", "Fasciola", "Flavobacterium", "Fonsecaea",
|
||||
"Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Dysgonomonas", "Echinostoma", "Elizabethkingia",
|
||||
"Empedobacter", "Entamoeba", "Enterobius", "Exophiala", "Exserohilum", "Fasciola", "Flavobacterium", "Fonsecaea",
|
||||
"Fusarium", "Fusobacterium", "Giardia", "Haloarcula", "Halobacterium", "Halococcus", "Hendersonula",
|
||||
"Heterophyes", "Histoplasma", "Hymenolepis", "Hypomyces", "Hysterothylacium", "Lelliottia",
|
||||
"Leptosphaeria", "Leptotrichia", "Lucilia", "Lumbricus", "Malassezia", "Malbranchea", "Metagonimus",
|
||||
"Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Myroides", "Necator",
|
||||
"Heterophyes", "Histomonas", "Histoplasma", "Hymenolepis", "Hypomyces", "Hysterothylacium", "Leishmania", "Lelliottia",
|
||||
"Leptosphaeria", "Leptotrichia", "Lucilia", "Lumbricus", "Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma",
|
||||
"Microsporidium", "Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Myroides", "Necator",
|
||||
"Nectria", "Ochroconis", "Odoribacter", "Oesophagostomum", "Oidiodendron", "Opisthorchis",
|
||||
"Ornithobacterium", "Parabacteroides", "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola",
|
||||
"Phocanema", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Porphyromonas", "Prevotella",
|
||||
"Phocanema", "Phoma", "Pichia", "Piedraia", "Pithomyces", "Pityrosporum", "Pneumocystis", "Porphyromonas", "Prevotella",
|
||||
"Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula", "Riemerella",
|
||||
"Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
|
||||
"Spirometra", "Spiroplasma", "Sporobolomyces", "Stachybotrys", "Streptobacillus", "Strongyloides",
|
||||
"Syngamus", "Taenia", "Tannerella", "Tenacibaculum", "Terrimonas", "Toxocara", "Treponema", "Trichinella",
|
||||
"Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus",
|
||||
"Trichuris", "Tritirachium", "Trombicula", "Tunga", "Ureaplasma", "Victivallis", "Wautersiella",
|
||||
"Trichuris", "Tritirachium", "Trypanosoma", "Trombicula", "Tunga", "Ureaplasma", "Victivallis", "Wautersiella",
|
||||
"Weeksella", "Wuchereria"
|
||||
)
|
||||
|
||||
@ -281,7 +293,7 @@ create_AB_lookup <- function() {
|
||||
AB_LOOKUP <- create_AB_lookup()
|
||||
|
||||
# Export to package as internal data ----
|
||||
usethis::ui_info(paste0("Saving {usethis::ui_value('sysdata.rda')} to {usethis::ui_value('R/')}"))
|
||||
usethis::ui_info(paste0("Updating internal package data"))
|
||||
suppressMessages(usethis::use_data(EUCAST_RULES_DF,
|
||||
TRANSLATIONS,
|
||||
LANGUAGES_SUPPORTED_NAMES,
|
||||
@ -360,7 +372,7 @@ changed_md5 <- function(object) {
|
||||
|
||||
# give official names to ABs and MOs
|
||||
rsi <- rsi_translation %>%
|
||||
mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
|
||||
mutate(mo_name = mo_name(mo, language = NULL, keep_synonyms = TRUE, info = FALSE), .after = mo) %>%
|
||||
mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
|
||||
if (changed_md5(rsi)) {
|
||||
usethis::ui_info(paste0("Saving {usethis::ui_value('rsi_translation')} to {usethis::ui_value('data-raw/')}"))
|
||||
@ -392,19 +404,6 @@ if (changed_md5(microorganisms)) {
|
||||
try(arrow::write_parquet(microorganisms, "data-raw/microorganisms.parquet"), silent = TRUE)
|
||||
}
|
||||
|
||||
if (changed_md5(microorganisms.old)) {
|
||||
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.old')} to {usethis::ui_value('data-raw/')}"))
|
||||
write_md5(microorganisms.old)
|
||||
try(saveRDS(microorganisms.old, "data-raw/microorganisms.old.rds", version = 2, compress = "xz"), silent = TRUE)
|
||||
try(write.table(microorganisms.old, "data-raw/microorganisms.old.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
||||
try(haven::write_sas(microorganisms.old, "data-raw/microorganisms.old.sas"), silent = TRUE)
|
||||
try(haven::write_sav(microorganisms.old, "data-raw/microorganisms.old.sav"), silent = TRUE)
|
||||
try(haven::write_dta(microorganisms.old, "data-raw/microorganisms.old.dta"), silent = TRUE)
|
||||
try(openxlsx::write.xlsx(microorganisms.old, "data-raw/microorganisms.old.xlsx"), silent = TRUE)
|
||||
try(arrow::write_feather(microorganisms.old, "data-raw/microorganisms.old.feather"), silent = TRUE)
|
||||
try(arrow::write_parquet(microorganisms.old, "data-raw/microorganisms.old.parquet"), silent = TRUE)
|
||||
}
|
||||
|
||||
ab <- dplyr::mutate_if(antibiotics, ~ !is.numeric(.), as.character)
|
||||
if (changed_md5(ab)) {
|
||||
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
|
||||
@ -435,7 +434,7 @@ if (changed_md5(av)) {
|
||||
|
||||
# give official names to ABs and MOs
|
||||
intrinsicR <- data.frame(
|
||||
microorganism = mo_name(intrinsic_resistant$mo, language = NULL),
|
||||
microorganism = mo_name(intrinsic_resistant$mo, language = NULL, keep_synonyms = TRUE, info = FALSE),
|
||||
antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
@ -486,16 +485,14 @@ suppressMessages(devtools::document(quiet = TRUE))
|
||||
|
||||
|
||||
# Style pkg ---------------------------------------------------------------
|
||||
usethis::ui_info("Styling package")
|
||||
invisible(capture.output(styler::style_pkg(
|
||||
style = styler::tidyverse_style,
|
||||
filetype = c("R", "Rmd")
|
||||
)))
|
||||
invisible(capture.output(styler::style_dir(
|
||||
path = "inst", # unit tests
|
||||
style = styler::tidyverse_style,
|
||||
filetype = c("R", "Rmd")
|
||||
)))
|
||||
if (interactive()) {
|
||||
# only when sourcing this file ourselves
|
||||
usethis::ui_info("Styling package")
|
||||
styler::style_pkg(
|
||||
style = styler::tidyverse_style,
|
||||
filetype = c("R", "Rmd")
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
# Finished ----------------------------------------------------------------
|
||||
|
||||
@ -1 +1 @@
|
||||
56b3cea0e28d8a54e0fcbd3e50af96fc
|
||||
a6dcb362ffa737670ed4663968fbff26
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -7617,11 +7617,11 @@
|
||||
"Actinoalloteichus spitiensis" "Nalidixic acid"
|
||||
"Actinoalloteichus spitiensis" "Polymyxin B"
|
||||
"Actinoalloteichus spitiensis" "Temocillin"
|
||||
"Actinobacteria" "Aztreonam"
|
||||
"Actinobacteria" "Colistin"
|
||||
"Actinobacteria" "Nalidixic acid"
|
||||
"Actinobacteria" "Polymyxin B"
|
||||
"Actinobacteria" "Temocillin"
|
||||
"Actinobacteriota" "Aztreonam"
|
||||
"Actinobacteriota" "Colistin"
|
||||
"Actinobacteriota" "Nalidixic acid"
|
||||
"Actinobacteriota" "Polymyxin B"
|
||||
"Actinobacteriota" "Temocillin"
|
||||
"Actinobaculum" "Aztreonam"
|
||||
"Actinobaculum" "Colistin"
|
||||
"Actinobaculum" "Nalidixic acid"
|
||||
@ -8877,11 +8877,6 @@
|
||||
"Actinopolysporaceae" "Nalidixic acid"
|
||||
"Actinopolysporaceae" "Polymyxin B"
|
||||
"Actinopolysporaceae" "Temocillin"
|
||||
"Actinopolysporales" "Aztreonam"
|
||||
"Actinopolysporales" "Colistin"
|
||||
"Actinopolysporales" "Nalidixic acid"
|
||||
"Actinopolysporales" "Polymyxin B"
|
||||
"Actinopolysporales" "Temocillin"
|
||||
"Actinorectispora" "Aztreonam"
|
||||
"Actinorectispora" "Colistin"
|
||||
"Actinorectispora" "Nalidixic acid"
|
||||
@ -9272,16 +9267,6 @@
|
||||
"Aestuariimicrobium" "Nalidixic acid"
|
||||
"Aestuariimicrobium" "Polymyxin B"
|
||||
"Aestuariimicrobium" "Temocillin"
|
||||
"Aestuariimicrobium kwangyangense" "Aztreonam"
|
||||
"Aestuariimicrobium kwangyangense" "Colistin"
|
||||
"Aestuariimicrobium kwangyangense" "Nalidixic acid"
|
||||
"Aestuariimicrobium kwangyangense" "Polymyxin B"
|
||||
"Aestuariimicrobium kwangyangense" "Temocillin"
|
||||
"Aestuariimicrobium soli" "Aztreonam"
|
||||
"Aestuariimicrobium soli" "Colistin"
|
||||
"Aestuariimicrobium soli" "Nalidixic acid"
|
||||
"Aestuariimicrobium soli" "Polymyxin B"
|
||||
"Aestuariimicrobium soli" "Temocillin"
|
||||
"Agathobacter" "Aztreonam"
|
||||
"Agathobacter" "Colistin"
|
||||
"Agathobacter" "Nalidixic acid"
|
||||
@ -11265,11 +11250,11 @@
|
||||
"Amycolatopsis alba" "Nalidixic acid"
|
||||
"Amycolatopsis alba" "Polymyxin B"
|
||||
"Amycolatopsis alba" "Temocillin"
|
||||
"Amycolatopsis albidiflava" "Aztreonam"
|
||||
"Amycolatopsis albidiflava" "Colistin"
|
||||
"Amycolatopsis albidiflava" "Nalidixic acid"
|
||||
"Amycolatopsis albidiflava" "Polymyxin B"
|
||||
"Amycolatopsis albidiflava" "Temocillin"
|
||||
"Amycolatopsis albidoflava" "Aztreonam"
|
||||
"Amycolatopsis albidoflava" "Colistin"
|
||||
"Amycolatopsis albidoflava" "Nalidixic acid"
|
||||
"Amycolatopsis albidoflava" "Polymyxin B"
|
||||
"Amycolatopsis albidoflava" "Temocillin"
|
||||
"Amycolatopsis albispora" "Aztreonam"
|
||||
"Amycolatopsis albispora" "Colistin"
|
||||
"Amycolatopsis albispora" "Nalidixic acid"
|
||||
@ -22103,11 +22088,6 @@
|
||||
"Catabacter honkongensis" "Nalidixic acid"
|
||||
"Catabacter honkongensis" "Polymyxin B"
|
||||
"Catabacter honkongensis" "Temocillin"
|
||||
"Catabacteraceae" "Aztreonam"
|
||||
"Catabacteraceae" "Colistin"
|
||||
"Catabacteraceae" "Nalidixic acid"
|
||||
"Catabacteraceae" "Polymyxin B"
|
||||
"Catabacteraceae" "Temocillin"
|
||||
"Catellatospora" "Aztreonam"
|
||||
"Catellatospora" "Colistin"
|
||||
"Catellatospora" "Nalidixic acid"
|
||||
@ -23053,11 +23033,6 @@
|
||||
"Chloroflexales" "Nalidixic acid"
|
||||
"Chloroflexales" "Polymyxin B"
|
||||
"Chloroflexales" "Temocillin"
|
||||
"Chloroflexi" "Aztreonam"
|
||||
"Chloroflexi" "Colistin"
|
||||
"Chloroflexi" "Nalidixic acid"
|
||||
"Chloroflexi" "Polymyxin B"
|
||||
"Chloroflexi" "Temocillin"
|
||||
"Chloroflexia" "Aztreonam"
|
||||
"Chloroflexia" "Colistin"
|
||||
"Chloroflexia" "Nalidixic acid"
|
||||
@ -30752,12 +30727,6 @@
|
||||
"Corynebacterium appendicis" "Nalidixic acid"
|
||||
"Corynebacterium appendicis" "Polymyxin B"
|
||||
"Corynebacterium appendicis" "Temocillin"
|
||||
"Corynebacterium aquaticum" "Aztreonam"
|
||||
"Corynebacterium aquaticum" "Colistin"
|
||||
"Corynebacterium aquaticum" "Fosfomycin"
|
||||
"Corynebacterium aquaticum" "Nalidixic acid"
|
||||
"Corynebacterium aquaticum" "Polymyxin B"
|
||||
"Corynebacterium aquaticum" "Temocillin"
|
||||
"Corynebacterium aquatimens" "Aztreonam"
|
||||
"Corynebacterium aquatimens" "Colistin"
|
||||
"Corynebacterium aquatimens" "Fosfomycin"
|
||||
@ -32711,11 +32680,6 @@
|
||||
"Dehalococcoides mccartyi" "Nalidixic acid"
|
||||
"Dehalococcoides mccartyi" "Polymyxin B"
|
||||
"Dehalococcoides mccartyi" "Temocillin"
|
||||
"Dehalococcoidetes" "Aztreonam"
|
||||
"Dehalococcoidetes" "Colistin"
|
||||
"Dehalococcoidetes" "Nalidixic acid"
|
||||
"Dehalococcoidetes" "Polymyxin B"
|
||||
"Dehalococcoidetes" "Temocillin"
|
||||
"Dehalogenimonas" "Aztreonam"
|
||||
"Dehalogenimonas" "Colistin"
|
||||
"Dehalogenimonas" "Nalidixic acid"
|
||||
@ -33146,11 +33110,6 @@
|
||||
"Desulfofundulus thermobenzoicus thermobenzoicus" "Nalidixic acid"
|
||||
"Desulfofundulus thermobenzoicus thermobenzoicus" "Polymyxin B"
|
||||
"Desulfofundulus thermobenzoicus thermobenzoicus" "Temocillin"
|
||||
"Desulfofundulus thermobenzoicus thermosyntrophicus" "Aztreonam"
|
||||
"Desulfofundulus thermobenzoicus thermosyntrophicus" "Colistin"
|
||||
"Desulfofundulus thermobenzoicus thermosyntrophicus" "Nalidixic acid"
|
||||
"Desulfofundulus thermobenzoicus thermosyntrophicus" "Polymyxin B"
|
||||
"Desulfofundulus thermobenzoicus thermosyntrophicus" "Temocillin"
|
||||
"Desulfofundulus thermocisternus" "Aztreonam"
|
||||
"Desulfofundulus thermocisternus" "Colistin"
|
||||
"Desulfofundulus thermocisternus" "Nalidixic acid"
|
||||
@ -60316,11 +60275,6 @@
|
||||
"Geobacillus thermodenitrificans calidus" "Nalidixic acid"
|
||||
"Geobacillus thermodenitrificans calidus" "Polymyxin B"
|
||||
"Geobacillus thermodenitrificans calidus" "Temocillin"
|
||||
"Geobacillus thermodenitrificans thermodenitrificans" "Aztreonam"
|
||||
"Geobacillus thermodenitrificans thermodenitrificans" "Colistin"
|
||||
"Geobacillus thermodenitrificans thermodenitrificans" "Nalidixic acid"
|
||||
"Geobacillus thermodenitrificans thermodenitrificans" "Polymyxin B"
|
||||
"Geobacillus thermodenitrificans thermodenitrificans" "Temocillin"
|
||||
"Geobacillus thermoleovorans" "Aztreonam"
|
||||
"Geobacillus thermoleovorans" "Colistin"
|
||||
"Geobacillus thermoleovorans" "Nalidixic acid"
|
||||
@ -62185,11 +62139,6 @@
|
||||
"Haloechinothrix" "Nalidixic acid"
|
||||
"Haloechinothrix" "Polymyxin B"
|
||||
"Haloechinothrix" "Temocillin"
|
||||
"Haloechinothrix aidingensis" "Aztreonam"
|
||||
"Haloechinothrix aidingensis" "Colistin"
|
||||
"Haloechinothrix aidingensis" "Nalidixic acid"
|
||||
"Haloechinothrix aidingensis" "Polymyxin B"
|
||||
"Haloechinothrix aidingensis" "Temocillin"
|
||||
"Haloechinothrix alba" "Aztreonam"
|
||||
"Haloechinothrix alba" "Colistin"
|
||||
"Haloechinothrix alba" "Nalidixic acid"
|
||||
@ -67423,20 +67372,13 @@
|
||||
"Lactobacillus bombicola" "Teicoplanin"
|
||||
"Lactobacillus bombicola" "Temocillin"
|
||||
"Lactobacillus bombicola" "Vancomycin"
|
||||
"Lactobacillus casei casei" "Aztreonam"
|
||||
"Lactobacillus casei casei" "Colistin"
|
||||
"Lactobacillus casei casei" "Nalidixic acid"
|
||||
"Lactobacillus casei casei" "Polymyxin B"
|
||||
"Lactobacillus casei casei" "Teicoplanin"
|
||||
"Lactobacillus casei casei" "Temocillin"
|
||||
"Lactobacillus casei casei" "Vancomycin"
|
||||
"Lactobacillus casei pseudoplantarum" "Aztreonam"
|
||||
"Lactobacillus casei pseudoplantarum" "Colistin"
|
||||
"Lactobacillus casei pseudoplantarum" "Nalidixic acid"
|
||||
"Lactobacillus casei pseudoplantarum" "Polymyxin B"
|
||||
"Lactobacillus casei pseudoplantarum" "Teicoplanin"
|
||||
"Lactobacillus casei pseudoplantarum" "Temocillin"
|
||||
"Lactobacillus casei pseudoplantarum" "Vancomycin"
|
||||
"Lactobacillus casei" "Aztreonam"
|
||||
"Lactobacillus casei" "Colistin"
|
||||
"Lactobacillus casei" "Nalidixic acid"
|
||||
"Lactobacillus casei" "Polymyxin B"
|
||||
"Lactobacillus casei" "Teicoplanin"
|
||||
"Lactobacillus casei" "Temocillin"
|
||||
"Lactobacillus casei" "Vancomycin"
|
||||
"Lactobacillus colini" "Aztreonam"
|
||||
"Lactobacillus colini" "Colistin"
|
||||
"Lactobacillus colini" "Nalidixic acid"
|
||||
@ -67731,13 +67673,13 @@
|
||||
"Lactobacillus rogosae" "Teicoplanin"
|
||||
"Lactobacillus rogosae" "Temocillin"
|
||||
"Lactobacillus rogosae" "Vancomycin"
|
||||
"Lactobacillus sakei sake" "Aztreonam"
|
||||
"Lactobacillus sakei sake" "Colistin"
|
||||
"Lactobacillus sakei sake" "Nalidixic acid"
|
||||
"Lactobacillus sakei sake" "Polymyxin B"
|
||||
"Lactobacillus sakei sake" "Teicoplanin"
|
||||
"Lactobacillus sakei sake" "Temocillin"
|
||||
"Lactobacillus sakei sake" "Vancomycin"
|
||||
"Lactobacillus sakei" "Aztreonam"
|
||||
"Lactobacillus sakei" "Colistin"
|
||||
"Lactobacillus sakei" "Nalidixic acid"
|
||||
"Lactobacillus sakei" "Polymyxin B"
|
||||
"Lactobacillus sakei" "Teicoplanin"
|
||||
"Lactobacillus sakei" "Temocillin"
|
||||
"Lactobacillus sakei" "Vancomycin"
|
||||
"Lactobacillus salivarius salivarius" "Aztreonam"
|
||||
"Lactobacillus salivarius salivarius" "Colistin"
|
||||
"Lactobacillus salivarius salivarius" "Nalidixic acid"
|
||||
@ -68824,11 +68766,6 @@
|
||||
"Lentzea albidocapillata" "Nalidixic acid"
|
||||
"Lentzea albidocapillata" "Polymyxin B"
|
||||
"Lentzea albidocapillata" "Temocillin"
|
||||
"Lentzea albidocapillata albidocapillata" "Aztreonam"
|
||||
"Lentzea albidocapillata albidocapillata" "Colistin"
|
||||
"Lentzea albidocapillata albidocapillata" "Nalidixic acid"
|
||||
"Lentzea albidocapillata albidocapillata" "Polymyxin B"
|
||||
"Lentzea albidocapillata albidocapillata" "Temocillin"
|
||||
"Lentzea albidocapillata violacea" "Aztreonam"
|
||||
"Lentzea albidocapillata violacea" "Colistin"
|
||||
"Lentzea albidocapillata violacea" "Nalidixic acid"
|
||||
@ -75113,11 +75050,6 @@
|
||||
"Mycobacterium intracellulare chimaera" "Nalidixic acid"
|
||||
"Mycobacterium intracellulare chimaera" "Polymyxin B"
|
||||
"Mycobacterium intracellulare chimaera" "Temocillin"
|
||||
"Mycobacterium intracellulare intracellulare" "Aztreonam"
|
||||
"Mycobacterium intracellulare intracellulare" "Colistin"
|
||||
"Mycobacterium intracellulare intracellulare" "Nalidixic acid"
|
||||
"Mycobacterium intracellulare intracellulare" "Polymyxin B"
|
||||
"Mycobacterium intracellulare intracellulare" "Temocillin"
|
||||
"Mycobacterium iranicum" "Aztreonam"
|
||||
"Mycobacterium iranicum" "Colistin"
|
||||
"Mycobacterium iranicum" "Nalidixic acid"
|
||||
@ -75718,11 +75650,6 @@
|
||||
"Mycoplasma cavipharyngis" "Nalidixic acid"
|
||||
"Mycoplasma cavipharyngis" "Polymyxin B"
|
||||
"Mycoplasma cavipharyngis" "Temocillin"
|
||||
"Mycoplasma coccoides" "Aztreonam"
|
||||
"Mycoplasma coccoides" "Colistin"
|
||||
"Mycoplasma coccoides" "Nalidixic acid"
|
||||
"Mycoplasma coccoides" "Polymyxin B"
|
||||
"Mycoplasma coccoides" "Temocillin"
|
||||
"Mycoplasma collis" "Aztreonam"
|
||||
"Mycoplasma collis" "Colistin"
|
||||
"Mycoplasma collis" "Nalidixic acid"
|
||||
@ -78993,11 +78920,6 @@
|
||||
"Nocardioides zhouii" "Nalidixic acid"
|
||||
"Nocardioides zhouii" "Polymyxin B"
|
||||
"Nocardioides zhouii" "Temocillin"
|
||||
"Nocardiopsaceae" "Aztreonam"
|
||||
"Nocardiopsaceae" "Colistin"
|
||||
"Nocardiopsaceae" "Nalidixic acid"
|
||||
"Nocardiopsaceae" "Polymyxin B"
|
||||
"Nocardiopsaceae" "Temocillin"
|
||||
"Nocardiopsis" "Aztreonam"
|
||||
"Nocardiopsis" "Colistin"
|
||||
"Nocardiopsis" "Nalidixic acid"
|
||||
@ -80958,11 +80880,6 @@
|
||||
"Paenibacillus graminis" "Nalidixic acid"
|
||||
"Paenibacillus graminis" "Polymyxin B"
|
||||
"Paenibacillus graminis" "Temocillin"
|
||||
"Paenibacillus granivorans" "Aztreonam"
|
||||
"Paenibacillus granivorans" "Colistin"
|
||||
"Paenibacillus granivorans" "Nalidixic acid"
|
||||
"Paenibacillus granivorans" "Polymyxin B"
|
||||
"Paenibacillus granivorans" "Temocillin"
|
||||
"Paenibacillus guangzhouensis" "Aztreonam"
|
||||
"Paenibacillus guangzhouensis" "Colistin"
|
||||
"Paenibacillus guangzhouensis" "Nalidixic acid"
|
||||
@ -90318,78 +90235,6 @@
|
||||
"Pseudomonas agarici" "Tedizolid"
|
||||
"Pseudomonas agarici" "Vancomycin"
|
||||
"Pseudomonas agarici" "Nafithromycin"
|
||||
"Pseudomonas akapageensis" "Acetylmidecamycin"
|
||||
"Pseudomonas akapageensis" "Acetylspiramycin"
|
||||
"Pseudomonas akapageensis" "Avoparcin"
|
||||
"Pseudomonas akapageensis" "Azithromycin"
|
||||
"Pseudomonas akapageensis" "Cefacetrile"
|
||||
"Pseudomonas akapageensis" "Cadazolid"
|
||||
"Pseudomonas akapageensis" "Cefaclor"
|
||||
"Pseudomonas akapageensis" "Cephradine"
|
||||
"Pseudomonas akapageensis" "Cephalothin"
|
||||
"Pseudomonas akapageensis" "Cefadroxil"
|
||||
"Pseudomonas akapageensis" "Cefonicid"
|
||||
"Pseudomonas akapageensis" "Clindamycin"
|
||||
"Pseudomonas akapageensis" "Clarithromycin"
|
||||
"Pseudomonas akapageensis" "Cefmetazole"
|
||||
"Pseudomonas akapageensis" "Ceforanide"
|
||||
"Pseudomonas akapageensis" "Cefprozil"
|
||||
"Pseudomonas akapageensis" "Cefroxadine"
|
||||
"Pseudomonas akapageensis" "Cefotiam"
|
||||
"Pseudomonas akapageensis" "Ceftezole"
|
||||
"Pseudomonas akapageensis" "Cefotetan"
|
||||
"Pseudomonas akapageensis" "Cefatrizine"
|
||||
"Pseudomonas akapageensis" "Cefuroxime axetil"
|
||||
"Pseudomonas akapageensis" "Cefuroxime"
|
||||
"Pseudomonas akapageensis" "Cycloserine"
|
||||
"Pseudomonas akapageensis" "Cefazedone"
|
||||
"Pseudomonas akapageensis" "Cefazolin"
|
||||
"Pseudomonas akapageensis" "Dalbavancin"
|
||||
"Pseudomonas akapageensis" "Dirithromycin"
|
||||
"Pseudomonas akapageensis" "Erythromycin"
|
||||
"Pseudomonas akapageensis" "Flurithromycin"
|
||||
"Pseudomonas akapageensis" "Cefoxitin"
|
||||
"Pseudomonas akapageensis" "Fusidic acid"
|
||||
"Pseudomonas akapageensis" "Gamithromycin"
|
||||
"Pseudomonas akapageensis" "Cephapirin"
|
||||
"Pseudomonas akapageensis" "Josamycin"
|
||||
"Pseudomonas akapageensis" "Kitasamycin"
|
||||
"Pseudomonas akapageensis" "Cephalexin"
|
||||
"Pseudomonas akapageensis" "Lincomycin"
|
||||
"Pseudomonas akapageensis" "Linezolid"
|
||||
"Pseudomonas akapageensis" "Loracarbef"
|
||||
"Pseudomonas akapageensis" "Cefamandole"
|
||||
"Pseudomonas akapageensis" "Miocamycin"
|
||||
"Pseudomonas akapageensis" "Meleumycin"
|
||||
"Pseudomonas akapageensis" "Midecamycin"
|
||||
"Pseudomonas akapageensis" "Norvancomycin"
|
||||
"Pseudomonas akapageensis" "Oleandomycin"
|
||||
"Pseudomonas akapageensis" "Oritavancin"
|
||||
"Pseudomonas akapageensis" "Benzylpenicillin"
|
||||
"Pseudomonas akapageensis" "Pristinamycin"
|
||||
"Pseudomonas akapageensis" "Pirlimycin"
|
||||
"Pseudomonas akapageensis" "Primycin"
|
||||
"Pseudomonas akapageensis" "Quinupristin/dalfopristin"
|
||||
"Pseudomonas akapageensis" "Ramoplanin"
|
||||
"Pseudomonas akapageensis" "Cefaloridine"
|
||||
"Pseudomonas akapageensis" "Rifampicin"
|
||||
"Pseudomonas akapageensis" "Rokitamycin"
|
||||
"Pseudomonas akapageensis" "Roxithromycin"
|
||||
"Pseudomonas akapageensis" "Solithromycin"
|
||||
"Pseudomonas akapageensis" "Spiramycin"
|
||||
"Pseudomonas akapageensis" "Teicoplanin"
|
||||
"Pseudomonas akapageensis" "Thiacetazone"
|
||||
"Pseudomonas akapageensis" "Tilmicosin"
|
||||
"Pseudomonas akapageensis" "Tildipirosin"
|
||||
"Pseudomonas akapageensis" "Telithromycin"
|
||||
"Pseudomonas akapageensis" "Telavancin"
|
||||
"Pseudomonas akapageensis" "Troleandomycin"
|
||||
"Pseudomonas akapageensis" "Tulathromycin"
|
||||
"Pseudomonas akapageensis" "Tylosin"
|
||||
"Pseudomonas akapageensis" "Tylvalosin"
|
||||
"Pseudomonas akapageensis" "Tedizolid"
|
||||
"Pseudomonas akapageensis" "Vancomycin"
|
||||
"Pseudomonas akapageensis" "Nafithromycin"
|
||||
"Pseudomonas alcaligenes" "Acetylmidecamycin"
|
||||
"Pseudomonas alcaligenes" "Acetylspiramycin"
|
||||
"Pseudomonas alcaligenes" "Avoparcin"
|
||||
@ -114794,36 +114639,6 @@
|
||||
"Sanguibacter suarezii" "Nalidixic acid"
|
||||
"Sanguibacter suarezii" "Polymyxin B"
|
||||
"Sanguibacter suarezii" "Temocillin"
|
||||
"Sanguibacteraceae" "Aztreonam"
|
||||
"Sanguibacteraceae" "Colistin"
|
||||
"Sanguibacteraceae" "Nalidixic acid"
|
||||
"Sanguibacteraceae" "Polymyxin B"
|
||||
"Sanguibacteraceae" "Temocillin"
|
||||
"Sapromyces" "Aztreonam"
|
||||
"Sapromyces" "Colistin"
|
||||
"Sapromyces" "Nalidixic acid"
|
||||
"Sapromyces" "Polymyxin B"
|
||||
"Sapromyces" "Temocillin"
|
||||
"Sapromyces androgynus" "Aztreonam"
|
||||
"Sapromyces androgynus" "Colistin"
|
||||
"Sapromyces androgynus" "Nalidixic acid"
|
||||
"Sapromyces androgynus" "Polymyxin B"
|
||||
"Sapromyces androgynus" "Temocillin"
|
||||
"Sapromyces dubius" "Aztreonam"
|
||||
"Sapromyces dubius" "Colistin"
|
||||
"Sapromyces dubius" "Nalidixic acid"
|
||||
"Sapromyces dubius" "Polymyxin B"
|
||||
"Sapromyces dubius" "Temocillin"
|
||||
"Sapromyces elongatus" "Aztreonam"
|
||||
"Sapromyces elongatus" "Colistin"
|
||||
"Sapromyces elongatus" "Nalidixic acid"
|
||||
"Sapromyces elongatus" "Polymyxin B"
|
||||
"Sapromyces elongatus" "Temocillin"
|
||||
"Sapromyces indicus" "Aztreonam"
|
||||
"Sapromyces indicus" "Colistin"
|
||||
"Sapromyces indicus" "Nalidixic acid"
|
||||
"Sapromyces indicus" "Polymyxin B"
|
||||
"Sapromyces indicus" "Temocillin"
|
||||
"Sarcina" "Aztreonam"
|
||||
"Sarcina" "Colistin"
|
||||
"Sarcina" "Nalidixic acid"
|
||||
@ -120612,38 +120427,6 @@
|
||||
"Streptococcus caprae" "Streptomycin"
|
||||
"Streptococcus caprae" "Temocillin"
|
||||
"Streptococcus caprae" "Tobramycin"
|
||||
"Streptococcus casseliflavus" "Amikacin/fosfomycin"
|
||||
"Streptococcus casseliflavus" "Amikacin"
|
||||
"Streptococcus casseliflavus" "Apramycin"
|
||||
"Streptococcus casseliflavus" "Arbekacin"
|
||||
"Streptococcus casseliflavus" "Astromicin"
|
||||
"Streptococcus casseliflavus" "Aztreonam"
|
||||
"Streptococcus casseliflavus" "Bekanamycin"
|
||||
"Streptococcus casseliflavus" "Ceftazidime"
|
||||
"Streptococcus casseliflavus" "Colistin"
|
||||
"Streptococcus casseliflavus" "Dibekacin"
|
||||
"Streptococcus casseliflavus" "Framycetin"
|
||||
"Streptococcus casseliflavus" "Fusidic acid"
|
||||
"Streptococcus casseliflavus" "Gentamicin"
|
||||
"Streptococcus casseliflavus" "Habekacin"
|
||||
"Streptococcus casseliflavus" "Hygromycin"
|
||||
"Streptococcus casseliflavus" "Isepamicin"
|
||||
"Streptococcus casseliflavus" "Kanamycin/cephalexin"
|
||||
"Streptococcus casseliflavus" "Kanamycin"
|
||||
"Streptococcus casseliflavus" "Micronomicin"
|
||||
"Streptococcus casseliflavus" "Nalidixic acid"
|
||||
"Streptococcus casseliflavus" "Neomycin"
|
||||
"Streptococcus casseliflavus" "Netilmicin"
|
||||
"Streptococcus casseliflavus" "Pentisomicin"
|
||||
"Streptococcus casseliflavus" "Propikacin"
|
||||
"Streptococcus casseliflavus" "Polymyxin B"
|
||||
"Streptococcus casseliflavus" "Plazomicin"
|
||||
"Streptococcus casseliflavus" "Ribostamycin"
|
||||
"Streptococcus casseliflavus" "Sisomicin"
|
||||
"Streptococcus casseliflavus" "Streptoduocin"
|
||||
"Streptococcus casseliflavus" "Streptomycin"
|
||||
"Streptococcus casseliflavus" "Temocillin"
|
||||
"Streptococcus casseliflavus" "Tobramycin"
|
||||
"Streptococcus castoreus" "Amikacin/fosfomycin"
|
||||
"Streptococcus castoreus" "Amikacin"
|
||||
"Streptococcus castoreus" "Apramycin"
|
||||
@ -124918,11 +124701,6 @@
|
||||
"Streptomyces albospinus" "Nalidixic acid"
|
||||
"Streptomyces albospinus" "Polymyxin B"
|
||||
"Streptomyces albospinus" "Temocillin"
|
||||
"Streptomyces albosporeus albosporeus" "Aztreonam"
|
||||
"Streptomyces albosporeus albosporeus" "Colistin"
|
||||
"Streptomyces albosporeus albosporeus" "Nalidixic acid"
|
||||
"Streptomyces albosporeus albosporeus" "Polymyxin B"
|
||||
"Streptomyces albosporeus albosporeus" "Temocillin"
|
||||
"Streptomyces albosporeus labilomyceticus" "Aztreonam"
|
||||
"Streptomyces albosporeus labilomyceticus" "Colistin"
|
||||
"Streptomyces albosporeus labilomyceticus" "Nalidixic acid"
|
||||
@ -125468,11 +125246,6 @@
|
||||
"Streptomyces cavourensis" "Nalidixic acid"
|
||||
"Streptomyces cavourensis" "Polymyxin B"
|
||||
"Streptomyces cavourensis" "Temocillin"
|
||||
"Streptomyces cavourensis cavourensis" "Aztreonam"
|
||||
"Streptomyces cavourensis cavourensis" "Colistin"
|
||||
"Streptomyces cavourensis cavourensis" "Nalidixic acid"
|
||||
"Streptomyces cavourensis cavourensis" "Polymyxin B"
|
||||
"Streptomyces cavourensis cavourensis" "Temocillin"
|
||||
"Streptomyces cellostaticus" "Aztreonam"
|
||||
"Streptomyces cellostaticus" "Colistin"
|
||||
"Streptomyces cellostaticus" "Nalidixic acid"
|
||||
@ -125548,11 +125321,6 @@
|
||||
"Streptomyces chryseus" "Nalidixic acid"
|
||||
"Streptomyces chryseus" "Polymyxin B"
|
||||
"Streptomyces chryseus" "Temocillin"
|
||||
"Streptomyces chrysomallus chrysomallus" "Aztreonam"
|
||||
"Streptomyces chrysomallus chrysomallus" "Colistin"
|
||||
"Streptomyces chrysomallus chrysomallus" "Nalidixic acid"
|
||||
"Streptomyces chrysomallus chrysomallus" "Polymyxin B"
|
||||
"Streptomyces chrysomallus chrysomallus" "Temocillin"
|
||||
"Streptomyces chrysomallus fumigatus" "Aztreonam"
|
||||
"Streptomyces chrysomallus fumigatus" "Colistin"
|
||||
"Streptomyces chrysomallus fumigatus" "Nalidixic acid"
|
||||
@ -125613,11 +125381,6 @@
|
||||
"Streptomyces cinnamoneus albosporus" "Nalidixic acid"
|
||||
"Streptomyces cinnamoneus albosporus" "Polymyxin B"
|
||||
"Streptomyces cinnamoneus albosporus" "Temocillin"
|
||||
"Streptomyces cinnamoneus cinnamoneus" "Aztreonam"
|
||||
"Streptomyces cinnamoneus cinnamoneus" "Colistin"
|
||||
"Streptomyces cinnamoneus cinnamoneus" "Nalidixic acid"
|
||||
"Streptomyces cinnamoneus cinnamoneus" "Polymyxin B"
|
||||
"Streptomyces cinnamoneus cinnamoneus" "Temocillin"
|
||||
"Streptomyces cirratus" "Aztreonam"
|
||||
"Streptomyces cirratus" "Colistin"
|
||||
"Streptomyces cirratus" "Nalidixic acid"
|
||||
@ -126088,11 +125851,6 @@
|
||||
"Streptomyces globisporus" "Nalidixic acid"
|
||||
"Streptomyces globisporus" "Polymyxin B"
|
||||
"Streptomyces globisporus" "Temocillin"
|
||||
"Streptomyces globisporus globisporus" "Aztreonam"
|
||||
"Streptomyces globisporus globisporus" "Colistin"
|
||||
"Streptomyces globisporus globisporus" "Nalidixic acid"
|
||||
"Streptomyces globisporus globisporus" "Polymyxin B"
|
||||
"Streptomyces globisporus globisporus" "Temocillin"
|
||||
"Streptomyces globosus" "Aztreonam"
|
||||
"Streptomyces globosus" "Colistin"
|
||||
"Streptomyces globosus" "Nalidixic acid"
|
||||
@ -126233,11 +125991,6 @@
|
||||
"Streptomyces griseus" "Nalidixic acid"
|
||||
"Streptomyces griseus" "Polymyxin B"
|
||||
"Streptomyces griseus" "Temocillin"
|
||||
"Streptomyces griseus griseus" "Aztreonam"
|
||||
"Streptomyces griseus griseus" "Colistin"
|
||||
"Streptomyces griseus griseus" "Nalidixic acid"
|
||||
"Streptomyces griseus griseus" "Polymyxin B"
|
||||
"Streptomyces griseus griseus" "Temocillin"
|
||||
"Streptomyces guanduensis" "Aztreonam"
|
||||
"Streptomyces guanduensis" "Colistin"
|
||||
"Streptomyces guanduensis" "Nalidixic acid"
|
||||
@ -126608,11 +126361,6 @@
|
||||
"Streptomyces lavendulae grasserius" "Nalidixic acid"
|
||||
"Streptomyces lavendulae grasserius" "Polymyxin B"
|
||||
"Streptomyces lavendulae grasserius" "Temocillin"
|
||||
"Streptomyces lavendulae lavendulae" "Aztreonam"
|
||||
"Streptomyces lavendulae lavendulae" "Colistin"
|
||||
"Streptomyces lavendulae lavendulae" "Nalidixic acid"
|
||||
"Streptomyces lavendulae lavendulae" "Polymyxin B"
|
||||
"Streptomyces lavendulae lavendulae" "Temocillin"
|
||||
"Streptomyces lavenduligriseus" "Aztreonam"
|
||||
"Streptomyces lavenduligriseus" "Colistin"
|
||||
"Streptomyces lavenduligriseus" "Nalidixic acid"
|
||||
@ -127883,11 +127631,6 @@
|
||||
"Streptomyces thermoviolaceus apingens" "Nalidixic acid"
|
||||
"Streptomyces thermoviolaceus apingens" "Polymyxin B"
|
||||
"Streptomyces thermoviolaceus apingens" "Temocillin"
|
||||
"Streptomyces thermoviolaceus thermoviolaceus" "Aztreonam"
|
||||
"Streptomyces thermoviolaceus thermoviolaceus" "Colistin"
|
||||
"Streptomyces thermoviolaceus thermoviolaceus" "Nalidixic acid"
|
||||
"Streptomyces thermoviolaceus thermoviolaceus" "Polymyxin B"
|
||||
"Streptomyces thermoviolaceus thermoviolaceus" "Temocillin"
|
||||
"Streptomyces thermovulgaris" "Aztreonam"
|
||||
"Streptomyces thermovulgaris" "Colistin"
|
||||
"Streptomyces thermovulgaris" "Nalidixic acid"
|
||||
@ -128463,36 +128206,11 @@
|
||||
"Streptoverticillium" "Nalidixic acid"
|
||||
"Streptoverticillium" "Polymyxin B"
|
||||
"Streptoverticillium" "Temocillin"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Aztreonam"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Colistin"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Nalidixic acid"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Polymyxin B"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Temocillin"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Aztreonam"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Colistin"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Nalidixic acid"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Polymyxin B"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Temocillin"
|
||||
"Streptoverticillium olivoreticuli olivoreticuli" "Aztreonam"
|
||||
"Streptoverticillium olivoreticuli olivoreticuli" "Colistin"
|
||||
"Streptoverticillium olivoreticuli olivoreticuli" "Nalidixic acid"
|
||||
"Streptoverticillium olivoreticuli olivoreticuli" "Polymyxin B"
|
||||
"Streptoverticillium olivoreticuli olivoreticuli" "Temocillin"
|
||||
"Streptoverticillium reticulum protomycicum" "Aztreonam"
|
||||
"Streptoverticillium reticulum protomycicum" "Colistin"
|
||||
"Streptoverticillium reticulum protomycicum" "Nalidixic acid"
|
||||
"Streptoverticillium reticulum protomycicum" "Polymyxin B"
|
||||
"Streptoverticillium reticulum protomycicum" "Temocillin"
|
||||
"Streptoverticillium verticillium quintum" "Aztreonam"
|
||||
"Streptoverticillium verticillium quintum" "Colistin"
|
||||
"Streptoverticillium verticillium quintum" "Nalidixic acid"
|
||||
"Streptoverticillium verticillium quintum" "Polymyxin B"
|
||||
"Streptoverticillium verticillium quintum" "Temocillin"
|
||||
"Streptoverticillium verticillium tsukushiense" "Aztreonam"
|
||||
"Streptoverticillium verticillium tsukushiense" "Colistin"
|
||||
"Streptoverticillium verticillium tsukushiense" "Nalidixic acid"
|
||||
"Streptoverticillium verticillium tsukushiense" "Polymyxin B"
|
||||
"Streptoverticillium verticillium tsukushiense" "Temocillin"
|
||||
"Streptoverticillium cinnamoneum" "Aztreonam"
|
||||
"Streptoverticillium cinnamoneum" "Colistin"
|
||||
"Streptoverticillium cinnamoneum" "Nalidixic acid"
|
||||
"Streptoverticillium cinnamoneum" "Polymyxin B"
|
||||
"Streptoverticillium cinnamoneum" "Temocillin"
|
||||
"Subdoligranulum" "Aztreonam"
|
||||
"Subdoligranulum" "Colistin"
|
||||
"Subdoligranulum" "Nalidixic acid"
|
||||
@ -129109,11 +128827,6 @@
|
||||
"Tatumella terrea" "Tedizolid"
|
||||
"Tatumella terrea" "Vancomycin"
|
||||
"Tatumella terrea" "Nafithromycin"
|
||||
"Tenericutes" "Aztreonam"
|
||||
"Tenericutes" "Colistin"
|
||||
"Tenericutes" "Nalidixic acid"
|
||||
"Tenericutes" "Polymyxin B"
|
||||
"Tenericutes" "Temocillin"
|
||||
"Tenggerimyces" "Aztreonam"
|
||||
"Tenggerimyces" "Colistin"
|
||||
"Tenggerimyces" "Nalidixic acid"
|
||||
@ -130753,11 +130466,6 @@
|
||||
"Tropheryma whipplei" "Nalidixic acid"
|
||||
"Tropheryma whipplei" "Polymyxin B"
|
||||
"Tropheryma whipplei" "Temocillin"
|
||||
"Tropherymataceae" "Aztreonam"
|
||||
"Tropherymataceae" "Colistin"
|
||||
"Tropherymataceae" "Nalidixic acid"
|
||||
"Tropherymataceae" "Polymyxin B"
|
||||
"Tropherymataceae" "Temocillin"
|
||||
"Tropicihabitans" "Aztreonam"
|
||||
"Tropicihabitans" "Colistin"
|
||||
"Tropicihabitans" "Nalidixic acid"
|
||||
@ -133267,11 +132975,6 @@
|
||||
"Yaniella soli" "Nalidixic acid"
|
||||
"Yaniella soli" "Polymyxin B"
|
||||
"Yaniella soli" "Temocillin"
|
||||
"Yaniellaceae" "Aztreonam"
|
||||
"Yaniellaceae" "Colistin"
|
||||
"Yaniellaceae" "Nalidixic acid"
|
||||
"Yaniellaceae" "Polymyxin B"
|
||||
"Yaniellaceae" "Temocillin"
|
||||
"Yersinia" "Acetylmidecamycin"
|
||||
"Yersinia" "Acetylspiramycin"
|
||||
"Yersinia" "Avoparcin"
|
||||
|
||||
Binary file not shown.
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@ -1 +1 @@
|
||||
4108363bb220b8f85ab924afb8ffbbcf
|
||||
5ac1152c166d5d4f5763547d948fce79
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@ -1 +0,0 @@
|
||||
b57c9cc7380a233a2616a80e8e904a81
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
File diff suppressed because it is too large
Load Diff
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
File diff suppressed because it is too large
Load Diff
Binary file not shown.
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
@ -103,9 +107,9 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
|
||||
get_mo <- function(x) {
|
||||
for (i in seq_len(length(x))) {
|
||||
y <- trimws(unlist(strsplit(x[i], "(,|and)")))
|
||||
y <- trimws(gsub("[(].*[)]", "", y))
|
||||
y <- suppressWarnings(suppressMessages(as.mo(y, allow_uncertain = FALSE)))
|
||||
y <- trimws2(unlist(strsplit(x[i], "(,|and)")))
|
||||
y <- trimws2(gsub("[(].*[)]", "", y))
|
||||
y <- suppressWarnings(suppressMessages(as.mo(y)))
|
||||
if (!is.null(mo_uncertainties())) uncertainties <<- add_uncertainties(uncertainties, mo_uncertainties())
|
||||
y <- y[!is.na(y) & y != "UNKNOWN"]
|
||||
x[i] <- paste(y, collapse = "|")
|
||||
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,513 +0,0 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# #
|
||||
# Visit our website for the full manual and a complete tutorial about #
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# Go to https://lpsn.dsmz.de/downloads (register first) and download the latest CSV file.
|
||||
|
||||
file_location <- "data-raw/taxonomy.csv"
|
||||
|
||||
library(tidyverse)
|
||||
library(AMR)
|
||||
|
||||
# these should still work after this update
|
||||
test_fullname <- microorganisms$fullname
|
||||
test_mo <- microorganisms$mo
|
||||
|
||||
|
||||
# Helper functions --------------------------------------------------------
|
||||
|
||||
get_author_year <- function(ref) {
|
||||
# Only keep first author, e.g. transform 'Smith, Jones, 2011' to 'Smith et al., 2011'
|
||||
|
||||
authors2 <- iconv(ref, from = "UTF-8", to = "ASCII//TRANSLIT")
|
||||
authors2 <- gsub(" ?\\(Approved Lists [0-9]+\\) ?", " () ", authors2)
|
||||
authors2 <- gsub(" [)(]+ $", "", authors2)
|
||||
# remove leading and trailing brackets
|
||||
authors2 <- trimws(gsub("^[(](.*)[)]$", "\\1", authors2))
|
||||
# only take part after brackets if there's a name
|
||||
authors2 <- ifelse(grepl(".*[)] [a-zA-Z]+.*", authors2),
|
||||
gsub(".*[)] (.*)", "\\1", authors2),
|
||||
authors2
|
||||
)
|
||||
# get year from last 4 digits
|
||||
lastyear <- as.integer(gsub(".*([0-9]{4})$", "\\1", authors2))
|
||||
# can never be later than now
|
||||
lastyear <- ifelse(lastyear > as.integer(format(Sys.Date(), "%Y")),
|
||||
NA,
|
||||
lastyear
|
||||
)
|
||||
# get authors without last year
|
||||
authors <- gsub("(.*)[0-9]{4}$", "\\1", authors2)
|
||||
# remove nonsense characters from names
|
||||
authors <- gsub("[^a-zA-Z,'& -]", "", authors)
|
||||
# remove trailing and leading spaces
|
||||
authors <- trimws(authors)
|
||||
# only keep first author and replace all others by 'et al'
|
||||
authors <- gsub("(,| and| et| &| ex| emend\\.?) .*", " et al.", authors)
|
||||
# et al. always with ending dot
|
||||
authors <- gsub(" et al\\.?", " et al.", authors)
|
||||
authors <- gsub(" ?,$", "", authors)
|
||||
# don't start with 'sensu' or 'ehrenb'
|
||||
authors <- gsub("^(sensu|Ehrenb.?) ", "", authors, ignore.case = TRUE)
|
||||
# no initials, only surname
|
||||
authors <- gsub("^([A-Z]+ )+", "", authors, ignore.case = FALSE)
|
||||
# combine author and year if year is available
|
||||
ref <- ifelse(!is.na(lastyear),
|
||||
paste0(authors, ", ", lastyear),
|
||||
authors
|
||||
)
|
||||
# fix beginning and ending
|
||||
ref <- gsub(", $", "", ref)
|
||||
ref <- gsub("^, ", "", ref)
|
||||
ref <- gsub("^(emend|et al.,?)", "", ref)
|
||||
ref <- trimws(ref)
|
||||
ref <- gsub("'", "", ref)
|
||||
|
||||
# a lot start with a lowercase character - fix that
|
||||
ref[!grepl("^d[A-Z]", ref)] <- gsub("^([a-z])", "\\U\\1", ref[!grepl("^d[A-Z]", ref)], perl = TRUE)
|
||||
# specific one for the French that are named dOrbigny
|
||||
ref[grepl("^d[A-Z]", ref)] <- gsub("^d", "d'", ref[grepl("^d[A-Z]", ref)])
|
||||
ref <- gsub(" +", " ", ref)
|
||||
ref
|
||||
}
|
||||
|
||||
df_remove_nonASCII <- function(df) {
|
||||
# Remove non-ASCII characters (these are not allowed by CRAN)
|
||||
df %>%
|
||||
mutate_if(is.character, iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
|
||||
# also remove invalid characters
|
||||
mutate_if(is.character, ~ gsub("[\"'`]+", "", .)) %>%
|
||||
AMR:::dataset_UTF8_to_ASCII()
|
||||
}
|
||||
|
||||
abbreviate_mo <- function(x, minlength = 5, prefix = "", ...) {
|
||||
# keep a starting Latin ae
|
||||
suppressWarnings(
|
||||
gsub("^ae", "\u00E6\u00E6", x, ignore.case = TRUE) %>%
|
||||
abbreviate(
|
||||
minlength = minlength,
|
||||
use.classes = TRUE,
|
||||
method = "both.sides", ...
|
||||
) %>%
|
||||
paste0(prefix, .) %>%
|
||||
toupper() %>%
|
||||
gsub("(\u00C6|\u00E6)+", "AE", .)
|
||||
)
|
||||
}
|
||||
|
||||
# Read data ---------------------------------------------------------------
|
||||
|
||||
taxonomy <- read_csv(file_location)
|
||||
|
||||
# Create synonyms ---------------------------------------------------------
|
||||
|
||||
new_synonyms <- taxonomy %>%
|
||||
left_join(taxonomy,
|
||||
by = c("record_lnk" = "record_no"),
|
||||
suffix = c("", ".new")
|
||||
) %>%
|
||||
filter(!is.na(record_lnk)) %>%
|
||||
mutate_all(~ ifelse(is.na(.), "", .)) %>%
|
||||
transmute(
|
||||
fullname = trimws(paste(genus_name, sp_epithet, subsp_epithet)),
|
||||
fullname_new = trimws(paste(genus_name.new, sp_epithet.new, subsp_epithet.new)),
|
||||
ref = get_author_year(authors),
|
||||
prevalence = 0
|
||||
) %>%
|
||||
distinct(fullname, .keep_all = TRUE) %>%
|
||||
filter(fullname != fullname_new) %>%
|
||||
# this part joins this table to itself to correct for entries that had >1 renames,
|
||||
# such as:
|
||||
# Bacteroides tectum -> Bacteroides tectus -> Bacteroides pyogenes
|
||||
left_join(., .,
|
||||
by = c("fullname_new" = "fullname"),
|
||||
suffix = c("", ".2")
|
||||
) %>%
|
||||
mutate(
|
||||
fullname_new = ifelse(!is.na(fullname_new.2), fullname_new.2, fullname_new),
|
||||
ref = ifelse(!is.na(ref.2), ref.2, ref)
|
||||
) %>%
|
||||
select(-ends_with(".2"))
|
||||
|
||||
mo_became_synonym <- microorganisms %>%
|
||||
filter(fullname %in% new_synonyms$fullname)
|
||||
|
||||
updated_microorganisms <- taxonomy %>%
|
||||
filter(is.na(record_lnk)) %>%
|
||||
mutate_all(~ ifelse(is.na(.), "", .)) %>%
|
||||
transmute(
|
||||
mo = "",
|
||||
fullname = trimws(paste(genus_name, sp_epithet, subsp_epithet)),
|
||||
kingdom = "Bacteria",
|
||||
phylum = "",
|
||||
class = "",
|
||||
order = "",
|
||||
family = "",
|
||||
genus = trimws(genus_name),
|
||||
species = trimws(replace_na(sp_epithet, "")),
|
||||
subspecies = trimws(replace_na(subsp_epithet, "")),
|
||||
rank = case_when(
|
||||
subspecies == "" & species == "" ~ "genus",
|
||||
subspecies == "" ~ "species",
|
||||
TRUE ~ "subsp."
|
||||
),
|
||||
ref = get_author_year(authors),
|
||||
species_id = as.character(record_no),
|
||||
source = "LPSN",
|
||||
prevalence = 0,
|
||||
snomed = NA
|
||||
)
|
||||
|
||||
new_microorganisms <- updated_microorganisms %>%
|
||||
filter(!fullname %in% microorganisms$fullname)
|
||||
|
||||
genera_with_mo_code <- updated_microorganisms %>%
|
||||
filter(genus %in% (microorganisms %>% filter(kingdom == "Bacteria", rank == "genus") %>% pull(genus))) %>%
|
||||
distinct(genus) %>%
|
||||
left_join(microorganisms %>% filter(kingdom == "Bacteria", rank == "genus") %>% select(mo, genus),
|
||||
by = "genus"
|
||||
)
|
||||
|
||||
genera_without_mo_code <- updated_microorganisms %>%
|
||||
filter(!genus %in% genera_with_mo_code$genus) %>%
|
||||
pull(genus) %>%
|
||||
unique()
|
||||
|
||||
genera_without_mo_code_abbr <- genera_without_mo_code %>% abbreviate_mo(5, prefix = "B_")
|
||||
genera_without_mo_code_abbr[genera_without_mo_code_abbr %in% microorganisms$mo] <- abbreviate_mo(genera_without_mo_code[genera_without_mo_code_abbr %in% microorganisms$mo], 6, prefix = "B_")
|
||||
genera_without_mo_code_abbr[genera_without_mo_code_abbr %in% microorganisms$mo] <- abbreviate_mo(genera_without_mo_code[genera_without_mo_code_abbr %in% microorganisms$mo], 7, prefix = "B_")
|
||||
# all unique??
|
||||
sum(genera_without_mo_code_abbr %in% microorganisms$mo) == 0
|
||||
|
||||
genus_abb <- tibble(
|
||||
genus = genera_without_mo_code,
|
||||
abbr = genera_without_mo_code_abbr
|
||||
) %>%
|
||||
bind_rows(microorganisms %>%
|
||||
filter(kingdom == "Bacteria", rank == "genus", !genus %in% genera_without_mo_code) %>%
|
||||
transmute(genus, abbr = as.character(mo))) %>%
|
||||
arrange(genus)
|
||||
|
||||
|
||||
# Update taxonomy ---------------------------------------------------------
|
||||
|
||||
# fill in the taxonomy of new genera
|
||||
updated_taxonomy <- tibble(
|
||||
phylum = character(0),
|
||||
class = character(0),
|
||||
order = character(0),
|
||||
family = character(0),
|
||||
genus = character(0)
|
||||
)
|
||||
for (page in LETTERS) {
|
||||
message("Downloading page ", page, "... ", appendLF = FALSE)
|
||||
url <- paste0("https://lpsn.dsmz.de/genus?page=", page)
|
||||
|
||||
x <- xml2::read_html(url) %>%
|
||||
rvest::html_node(".main-list") %>%
|
||||
# evety list element with a set <id> attribute
|
||||
rvest::html_nodes("li[id]")
|
||||
for (i in seq_len(length(x))) {
|
||||
txt <- x %>%
|
||||
magrittr::extract2(i) %>%
|
||||
rvest::html_text() %>%
|
||||
gsub("\\[[A-Za-z]+, no [a-z]+\\]", "NA", .) %>%
|
||||
gsub("Candidatus ", "", ., fixed = TRUE) %>%
|
||||
gsub("[ \t\r\n\"]+", "|", .) %>%
|
||||
gsub("\\|ShowHide.*", "", .) %>%
|
||||
gsub("[\\[\\]]", "", ., fixed = TRUE) %>%
|
||||
gsub("^\\|", "", .) %>%
|
||||
strsplit("|", fixed = TRUE) %>%
|
||||
unlist()
|
||||
txt[txt == "NA"] <- ""
|
||||
txt <- gsub("[^A-Za-z]+", "", txt)
|
||||
updated_taxonomy <- updated_taxonomy %>%
|
||||
bind_rows(tibble(
|
||||
phylum = txt[2],
|
||||
class = txt[3],
|
||||
order = txt[4],
|
||||
family = txt[5],
|
||||
genus = txt[6]
|
||||
))
|
||||
}
|
||||
message(length(x), " entries (total ", nrow(updated_taxonomy), ")")
|
||||
}
|
||||
|
||||
# Create new microorganisms -----------------------------------------------
|
||||
|
||||
new_microorganisms <- new_microorganisms %>%
|
||||
left_join(genus_abb, by = "genus") %>%
|
||||
group_by(genus) %>%
|
||||
mutate(species_abb = abbreviate_mo(species, 4)) %>%
|
||||
group_by(genus, species) %>%
|
||||
mutate(subspecies_abb = abbreviate_mo(subspecies, 4)) %>%
|
||||
ungroup() %>%
|
||||
mutate(
|
||||
mo = paste(abbr, species_abb, subspecies_abb, sep = "_"),
|
||||
mo = gsub("_+$", "", mo)
|
||||
) %>%
|
||||
select(-matches("abb"))
|
||||
|
||||
# add taxonomy new microorganisms
|
||||
MOs <- microorganisms %>%
|
||||
mutate(mo = as.character(mo)) %>%
|
||||
bind_rows(new_microorganisms) %>%
|
||||
arrange(fullname)
|
||||
|
||||
# unique MO codes
|
||||
MOs$mo[which(duplicated(MOs$mo))] <- paste0(MOs$mo[which(duplicated(MOs$mo))], 1)
|
||||
# all unique?
|
||||
!any(duplicated(MOs$mo))
|
||||
|
||||
MOs <- MOs %>%
|
||||
# remove entries that are now a synonym
|
||||
filter(!fullname %in% new_synonyms$fullname) %>%
|
||||
# update the taxonomy
|
||||
left_join(updated_taxonomy, by = "genus", suffix = c("", ".new")) %>%
|
||||
mutate(
|
||||
phylum = ifelse(!is.na(phylum.new), phylum.new, phylum),
|
||||
class = ifelse(!is.na(class.new), class.new, class),
|
||||
order = ifelse(!is.na(order.new), order.new, order),
|
||||
family = ifelse(!is.na(family.new), family.new, family)
|
||||
) %>%
|
||||
select(-ends_with(".new")) %>%
|
||||
# update prevalence based on taxonomy (Berends et al., 2021)
|
||||
mutate(prevalence = case_when(
|
||||
class == "Gammaproteobacteria" |
|
||||
genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
|
||||
~ 1,
|
||||
kingdom %in% c("Archaea", "Bacteria", "Chromista", "Fungi") &
|
||||
(phylum %in% c(
|
||||
"Proteobacteria",
|
||||
"Firmicutes",
|
||||
"Actinobacteria",
|
||||
"Sarcomastigophora"
|
||||
) |
|
||||
genus %in% MO_PREVALENT_GENERA |
|
||||
rank %in% c("kingdom", "phylum", "class", "order", "family"))
|
||||
~ 2,
|
||||
TRUE ~ 3
|
||||
))
|
||||
|
||||
# add all mssing genera, families and orders
|
||||
MOs <- MOs %>%
|
||||
bind_rows(
|
||||
MOs %>%
|
||||
arrange(genus, species) %>%
|
||||
distinct(genus, .keep_all = TRUE) %>%
|
||||
filter(rank == "species", source != "manually added") %>%
|
||||
mutate(
|
||||
mo = gsub("^([A-Z]_[A-Z]+)_.*", "\\1", mo),
|
||||
fullname = genus,
|
||||
species = "",
|
||||
subspecies = "",
|
||||
rank = "genus",
|
||||
species_id = "",
|
||||
snomed = NA,
|
||||
ref = NA_character_
|
||||
),
|
||||
MOs %>%
|
||||
group_by(family) %>%
|
||||
filter(!any(rank == "family") & n() > 1) %>%
|
||||
ungroup() %>%
|
||||
arrange(family) %>%
|
||||
distinct(family, .keep_all = TRUE) %>%
|
||||
filter(!family %in% c("", NA), source != "manually added") %>%
|
||||
mutate(
|
||||
mo = paste0(
|
||||
substr(kingdom, 1, 1), "_[FAM]_",
|
||||
abbreviate(family,
|
||||
minlength = 8,
|
||||
use.classes = TRUE,
|
||||
method = "both.sides",
|
||||
strict = FALSE
|
||||
)
|
||||
),
|
||||
mo = toupper(mo),
|
||||
fullname = family,
|
||||
genus = "",
|
||||
species = "",
|
||||
subspecies = "",
|
||||
rank = "family",
|
||||
species_id = "",
|
||||
snomed = NA,
|
||||
ref = NA_character_
|
||||
),
|
||||
MOs %>%
|
||||
group_by(order) %>%
|
||||
filter(!any(rank == "order") & n() > 1) %>%
|
||||
ungroup() %>%
|
||||
arrange(order) %>%
|
||||
distinct(order, .keep_all = TRUE) %>%
|
||||
filter(!order %in% c("", NA), source != "manually added") %>%
|
||||
mutate(
|
||||
mo = paste0(
|
||||
substr(kingdom, 1, 1), "_[ORD]_",
|
||||
abbreviate(order,
|
||||
minlength = 8,
|
||||
use.classes = TRUE,
|
||||
method = "both.sides",
|
||||
strict = FALSE
|
||||
)
|
||||
),
|
||||
mo = toupper(mo),
|
||||
fullname = order,
|
||||
family = "",
|
||||
genus = "",
|
||||
species = "",
|
||||
subspecies = "",
|
||||
rank = "order",
|
||||
species_id = "",
|
||||
snomed = NA,
|
||||
ref = NA_character_
|
||||
)
|
||||
) %>%
|
||||
arrange(fullname)
|
||||
|
||||
# clean up
|
||||
MOs <- MOs %>%
|
||||
df_remove_nonASCII()
|
||||
|
||||
# Add LPSN record IDs -----------------------------------------------------
|
||||
|
||||
records_ids <- taxonomy %>%
|
||||
mutate(across(1:3, function(x) {
|
||||
x[is.na(x)] <- ""
|
||||
x
|
||||
}),
|
||||
fullname = trimws(paste(genus_name, sp_epithet, subsp_epithet))
|
||||
) %>%
|
||||
transmute(fullname, species_id = as.numeric(record_no)) %>%
|
||||
arrange(fullname, species_id) %>%
|
||||
distinct(fullname, .keep_all = TRUE)
|
||||
message("Adding ", sum(records_ids$fullname %in% microorganisms$fullname), " LPSN record IDs")
|
||||
MOs <- MOs %>%
|
||||
select(-species_id) %>%
|
||||
left_join(records_ids, by = "fullname") %>%
|
||||
relocate(species_id, .after = ref) %>%
|
||||
mutate(source = case_when(
|
||||
!is.na(species_id) ~ "LPSN",
|
||||
source %unlike% "manual" ~ "CoL",
|
||||
TRUE ~ source
|
||||
))
|
||||
|
||||
# Merge synonyms ----------------------------------------------------------
|
||||
|
||||
# remove synonyms that are now valid names
|
||||
MOs.old <- microorganisms.old %>%
|
||||
# add new synonyms
|
||||
bind_rows(new_synonyms) %>%
|
||||
filter(!fullname %in% MOs$fullname) %>%
|
||||
arrange(fullname) %>%
|
||||
distinct(fullname, fullname_new, .keep_all = TRUE) %>%
|
||||
# add prevalence to old taxonomic names
|
||||
select(-prevalence) %>%
|
||||
left_join(MOs %>% select(fullname, prevalence), by = c("fullname_new" = "fullname")) %>%
|
||||
# clean up
|
||||
df_remove_nonASCII()
|
||||
|
||||
message("microorganisms new: ", sum(!MOs$fullname %in% c(microorganisms$fullname, MOs.old$fullname)))
|
||||
message("microorganisms renamed: ", sum(!MOs.old$fullname %in% microorganisms.old$fullname))
|
||||
|
||||
|
||||
# Save --------------------------------------------------------------------
|
||||
|
||||
# class <mo>
|
||||
class(MOs$mo) <- c("mo", "character")
|
||||
|
||||
microorganisms <- MOs
|
||||
microorganisms.old <- MOs.old
|
||||
|
||||
# --- Moraxella catarrhalis was named Branhamella catarrhalis (Catlin, 1970), but this is unaccepted in clinical microbiology
|
||||
# we keep them both
|
||||
microorganisms <- microorganisms %>%
|
||||
bind_rows(microorganisms %>%
|
||||
filter(fullname == "Branhamella catarrhalis") %>%
|
||||
mutate(
|
||||
mo = "B_MRXLL_CTRR",
|
||||
fullname = "Moraxella catarrhalis",
|
||||
genus = "Moraxella",
|
||||
ref = "Henriksen et al., 1968",
|
||||
species_id = "a374f6f0868e05f9c0f5077b60ee0a6c",
|
||||
snomed = as.list(24226003)
|
||||
)) %>%
|
||||
arrange(fullname) %>%
|
||||
df_remove_nonASCII()
|
||||
microorganisms.old <- microorganisms.old %>%
|
||||
filter(fullname != "Moraxella catarrhalis")
|
||||
# ---
|
||||
|
||||
# (this would be a great moment to run data-raw/snomed.R as well)
|
||||
|
||||
# on the server, do:
|
||||
usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
|
||||
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2, compress = "xz")
|
||||
rm(microorganisms)
|
||||
rm(microorganisms.old)
|
||||
|
||||
# DON'T FORGET TO UPDATE R/globals.R!
|
||||
|
||||
# load new data sets
|
||||
devtools::load_all(".")
|
||||
|
||||
# reset previously changed mo codes
|
||||
rsi_translation$mo <- as.mo(rsi_translation$mo, language = NULL)
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE, version = 2, compress = "xz")
|
||||
rm(rsi_translation)
|
||||
|
||||
microorganisms.codes$mo <- as.mo(microorganisms.codes$mo, language = NULL)
|
||||
# new NAs introduced?
|
||||
any(is.na(microorganisms.codes$mo))
|
||||
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2, compress = "xz")
|
||||
rm(microorganisms.codes)
|
||||
|
||||
example_isolates$mo <- as.mo(example_isolates$mo, language = NULL)
|
||||
usethis::use_data(example_isolates, overwrite = TRUE, version = 2)
|
||||
rm(example_isolates)
|
||||
|
||||
intrinsic_resistant$microorganism <- suppressMessages(mo_name(intrinsic_resistant$microorganism))
|
||||
usethis::use_data(intrinsic_resistant, overwrite = TRUE, version = 2)
|
||||
rm(intrinsic_resistant)
|
||||
|
||||
# load new data sets again
|
||||
devtools::load_all(".")
|
||||
source("data-raw/_pre_commit_hook.R")
|
||||
devtools::load_all(".")
|
||||
|
||||
|
||||
# Test updates ------------------------------------------------------------
|
||||
|
||||
# and check: these codes should not be missing (will otherwise 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$mo)
|
||||
AMR::example_isolates %>% filter(!mo %in% MOs$mo)
|
||||
|
||||
# Don't forget to add SNOMED codes! (data-raw/snomed.R)
|
||||
|
||||
# run the unit tests
|
||||
Sys.setenv(NOT_CRAN = "true")
|
||||
testthat::test_file("tests/testthat/test-data.R")
|
||||
testthat::test_file("tests/testthat/test-mo.R")
|
||||
testthat::test_file("tests/testthat/test-mo_property.R")
|
||||
@ -1,12 +1,16 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -1,77 +0,0 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# #
|
||||
# Visit our website for the full manual and a complete tutorial about #
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
library(AMR)
|
||||
library(tidyverse)
|
||||
|
||||
# we will use Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)
|
||||
# as a source, which copies directly from the latest US SNOMED CT version
|
||||
# - go to https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009
|
||||
# - check that current online version is higher than SNOMED_VERSION$current_version
|
||||
# - if so, click on 'Download Value Set', choose 'TXT'
|
||||
snomed <- read_tsv("data-raw/SNOMED_PHVS_Microorganism_CDC_V12.txt", skip = 3) %>%
|
||||
select(1:2) %>%
|
||||
set_names(c("snomed", "mo"))
|
||||
|
||||
# save all valid genera, species and subspecies
|
||||
vctr <- unique(unlist(strsplit(c(microorganisms$fullname, microorganisms.old$fullname), " ")))
|
||||
vctr <- tolower(vctr[vctr %like% "^[a-z]+$"])
|
||||
|
||||
# remove all parts of the name that are no valid values in genera, species or subspecies
|
||||
# this takes ~20 seconds
|
||||
snomed <- snomed %>%
|
||||
mutate(
|
||||
fullname = vapply(
|
||||
FUN.VALUE = character(1),
|
||||
# split on space and/or comma
|
||||
strsplit(tolower(mo), "[ ,]"),
|
||||
function(x) trimws(paste0(x[x %in% vctr], collapse = " "))
|
||||
),
|
||||
# remove " group"
|
||||
fullname = gsub(" group", "", fullname, fixed = TRUE)
|
||||
)
|
||||
|
||||
snomed_keep <- snomed %>%
|
||||
filter(fullname %in% tolower(c(microorganisms$fullname, microorganisms.old$fullname))) %>%
|
||||
group_by(fullname_lower = fullname) %>%
|
||||
summarise(snomed = list(snomed))
|
||||
|
||||
message(nrow(snomed_keep), " MO's will get a SNOMED code.")
|
||||
|
||||
# save to microorganisms data set
|
||||
microorganisms <- microorganisms %>%
|
||||
# remove old snomed
|
||||
select(-snomed) %>%
|
||||
# create dummy var for joining
|
||||
mutate(fullname_lower = tolower(fullname)) %>%
|
||||
# join new snomed
|
||||
left_join(snomed_keep) %>%
|
||||
# remove dummy var
|
||||
select(-fullname_lower) %>%
|
||||
AMR:::dataset_UTF8_to_ASCII()
|
||||
|
||||
# don't forget to update the version number in SNOMED_VERSION in ./R/globals.R!
|
||||
|
||||
# usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
|
||||
BIN
data-raw/taxonomy.rds
Normal file
BIN
data-raw/taxonomy.rds
Normal file
Binary file not shown.
BIN
data-raw/taxonomy_gbif.rds
Normal file
BIN
data-raw/taxonomy_gbif.rds
Normal file
Binary file not shown.
BIN
data-raw/taxonomy_lpsn.rds
Normal file
BIN
data-raw/taxonomy_lpsn.rds
Normal file
Binary file not shown.
@ -32,8 +32,8 @@ biotype TRUE TRUE FALSE FALSE 生物型 biotype Biotyp βιότυπος biotip
|
||||
vegetative TRUE TRUE FALSE FALSE 无性系 vegetativ vegetatief végétatif vegetativ βλαστικός vegetativo ([[ ]*?)グループ wegetatywna vegetativo вегетативный vegetativo vegetativ vejetatif вегетативний
|
||||
([([ ]*?)group TRUE TRUE FALSE FALSE ([([]*?)组 \\1gruppe \\1groep \\1groupe \\1Gruppe ([([ ]*?)ομάδα \\1gruppo ([([ ]*?)grupa \\1grupo \\1группа \\1grupo \\1grupp ([([ ]*?)grup \\1група
|
||||
([([ ]*?)Group TRUE TRUE FALSE FALSE ([([]*?)组 \\1Gruppe \\1Groep \\1Groupe \\1Gruppe ([([ ]*;)ομάδα \\1Gruppo ない ([([ ]*?)Grupa \\1Grupo \\1Группа \\1Grupo \\1Grupp ([([ ]*?)Grup \\1Група
|
||||
no .*growth TRUE FALSE FALSE FALSE 无.*生长 ingen .*vækst geen .*groei pas .*croissance keine? .*wachstum όχι .*αύξηση sem .*crescimento 中間体 brak .*wzrostu sem .*crescimento отсутствие.*роста no .*crecimientonon ingen .*tillväxt büyüme yok відсутність .*росту
|
||||
no|not TRUE FALSE FALSE FALSE 不|不 nej|ikke geen|niet non keine? no|not sem 感受性の高い、被ばく量の増加 nie|nie sem нет? no|sin nej|inte hayır|değil|hayir|degil ні
|
||||
no .*growth FALSE FALSE FALSE FALSE 无.*生长 ingen .*vækst geen .*groei pas .*croissance keine(|n|m|r|s)|nicht .*wachstum όχι .*αύξηση sem .*crescimento 中間体 brak .*wzrostu sem .*crescimento отсутствие.*роста no .*crecimientonon ingen .*tillväxt büyüme yok відсутність .*росту
|
||||
no|not FALSE FALSE FALSE FALSE 不|不 nej|ikke geen|niet non keine? no|not sem 感受性の高い、被ばく量の増加 nie|nie sem нет? no|sin nej|inte hayır|değil|hayir|degil ні
|
||||
Intermediate TRUE FALSE FALSE FALSE 中级 Mellemliggende Intermediair Mittlere Ενδιάμεση 影響を受けやすい。 Pośrednia Intermedio Orta seviye Знижена чутливість
|
||||
Susceptible, incr. exp. FALSE TRUE FALSE FALSE 易感，暴露增加 Modtagelig, øget eksp. Gevoelig bij verh. blootstelling Empfindlich, erh Belastung Ευάλωτος, αυξημένη έκθεση 影響を受けやすい Podatne, zwiększone narażenie Duyarlı, enk. maruziyet Чутливий до підвищеної експозиції
|
||||
susceptible, incr. exp. FALSE TRUE FALSE FALSE 易感，接触增加 modtagelig, øget eksp. gevoelig bij verh. blootstelling empfindlich, erh Belastung Ευαίσθητος, αυξημένη έκθεση 曝露量増加 podatny, zwiększone narażenie duyarlı, enk. maruziyet чутливий до підвищеної експозиції
|
||||
|
||||
|
Reference in New Issue
Block a user