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Add add_if_missing parameter to control NA handling in interpretive rules (#264)

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Matthijs Berends
2026-04-21 21:53:43 +02:00
committed by GitHub
parent fb8758f36b
commit 8ff5d4472a
46 changed files with 1232 additions and 1016 deletions
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314
data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R
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@@ -262,9 +262,9 @@ get_synonyms <- function(CID, clean = TRUE) {
if (is.na(CID[i])) {
next
}
all_cids <- CID[i]
# we will now get the closest compounds with a 96% threshold
similar_cids <- tryCatch(
data.table::fread(
@@ -281,7 +281,7 @@ get_synonyms <- function(CID, clean = TRUE) {
# leave out all CIDs that we have in our antimicrobials dataset to prevent duplication
similar_cids <- similar_cids[!similar_cids %in% antimicrobials$cid[!is.na(antimicrobials$cid)]]
all_cids <- unique(c(all_cids, similar_cids))
# for each one, we are getting the synonyms
current_syns <- character(0)
for (j in seq_len(length(all_cids))) {
@@ -297,9 +297,9 @@ get_synonyms <- function(CID, clean = TRUE) {
)[[1]],
error = function(e) NA_character_
)
Sys.sleep(0.05)
if (clean == TRUE) {
# remove text between brackets
synonyms_txt <- trimws(gsub(
@@ -319,16 +319,16 @@ get_synonyms <- function(CID, clean = TRUE) {
synonyms_txt <- gsub("[^a-z]+$", "", ignore.case = TRUE, synonyms_txt)
# only length 5 to 20 and lower-case names starting with a capital letter
synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(5:20) &
grepl("^[A-Z][a-z]+$", synonyms_txt, ignore.case = FALSE)]
grepl("^[A-Z][a-z]+$", synonyms_txt, ignore.case = FALSE)]
synonyms_txt <- unlist(strsplit(synonyms_txt, ";", fixed = TRUE))
}
# synonyms must not be set for other agents, so remove the duplicates
synonyms_txt <- synonyms_txt[!synonyms_txt %in% unlist(synonyms)]
current_syns <- c(current_syns, synonyms_txt)
}
current_syns <- unique(trimws(current_syns[tolower(current_syns) %in% unique(tolower(current_syns))]))
synonyms[i] <- list(sort(current_syns))
}
@@ -763,10 +763,12 @@ antimicrobials[which(antimicrobials$ab %in% c("CYC", "LNZ", "THA", "TZD")), "gro
# add efflux
effl <- antimicrobials |>
filter(ab == "ACM") |>
mutate(ab = as.character("EFF"),
cid = NA_real_,
name = "Efflux",
group = "Other")
mutate(
ab = as.character("EFF"),
cid = NA_real_,
name = "Efflux",
group = "Other"
)
antimicrobials <- antimicrobials |>
mutate(ab = as.character(ab)) |>
bind_rows(effl)
@@ -777,9 +779,11 @@ antimicrobials[which(antimicrobials$ab == "EFF"), "abbreviations"][[1]] <- list(
# add clindamycin inducible screening
clin <- antimicrobials |>
filter(ab == "FOX1") |>
mutate(ab = as.character("CLI-S"),
name = "Clindamycin inducible screening",
group = "Macrolides/lincosamides")
mutate(
ab = as.character("CLI-S"),
name = "Clindamycin inducible screening",
group = "Macrolides/lincosamides"
)
antimicrobials <- antimicrobials |>
mutate(ab = as.character(ab)) |>
bind_rows(clin)
@@ -791,109 +795,123 @@ antimicrobials <- antimicrobials |>
bind_rows(
antimicrobials |>
filter(ab == "EFF") |>
mutate(ab = "BLA-S",
name = paste("Beta-lactamase", "screening test"),
cid = NA_real_,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("beta-lactamase", "betalactamase", "bl screen", "blt screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))),
mutate(
ab = "BLA-S",
name = paste("Beta-lactamase", "screening test"),
cid = NA_real_,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("beta-lactamase", "betalactamase", "bl screen", "blt screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))
),
antimicrobials |>
filter(ab == "PEN") |>
mutate(ab = "PEN-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("pen screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))),
mutate(
ab = "PEN-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("pen screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))
),
antimicrobials |>
filter(ab == "OXA") |>
mutate(ab = "OXA-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("oxa screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))),
mutate(
ab = "OXA-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("oxa screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))
),
antimicrobials |>
filter(ab == "PEF") |>
mutate(ab = "PEF-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("pef screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))),
mutate(
ab = "PEF-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("pef screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))
),
antimicrobials |>
filter(ab == "NAL") |>
mutate(ab = "NAL-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("nal screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))),
mutate(
ab = "NAL-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("nal screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))
),
antimicrobials |>
filter(ab == "NOR") |>
mutate(ab = "NOR-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("nor screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))),
mutate(
ab = "NOR-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("nor screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))
),
antimicrobials |>
filter(ab == "TCY") |>
mutate(ab = "TCY-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("tcy screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0)))
mutate(
ab = "TCY-S",
name = paste(name, "screening test"),
cid = NA,
atc = list(character(0)),
atc_group1 = NA_character_,
atc_group2 = NA_character_,
abbreviations = list(c("tcy screen")),
synonyms = list(character(0)),
oral_ddd = NA_real_,
oral_units = NA_character_,
iv_ddd = NA_real_,
iv_units = NA_character_,
loinc = list(character(0))
)
)
@@ -919,16 +937,20 @@ antimicrobials <- antimicrobials |>
antimicrobials |>
filter(ab == "FPE") |>
mutate(ab = as.character(ab)) |>
mutate(ab = "FTA",
name = "Cefepime/taniborbactam",
cid = NA_real_),
mutate(
ab = "FTA",
name = "Cefepime/taniborbactam",
cid = NA_real_
),
antimicrobials |>
filter(ab == "TBP") |>
mutate(ab = as.character(ab)) |>
mutate(ab = "TAN",
name = "Taniborbactam",
cid = 76902493,
abbreviations = list("VNRX-5133"))
mutate(
ab = "TAN",
name = "Taniborbactam",
cid = 76902493,
abbreviations = list("VNRX-5133")
)
)
antimicrobials <- antimicrobials |>
@@ -936,39 +958,51 @@ antimicrobials <- antimicrobials |>
bind_rows(
antimicrobials |>
filter(ab == "CTB") |>
mutate(ab = "CTA",
cid = NA_real_,
name = "Ceftibuten/avibactam") |>
mutate(
ab = "CTA",
cid = NA_real_,
name = "Ceftibuten/avibactam"
) |>
select(1:4),
antimicrobials |>
filter(ab == "KAC") |>
mutate(ab = "KAS",
cid = NA_real_,
name = "Kasugamycin") |>
mutate(
ab = "KAS",
cid = NA_real_,
name = "Kasugamycin"
) |>
select(1:4),
antimicrobials |>
filter(ab == "PRI") |>
mutate(ab = "OST",
cid = NA_real_,
name = "Ostreogrycin") |>
mutate(
ab = "OST",
cid = NA_real_,
name = "Ostreogrycin"
) |>
select(1:4),
antimicrobials |>
filter(ab == "PRI") |>
mutate(ab = "THS",
cid = NA_real_,
name = "Thiostrepton") |>
mutate(
ab = "THS",
cid = NA_real_,
name = "Thiostrepton"
) |>
select(1, 3),
antimicrobials |>
filter(ab == "CLA1") |>
mutate(ab = "XER",
cid = NA_real_,
name = "Xeruborbactam") |>
mutate(
ab = "XER",
cid = NA_real_,
name = "Xeruborbactam"
) |>
select(1:4),
antimicrobials |>
filter(ab == "BLM") |>
mutate(ab = "ZOR",
cid = NA_real_,
name = "Zorbamycin") |>
mutate(
ab = "ZOR",
cid = NA_real_,
name = "Zorbamycin"
) |>
select(1:4),
)
@@ -977,9 +1011,11 @@ antimicrobials <- antimicrobials |>
bind_rows(
antimicrobials |>
filter(ab == "NOV") |>
mutate(ab = "CLB",
cid = 54706138,
name = "Clorobiocin") |>
mutate(
ab = "CLB",
cid = 54706138,
name = "Clorobiocin"
) |>
select(1:4),
)
@@ -990,7 +1026,7 @@ get_atc_table <- function(ab_name, type = "human") {
if (type == "human") {
url <- "https://atcddd.fhi.no/atc_ddd_index/"
} else if (type == "veterinary") {
url <- "https://atcddd.fhi.no/atcvet/atcvet_index/"
url <- "https://atcddd.fhi.no/atcvet/atcvet_index/"
} else {
stop("invalid type")
}
@@ -1055,8 +1091,10 @@ to_update <- 1:nrow(antimicrobials)
# or just the empty ones:
to_update <- which(sapply(antimicrobials$atc, function(x) length(x[!is.na(x)])) == 0)
updated_atc <- lapply(seq_len(length(to_update)),
function(x) NA_character_)
updated_atc <- lapply(
seq_len(length(to_update)),
function(x) NA_character_
)
# this takes around 10 minutes for the whole table (some ABx are skipped and go faster)