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Fix some WHONET codes

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dr. M.S. (Matthijs) Berends
2023-04-14 11:12:26 +02:00
parent 549790c2a6
commit 147f9112e9
21 changed files with 109 additions and 60 deletions
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42
data-raw/reproduction_of_clinical_breakpoints.R
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@@ -44,10 +44,18 @@ whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("
# remove old taxonomic names
filter(TAXONOMIC_STATUS == "C") %>%
transmute(ORGANISM_CODE = tolower(WHONET_ORG_CODE), ORGANISM) %>%
# what's wrong here? 'sau' is both S. areus and S. aureus sp. aureus
mutate(
# what's wrong here? all these are only in the table on subspecies level (where species == subspecies), not on species level
ORGANISM = if_else(ORGANISM_CODE == "sau", "Staphylococcus aureus", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "pam", "Pasteurella multocida", ORGANISM)
ORGANISM = if_else(ORGANISM_CODE == "pam", "Pasteurella multocida", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "kpn", "Klebsiella pneumoniae", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "caj", "Campylobacter jejuni", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "mmo", "Morganella morganii", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "sap", "Staphylococcus saprophyticus", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "fne", "Fusobacterium necrophorum", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "fnu", "Fusobacterium nucleatum", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "sdy", "Streptococcus dysgalactiae", ORGANISM),
ORGANISM = if_else(ORGANISM_CODE == "axy", "Achromobacter xylosoxidans", ORGANISM)
)
whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
filter(BREAKPOINT_TYPE == "Human", GUIDELINES %in% c("CLSI", "EUCAST"))
@@ -64,6 +72,36 @@ whonet_organisms <- whonet_organisms %>%
ORGANISM = c("Enterobacterales", "Campylobacter")
))
mo_reset_session()
whonet_organisms.bak <- whonet_organisms
whonet_organisms <- whonet_organisms.bak %>%
mutate(mo = as.mo(gsub("(sero[a-z]*| complex| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
keep_synonyms = TRUE,
language = "en"),
mo = as.mo(ifelse(ORGANISM %like% "Anaerobic", "B_ANAER", mo)),
mo_name = mo_name(mo,
keep_synonyms = TRUE,
language = "en"))
# update microorganisms.codes with the latest WHONET codes
new_mo_codes <- whonet_organisms %>%
mutate(
first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other")
microorganisms.codes <- microorganisms.codes %>%
# remove all old WHONET codes, whether we (in the end) keep them or not
filter(!toupper(code) %in% toupper(new_mo_codes$ORGANISM_CODE)) %>%
bind_rows(new_mo_codes %>%
filter(keep == TRUE) %>%
transmute(code = toupper(ORGANISM_CODE),
mo = mo)) %>%
arrange(code)
# save to package
usethis::use_data(microorganisms.codes, overwrite = TRUE, compress = "xz", version = 2)
rm(microorganisms.codes)
devtools::load_all()
breakpoints <- whonet_breakpoints %>%
mutate(ORGANISM_CODE = tolower(ORGANISM_CODE)) %>%
left_join(whonet_organisms) %>%