mirror of
https://github.com/msberends/AMR.git
synced 2025-07-11 13:01:55 +02:00
styled, unit test fix
This commit is contained in:
@ -9,7 +9,7 @@
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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@ -33,34 +33,43 @@ library(dplyr)
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library(readxl)
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DRGLST <- read_excel("DRGLST.xlsx")
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abx <- DRGLST %>%
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select(ab = WHON5_CODE,
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name = ANTIBIOTIC) %>%
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select(
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ab = WHON5_CODE,
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name = ANTIBIOTIC
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) %>%
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# remove the ones without WHONET code
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filter(!is.na(ab)) %>%
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distinct(name, .keep_all = TRUE) %>%
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# add the ones without WHONET code
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bind_rows(
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DRGLST %>%
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select(ab = WHON5_CODE,
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name = ANTIBIOTIC) %>%
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select(
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ab = WHON5_CODE,
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name = ANTIBIOTIC
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) %>%
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filter(is.na(ab)) %>%
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distinct(name, .keep_all = TRUE)
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# add new ab code later
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# add new ab code later
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) %>%
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arrange(name)
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# add old ATC codes
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ab_old <- AMR::antibiotics %>%
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mutate(official = gsub("( and |, )", "/", official),
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abbr = tolower(paste(ifelse(is.na(abbr), "", abbr),
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ifelse(is.na(certe), "", certe),
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ifelse(is.na(umcg), "", umcg),
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sep = "|")))
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mutate(
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official = gsub("( and |, )", "/", official),
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abbr = tolower(paste(ifelse(is.na(abbr), "", abbr),
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ifelse(is.na(certe), "", certe),
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ifelse(is.na(umcg), "", umcg),
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sep = "|"
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))
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)
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for (i in 1:nrow(ab_old)) {
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abbr <- ab_old[i, "abbr"]
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abbr <- strsplit(abbr, "|", fixed = TRUE) %>% unlist() %>% unique()
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abbr <- strsplit(abbr, "|", fixed = TRUE) %>%
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unlist() %>%
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unique()
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abbr <- abbr[abbr != ""]
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#print(abbr)
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# print(abbr)
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if (length(abbr) == 0) {
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ab_old[i, "abbr"] <- NA_character_
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} else {
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@ -72,50 +81,54 @@ for (i in 1:nrow(ab_old)) {
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abx_atc1 <- abx %>%
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mutate(name_lower = tolower(name)) %>%
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left_join(ab_old %>%
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select(ears_net, atc), by = c(ab = "ears_net")) %>%
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select(ears_net, atc), by = c(ab = "ears_net")) %>%
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rename(atc1 = atc) %>%
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left_join(ab_old %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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rename(atc2 = atc) %>%
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left_join(ab_old %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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mutate(official = gsub("f", "ph", official)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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mutate(official = gsub("f", "ph", official)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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rename(atc3 = atc) %>%
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left_join(ab_old %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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mutate(official = gsub("t", "th", official)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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mutate(official = gsub("t", "th", official)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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rename(atc4 = atc) %>%
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left_join(ab_old %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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mutate(official = gsub("f", "ph", official)) %>%
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mutate(official = gsub("t", "th", official)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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mutate(official = gsub("f", "ph", official)) %>%
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mutate(official = gsub("t", "th", official)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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rename(atc5 = atc) %>%
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left_join(ab_old %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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mutate(official = gsub("f", "ph", official)) %>%
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mutate(official = gsub("t", "th", official)) %>%
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mutate(official = gsub("ine$", "in", official)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
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mutate(official = gsub("f", "ph", official)) %>%
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mutate(official = gsub("t", "th", official)) %>%
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mutate(official = gsub("ine$", "in", official)) %>%
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transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
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rename(atc6 = atc) %>%
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mutate(atc = case_when(!is.na(atc1) ~ atc1,
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!is.na(atc2) ~ atc2,
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!is.na(atc3) ~ atc3,
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!is.na(atc4) ~ atc4,
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!is.na(atc4) ~ atc5,
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TRUE ~ atc6)) %>%
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mutate(atc = case_when(
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!is.na(atc1) ~ atc1,
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!is.na(atc2) ~ atc2,
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!is.na(atc3) ~ atc3,
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!is.na(atc4) ~ atc4,
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!is.na(atc4) ~ atc5,
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TRUE ~ atc6
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)) %>%
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distinct(ab, name, .keep_all = TRUE) %>%
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select(ab, atc, name)
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abx_atc2 <- ab_old %>%
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filter(!atc %in% abx_atc1$atc,
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is.na(ears_net),
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!is.na(atc_group1),
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atc_group1 %unlike% ("virus|vaccin|viral|immun"),
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official %unlike% "(combinations| with )") %>%
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filter(
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!atc %in% abx_atc1$atc,
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is.na(ears_net),
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!is.na(atc_group1),
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atc_group1 %unlike% ("virus|vaccin|viral|immun"),
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official %unlike% "(combinations| with )"
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) %>%
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mutate(ab = NA_character_) %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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select(ab, atc, name = official)
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@ -125,12 +138,15 @@ abx2 <- bind_rows(abx_atc1, abx_atc2)
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rm(abx_atc1)
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rm(abx_atc2)
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abx2$ab[is.na(abx2$ab)] <- toupper(abbreviate(gsub("[/0-9-]",
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" ",
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abx2$name[is.na(abx2$ab)]),
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minlength = 3,
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method = "left.kept",
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strict = TRUE))
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abx2$ab[is.na(abx2$ab)] <- toupper(abbreviate(gsub(
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"[/0-9-]",
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" ",
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abx2$name[is.na(abx2$ab)]
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),
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minlength = 3,
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method = "left.kept",
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strict = TRUE
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))
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n_distinct(abx2$ab)
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@ -150,7 +166,9 @@ for (i in 2:nrow(abx2)) {
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abx2[i, "ab"] <- paste0(abx2[i, "ab", drop = TRUE], abx2[i, "seqnr", drop = TRUE])
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}
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}
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abx2 <- abx2 %>% select(-seqnr) %>% arrange(name)
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abx2 <- abx2 %>%
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select(-seqnr) %>%
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arrange(name)
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# everything unique??
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nrow(abx2) == n_distinct(abx2$ab)
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@ -158,8 +176,10 @@ nrow(abx2) == n_distinct(abx2$ab)
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# get ATC properties
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abx2 <- abx2 %>%
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left_join(ab_old %>%
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select(atc, abbr, atc_group1, atc_group2,
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oral_ddd, oral_units, iv_ddd, iv_units))
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select(
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atc, abbr, atc_group1, atc_group2,
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oral_ddd, oral_units, iv_ddd, iv_units
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))
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abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixed = TRUE)))
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@ -171,29 +191,41 @@ get_CID <- function(ab) {
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p$tick()$print()
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CID[i] <- tryCatch(
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data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
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URLencode(ab[i], reserved = TRUE),
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"/cids/TXT?name_type=complete"),
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showProgress = FALSE)[[1]][1],
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error = function(e) NA_integer_)
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data.table::fread(paste0(
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"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
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URLencode(ab[i], reserved = TRUE),
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"/cids/TXT?name_type=complete"
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),
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showProgress = FALSE
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)[[1]][1],
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error = function(e) NA_integer_
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)
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if (is.na(CID[i])) {
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# try with removing the text in brackets
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CID[i] <- tryCatch(
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data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
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URLencode(trimws(gsub("[(].*[)]", "", ab[i])), reserved = TRUE),
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"/cids/TXT?name_type=complete"),
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showProgress = FALSE)[[1]][1],
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error = function(e) NA_integer_)
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data.table::fread(paste0(
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"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
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URLencode(trimws(gsub("[(].*[)]", "", ab[i])), reserved = TRUE),
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"/cids/TXT?name_type=complete"
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),
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showProgress = FALSE
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)[[1]][1],
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error = function(e) NA_integer_
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)
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}
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if (is.na(CID[i])) {
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# try match on word and take the lowest CID value (sorted)
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ab[i] <- gsub("[^a-z0-9]+", " ", ab[i], ignore.case = TRUE)
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CID[i] <- tryCatch(
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data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
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URLencode(ab[i], reserved = TRUE),
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"/cids/TXT?name_type=word"),
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showProgress = FALSE)[[1]][1],
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error = function(e) NA_integer_)
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data.table::fread(paste0(
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"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
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URLencode(ab[i], reserved = TRUE),
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"/cids/TXT?name_type=word"
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),
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showProgress = FALSE
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)[[1]][1],
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error = function(e) NA_integer_
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)
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}
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Sys.sleep(0.1)
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}
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@ -203,15 +235,15 @@ get_CID <- function(ab) {
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# get CIDs (2-3 min)
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CIDs <- get_CID(abx2$name)
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# These could not be found:
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abx2[is.na(CIDs),] %>% View()
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abx2[is.na(CIDs), ] %>% View()
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# returns list with synonyms (brand names), with CIDs as names
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get_synonyms <- function(CID, clean = TRUE) {
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synonyms <- rep(NA_character_, length(CID))
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#p <- progress_ticker(n = length(CID), min_time = 0)
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# p <- progress_ticker(n = length(CID), min_time = 0)
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for (i in 1:length(CID)) {
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#p$tick()$print()
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# p$tick()$print()
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synonyms_txt <- ""
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@ -220,27 +252,37 @@ get_synonyms <- function(CID, clean = TRUE) {
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}
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synonyms_txt <- tryCatch(
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data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/",
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CID[i],
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"/synonyms/TXT"),
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sep = "\n",
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showProgress = FALSE)[[1]],
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error = function(e) NA_character_)
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data.table::fread(paste0(
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"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/",
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CID[i],
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"/synonyms/TXT"
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),
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sep = "\n",
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showProgress = FALSE
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)[[1]],
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error = function(e) NA_character_
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)
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Sys.sleep(0.1)
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if (clean == TRUE) {
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# remove text between brackets
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synonyms_txt <- trimws(gsub("[(].*[)]", "",
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gsub("[[].*[]]", "",
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gsub("[(].*[]]", "",
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gsub("[[].*[)]", "", synonyms_txt)))))
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synonyms_txt <- trimws(gsub(
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"[(].*[)]", "",
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gsub(
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"[[].*[]]", "",
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gsub(
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"[(].*[]]", "",
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gsub("[[].*[)]", "", synonyms_txt)
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)
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)
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))
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synonyms_txt <- gsub("Co-", "Co", synonyms_txt, fixed = TRUE)
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# only length 6 to 20 and no txt with reading marks or numbers and must start with capital letter (= brand)
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synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(6:20)
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& !grepl("[-&{},_0-9/]", synonyms_txt)
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& grepl("^[A-Z]", synonyms_txt, ignore.case = FALSE)]
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synonyms_txt <- unlist(strsplit(synonyms_txt, ";", fixed = TRUE))
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synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(6:20) &
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!grepl("[-&{},_0-9/]", synonyms_txt) &
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grepl("^[A-Z]", synonyms_txt, ignore.case = FALSE)]
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synonyms_txt <- unlist(strsplit(synonyms_txt, ";", fixed = TRUE))
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}
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synonyms_txt <- unique(trimws(synonyms_txt[tolower(synonyms_txt) %in% unique(tolower(synonyms_txt))]))
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synonyms[i] <- list(sort(synonyms_txt))
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@ -251,52 +293,56 @@ get_synonyms <- function(CID, clean = TRUE) {
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# get brand names from PubChem (2-3 min)
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synonyms <- get_synonyms(CIDs)
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synonyms <- lapply(synonyms,
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function(x) {
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if (length(x) == 0 | all(is.na(x))) {
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""
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} else {
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x
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}})
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synonyms <- lapply(
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synonyms,
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function(x) {
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if (length(x) == 0 | all(is.na(x))) {
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""
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} else {
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x
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}
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}
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)
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# add them to data set
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antibiotics <- abx2 %>%
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left_join(DRGLST %>%
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select(ab = WHON5_CODE, CLASS, SUBCLASS) %>%
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distinct(ab, .keep_all = TRUE), by = "ab") %>%
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select(ab = WHON5_CODE, CLASS, SUBCLASS) %>%
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distinct(ab, .keep_all = TRUE), by = "ab") %>%
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transmute(ab,
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atc,
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cid = CIDs,
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# no capital after a slash: Ampicillin/Sulbactam -> Ampicillin/sulbactam
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name = name %>%
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gsub("([/-])([A-Z])", "\\1\\L\\2", ., perl = TRUE) %>%
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gsub("edta", "EDTA", ., ignore.case = TRUE),
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group = case_when(
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "am(ph|f)enicol" ~ "Amphenicols",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "aminoglycoside" ~ "Aminoglycosides",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "carbapenem" | name %like% "(imipenem|meropenem)" ~ "Carbapenems",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "First-generation cephalosporin" ~ "Cephalosporins (1st gen.)",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Second-generation cephalosporin" ~ "Cephalosporins (2nd gen.)",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Third-generation cephalosporin" ~ "Cephalosporins (3rd gen.)",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Fourth-generation cephalosporin" ~ "Cephalosporins (4th gen.)",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(tuberculosis|mycobacter)" ~ "Antimycobacterials",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "cephalosporin" ~ "Cephalosporins",
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name %like% "^Ce" & is.na(atc_group1) & paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "beta-?lactam" ~ "Cephalosporins",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(beta-?lactam|penicillin)" ~ "Beta-lactams/penicillins",
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "quinolone" ~ "Quinolones",
|
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paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "glycopeptide" ~ "Glycopeptides",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "macrolide" ~ "Macrolides/lincosamides",
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||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "tetracycline" ~ "Tetracyclines",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "trimethoprim" ~ "Trimethoprims",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "polymyxin" ~ "Polymyxins",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(fungal|mycot)" ~ "Antifungals/antimycotics",
|
||||
TRUE ~ "Other antibacterials"
|
||||
),
|
||||
atc_group1, atc_group2,
|
||||
abbreviations = unname(abbr),
|
||||
synonyms = unname(synonyms),
|
||||
oral_ddd, oral_units,
|
||||
iv_ddd, iv_units) %>%
|
||||
atc,
|
||||
cid = CIDs,
|
||||
# no capital after a slash: Ampicillin/Sulbactam -> Ampicillin/sulbactam
|
||||
name = name %>%
|
||||
gsub("([/-])([A-Z])", "\\1\\L\\2", ., perl = TRUE) %>%
|
||||
gsub("edta", "EDTA", ., ignore.case = TRUE),
|
||||
group = case_when(
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "am(ph|f)enicol" ~ "Amphenicols",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "aminoglycoside" ~ "Aminoglycosides",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "carbapenem" | name %like% "(imipenem|meropenem)" ~ "Carbapenems",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "First-generation cephalosporin" ~ "Cephalosporins (1st gen.)",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Second-generation cephalosporin" ~ "Cephalosporins (2nd gen.)",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Third-generation cephalosporin" ~ "Cephalosporins (3rd gen.)",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Fourth-generation cephalosporin" ~ "Cephalosporins (4th gen.)",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(tuberculosis|mycobacter)" ~ "Antimycobacterials",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "cephalosporin" ~ "Cephalosporins",
|
||||
name %like% "^Ce" & is.na(atc_group1) & paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "beta-?lactam" ~ "Cephalosporins",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(beta-?lactam|penicillin)" ~ "Beta-lactams/penicillins",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "quinolone" ~ "Quinolones",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "glycopeptide" ~ "Glycopeptides",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "macrolide" ~ "Macrolides/lincosamides",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "tetracycline" ~ "Tetracyclines",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "trimethoprim" ~ "Trimethoprims",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "polymyxin" ~ "Polymyxins",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(fungal|mycot)" ~ "Antifungals/antimycotics",
|
||||
TRUE ~ "Other antibacterials"
|
||||
),
|
||||
atc_group1, atc_group2,
|
||||
abbreviations = unname(abbr),
|
||||
synonyms = unname(synonyms),
|
||||
oral_ddd, oral_units,
|
||||
iv_ddd, iv_units
|
||||
) %>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
|
||||
# some exceptions
|
||||
@ -329,13 +375,15 @@ antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]] <-
|
||||
antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt"))
|
||||
# Add cefoxitin screening
|
||||
class(antibiotics$ab) <- "character"
|
||||
antibiotics <- rbind(antibiotics,data.frame(ab = "FOX1", atc = NA, cid = NA,
|
||||
name = "Cefoxitin screening",
|
||||
group = "Cephalosporins (2nd gen.)", atc_group1 = NA, atc_group2 = NA,
|
||||
abbreviations = "cfsc", synonyms = NA,
|
||||
oral_ddd = NA, oral_units = NA, iv_ddd = NA, iv_units = NA,
|
||||
loinc = NA,
|
||||
stringsAsFactors = FALSE))
|
||||
antibiotics <- rbind(antibiotics, data.frame(
|
||||
ab = "FOX1", atc = NA, cid = NA,
|
||||
name = "Cefoxitin screening",
|
||||
group = "Cephalosporins (2nd gen.)", atc_group1 = NA, atc_group2 = NA,
|
||||
abbreviations = "cfsc", synonyms = NA,
|
||||
oral_ddd = NA, oral_units = NA, iv_ddd = NA, iv_units = NA,
|
||||
loinc = NA,
|
||||
stringsAsFactors = FALSE
|
||||
))
|
||||
# More GLIMS codes
|
||||
antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "AMB"), "abbreviations"][[1]], "amf"))
|
||||
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz"))
|
||||
@ -520,27 +568,33 @@ antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(sort(c
|
||||
antibiotics[which(antibiotics$ab == "RTP"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "RTP"), "abbreviations"][[1]], "RET")))
|
||||
antibiotics[which(antibiotics$ab == "TYL1"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "TYL1"), "abbreviations"][[1]], "TVN")))
|
||||
|
||||
antibiotics <- antibiotics %>%
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "GEH") %>%
|
||||
mutate(ab = "AMH",
|
||||
name = "Amphotericin B-high",
|
||||
abbreviations = list(c("amhl", "amfo b high", "ampho b high", "amphotericin high")))) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "GEH") %>%
|
||||
mutate(ab = "TOH",
|
||||
name = "Tobramycin-high",
|
||||
abbreviations = list(c("tohl", "tobra high", "tobramycin high")))) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "BUT") %>%
|
||||
mutate(ab = "CIX",
|
||||
atc = "D01AE14",
|
||||
name = "Ciclopirox",
|
||||
group = "Antifungals/antimycotics",
|
||||
atc_group1 = "Antifungals for topical use",
|
||||
atc_group2 = "Other antifungals for topical use",
|
||||
abbreviations = list(c("cipx"))))
|
||||
antibiotics <- antibiotics %>%
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "GEH") %>%
|
||||
mutate(
|
||||
ab = "AMH",
|
||||
name = "Amphotericin B-high",
|
||||
abbreviations = list(c("amhl", "amfo b high", "ampho b high", "amphotericin high"))
|
||||
)) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "GEH") %>%
|
||||
mutate(
|
||||
ab = "TOH",
|
||||
name = "Tobramycin-high",
|
||||
abbreviations = list(c("tohl", "tobra high", "tobramycin high"))
|
||||
)) %>%
|
||||
rbind(antibiotics %>%
|
||||
filter(ab == "BUT") %>%
|
||||
mutate(
|
||||
ab = "CIX",
|
||||
atc = "D01AE14",
|
||||
name = "Ciclopirox",
|
||||
group = "Antifungals/antimycotics",
|
||||
atc_group1 = "Antifungals for topical use",
|
||||
atc_group2 = "Other antifungals for topical use",
|
||||
abbreviations = list(c("cipx"))
|
||||
))
|
||||
antibiotics[which(antibiotics$ab == "SSS"), "name"] <- "Sulfonamide"
|
||||
# ESBL E-test codes:
|
||||
antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
|
||||
@ -600,13 +654,13 @@ antibiotics[which(antibiotics$ab == "RXT"), "name"] <- "Roxithromycin"
|
||||
antibiotics[which(antibiotics$ab == "PEN"), "atc"] <- "J01CE01"
|
||||
|
||||
# WHONET cleanup
|
||||
antibiotics[which(antibiotics$ab == "BCZ"), "name"] <- "Bicyclomycin"
|
||||
antibiotics[which(antibiotics$ab == "CCL"), "name"] <- "Cefetecol"
|
||||
antibiotics[which(antibiotics$ab == "ENV"), "name"] <- "Enviomycin"
|
||||
antibiotics[which(antibiotics$ab == "KIT"), "name"] <- "Kitasamycin"
|
||||
antibiotics[which(antibiotics$ab == "LSP"), "name"] <- "Linco-spectin"
|
||||
antibiotics[which(antibiotics$ab == "MEC"), "name"] <- "Mecillinam"
|
||||
antibiotics[which(antibiotics$ab == "PMR"), "name"] <- "Pimaricin"
|
||||
antibiotics[which(antibiotics$ab == "BCZ"), "name"] <- "Bicyclomycin"
|
||||
antibiotics[which(antibiotics$ab == "CCL"), "name"] <- "Cefetecol"
|
||||
antibiotics[which(antibiotics$ab == "ENV"), "name"] <- "Enviomycin"
|
||||
antibiotics[which(antibiotics$ab == "KIT"), "name"] <- "Kitasamycin"
|
||||
antibiotics[which(antibiotics$ab == "LSP"), "name"] <- "Linco-spectin"
|
||||
antibiotics[which(antibiotics$ab == "MEC"), "name"] <- "Mecillinam"
|
||||
antibiotics[which(antibiotics$ab == "PMR"), "name"] <- "Pimaricin"
|
||||
antibiotics[which(antibiotics$ab == "BCZ"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "BCZ"), "abbreviations"][[1]], "Bicozamycin"))))
|
||||
antibiotics[which(antibiotics$ab == "CCL"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "CCL"), "abbreviations"][[1]], "Cefcatacol"))))
|
||||
antibiotics[which(antibiotics$ab == "ENV"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "ENV"), "abbreviations"][[1]], "Tuberactinomycin"))))
|
||||
@ -617,7 +671,7 @@ antibiotics[which(antibiotics$ab == "PMR"), "abbreviations"][[1]] <- list(sort(u
|
||||
|
||||
|
||||
# set cephalosporins groups for the ones that could not be determined automatically:
|
||||
antibiotics <- antibiotics %>%
|
||||
antibiotics <- antibiotics %>%
|
||||
mutate(group = case_when(
|
||||
name == "Cefcapene" ~ "Cephalosporins (3rd gen.)",
|
||||
name == "Cefcapene pivoxil" ~ "Cephalosporins (3rd gen.)",
|
||||
@ -650,21 +704,24 @@ antibiotics <- antibiotics %>%
|
||||
name == "Ceftolozane/enzyme inhibitor" ~ "Cephalosporins (5th gen.)",
|
||||
name == "Ceftolozane/tazobactam" ~ "Cephalosporins (5th gen.)",
|
||||
name == "Cefuroxime axetil" ~ "Cephalosporins (2nd gen.)",
|
||||
TRUE ~ group))
|
||||
TRUE ~ group
|
||||
))
|
||||
antibiotics[which(antibiotics$ab %in% c("CYC", "LNZ", "THA", "TZD")), "group"] <- "Oxazolidinones"
|
||||
|
||||
# add pretomanid
|
||||
antibiotics <- antibiotics %>%
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
bind_rows(antibiotics %>%
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
filter(ab == "SMF") %>%
|
||||
mutate(ab = "PMD",
|
||||
atc = "J04AK08",
|
||||
cid = 456199,
|
||||
name = "Pretomanid",
|
||||
abbreviations = list(""),
|
||||
oral_ddd = NA_real_))
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
filter(ab == "SMF") %>%
|
||||
mutate(
|
||||
ab = "PMD",
|
||||
atc = "J04AK08",
|
||||
cid = 456199,
|
||||
name = "Pretomanid",
|
||||
abbreviations = list(""),
|
||||
oral_ddd = NA_real_
|
||||
))
|
||||
|
||||
|
||||
|
||||
@ -675,25 +732,24 @@ antibiotics <- antibiotics %>%
|
||||
updated_atc <- as.list(antibiotics$atc)
|
||||
|
||||
get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
|
||||
|
||||
ab_name <- gsub("/", " and ", tolower(ab_name), fixed = TRUE)
|
||||
|
||||
|
||||
# we will do a search on their website, which means:
|
||||
|
||||
|
||||
# go to the url
|
||||
atc_tbl <- read_html(url) %>%
|
||||
atc_tbl <- read_html(url) %>%
|
||||
# get all forms
|
||||
html_form() %>%
|
||||
# get the second form (the first form is a global website form)
|
||||
.[[2]] %>%
|
||||
.[[2]] %>%
|
||||
# set the name input box to our search parameter
|
||||
html_form_set(name = ab_name) %>%
|
||||
html_form_set(name = ab_name) %>%
|
||||
# hit Submit
|
||||
html_form_submit() %>%
|
||||
html_form_submit() %>%
|
||||
# read the resulting page
|
||||
read_html() %>%
|
||||
read_html() %>%
|
||||
# retrieve the table on it
|
||||
html_node("table") %>%
|
||||
html_node("table") %>%
|
||||
# transform it to an R data set
|
||||
html_table(header = FALSE)
|
||||
# and get the ATCs (first column) of only exact hits
|
||||
@ -702,9 +758,10 @@ get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
|
||||
|
||||
# this takes around 4 minutes (some are skipped and go faster)
|
||||
for (i in seq_len(nrow(antibiotics))) {
|
||||
message(percentage(i / nrow(antibiotics), digits = 1),
|
||||
" - Downloading ", antibiotics$name[i],
|
||||
appendLF = FALSE)
|
||||
message(percentage(i / nrow(antibiotics), digits = 1),
|
||||
" - Downloading ", antibiotics$name[i],
|
||||
appendLF = FALSE
|
||||
)
|
||||
atcs <- get_atcs(antibiotics$name[i])
|
||||
if (length(atcs) > 0) {
|
||||
updated_atc[[i]] <- atcs
|
||||
|
||||
Reference in New Issue
Block a user