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(v2.1.1.9193) new antimicrobials for screening

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dr. M.S. (Matthijs) Berends
2025-03-12 15:09:28 +01:00
parent 067a8aca66
commit e1b7252ff6
30 changed files with 319 additions and 174 deletions
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103
data-raw/reproduction_of_antimicrobials.R
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@@ -777,14 +777,110 @@ antimicrobials[which(antimicrobials$ab == "EFF"), "abbreviations"][[1]] <- list(
# add clindamycin inducible screening
clin <- antimicrobials |>
filter(ab == "FOX1") |>
mutate(ab = as.character("CLI1"),
mutate(ab = as.character("CLI-S"),
name = "Clindamycin inducible screening",
group = "Macrolides/lincosamides")
antimicrobials <- antimicrobials |>
mutate(ab = as.character(ab)) |>
bind_rows(clin)
class(antimicrobials$ab) <- c("ab", "character")
antimicrobials[which(antimicrobials$ab == "CLI1"), "abbreviations"][[1]] <- list(c("clindamycin inducible", "clinda inducible", "clin inducible"))
antimicrobials[which(antimicrobials$ab == "CLI-S"), "abbreviations"][[1]] <- list(c("clindamycin inducible", "clinda inducible", "clin inducible"))
# add all screenings
antimicrobials <- antimicrobials |>
bind_rows(
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))),
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))),
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))),
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))),
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))),
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)))
)
# add pretomanid
antimicrobials <- antimicrobials %>%
@@ -918,6 +1014,8 @@ antimicrobials <- dplyr::arrange(antimicrobials, name)
# make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
for (i in 1:nrow(antimicrobials)) {
atc <- as.character(sort(unique(toupper(antimicrobials[i, "atc", drop = TRUE][[1]]))))
atc <- atc[atc != "" & atc %unlike% ":"]
abb <- as.character(sort(unique(tolower(antimicrobials[i, "abbreviations", drop = TRUE][[1]]))))
abb <- abb[abb != "" & abb %unlike% ":"]
syn <- as.character(sort(unique(tolower(unname(unlist(antimicrobials[i, "synonyms", drop = TRUE]))))))
@@ -934,6 +1032,7 @@ for (i in 1:nrow(antimicrobials)) {
# special cases
if (antimicrobials$ab[i] == "VAN") syn <- syn[syn %unlike% "^tei?ch?o"]
if (antimicrobials$ab[i] == "CLR") syn <- syn[syn %unlike% "^ery"]
antimicrobials[i, "atc"][[1]] <- ifelse(length(atc) == 0, list(NA_character_), list(atc))
antimicrobials[i, "abbreviations"][[1]] <- ifelse(length(abb) == 0, list(""), list(abb))
antimicrobials[i, "synonyms"][[1]] <- ifelse(length(syn) == 0, list(""), list(syn))
if ("loinc" %in% colnames(antimicrobials)) {