AMR/data-raw/reproduction_of_antivirals.R

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# ==================================================================== #
# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
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# 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 #
# #
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# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
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# 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. #
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# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
library(dplyr)
library(tidyr)
library(rvest)
# get all data from the WHOCC website
get_atc_table <- function(atc_group) {
# give as input J0XXX, like atc_group = "J05AB"
downloaded <- read_html(paste0("https://www.whocc.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
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table_title <- downloaded %>%
html_nodes(paste0('a[href^="./?code=', atc_group, '&"]')) %>%
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html_text()
table_title <- table_title[tolower(table_title) != "show text from guidelines"][1]
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table_content <- downloaded %>%
html_nodes("table") %>%
html_table(header = TRUE) %>%
# returns list, so make data.frame out of it
as.data.frame(stringsAsFactors = FALSE) %>%
# select right columns
select(atc = ATC.code, name = Name, ddd = DDD, unit = U, ddd_type = Adm.R) %>%
# fill empty rows
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mutate(atc = ifelse(atc == "", lag(atc), atc), name = ifelse(name == "", lag(name), name)) %>%
pivot_wider(names_from = ddd_type, values_from = c(ddd, unit)) %>%
mutate(atc_group = table_title)
if (!"ddd_O" %in% colnames(table_content)) {
table_content <- table_content %>% mutate(ddd_O = NA_real_, unit_O = NA_character_)
}
if (!"ddd_P" %in% colnames(table_content)) {
table_content <- table_content %>% mutate(ddd_P = NA_real_, unit_P = NA_character_)
}
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table_content %>% select(atc, name, atc_group,
oral_ddd = ddd_O, oral_units = unit_O,
iv_ddd = ddd_P, iv_units = unit_P
)
}
# these are the relevant groups for input: https://www.whocc.no/atc_ddd_index/?code=J05A (J05 only contains J05A)
atc_groups <- c("J05AA", "J05AB", "J05AC", "J05AD", "J05AE", "J05AF", "J05AG", "J05AH", "J05AJ", "J05AP", "J05AR", "J05AX")
# get the first
antivirals <- get_atc_table(atc_groups[1])
# bind all others to it
for (i in 2:length(atc_groups)) {
message(atc_groups[i], "...")
antivirals <- rbind(antivirals, get_atc_table(atc_groups[i]))
}
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# arrange on name, untibble it
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antivirals <- antivirals %>%
arrange(name) %>%
as.data.frame(stringsAsFactors = FALSE)
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# add PubChem Compound ID (cid) and their trade names
# see `data-raw/reproduction_of_antibiotics` for get_CID() and get_synonyms()
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CIDs <- get_CID(antivirals$name)
# these could not be found:
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antivirals[is.na(CIDs), ] %>% View()
# get brand names from PubChem
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synonyms <- get_synonyms(CIDs)
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synonyms <- lapply(
synonyms,
function(x) {
if (length(x) == 0 | all(is.na(x))) {
""
} else {
x
}
}
)
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antivirals <- antivirals %>%
transmute(atc,
cid = as.double(CIDs),
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name,
atc_group,
synonyms = unname(synonyms),
oral_ddd,
oral_units,
iv_ddd,
iv_units
) %>%
AMR:::dataset_UTF8_to_ASCII()
av_codes <- tibble(name = antivirals$name %>%
strsplit("(, | and )") %>%
unlist() %>%
unique() %>%
sort()) %>%
mutate(av_1st = toupper(abbreviate(name, minlength = 3, use.classes = FALSE))) %>%
filter(!name %in% c("acid", "dipivoxil", "disoproxil", "marboxil", "alafenamide"))
replace_with_av_code <- function(name) {
unname(av_codes$av_1st[match(name, av_codes$name)])
}
names_codes <- antivirals %>%
separate(name,
into = paste0("name", c(1:7)),
sep = "(, | and )",
remove = FALSE,
fill = "right") %>%
# remove empty columns
select(!where(function(x) all(is.na(x)))) %>%
mutate_at(vars(matches("name[1-9]")), replace_with_av_code) %>%
unite(av, matches("name[1-9]"), sep = "+", na.rm = TRUE) %>%
mutate(name = gsub("(, | and )", "/", name))
substr(names_codes$name, 1, 1) <- toupper(substr(names_codes$name, 1, 1))
antivirals <- bind_cols(
names_codes %>% select(av, name),
antivirals %>% select(-name)
)
class(antivirals$av) <- c("av", "character")
antivirals <- antivirals %>% AMR:::dataset_UTF8_to_ASCII()
# add loinc, see 'data-raw/loinc.R'
loinc_df <- read.csv("data-raw/Loinc.csv",
row.names = NULL,
stringsAsFactors = FALSE)
loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
av_names <- antivirals %>%
pull(name) %>%
paste0(collapse = "|") %>%
paste0("(", ., ")")
antivirals$loinc <- as.list(rep(NA_character_, nrow(antivirals)))
for (i in seq_len(nrow(antivirals))) {
message(i)
loinc_ab <- loinc_df %>%
filter(COMPONENT %like% paste0("^", antivirals$name[i])) %>%
pull(LOINC_NUM)
if (length(loinc_ab) > 0) {
antivirals$loinc[i] <- list(loinc_ab)
}
}
# sort and fix for empty values
for (i in 1:nrow(antivirals)) {
loinc <- as.character(sort(unique(tolower(antivirals[i, "loinc", drop = TRUE][[1]]))))
antivirals[i, "loinc"][[1]] <- ifelse(length(loinc[!loinc == ""]) == 0, list(""), list(loinc))
}
# de-duplicate synonyms
for (i in 1:nrow(antivirals)) {
syn <- as.character(sort(unique(tolower(antivirals[i, "synonyms", drop = TRUE][[1]]))))
syn <- syn[!syn %in% tolower(antivirals[i, "name", drop = TRUE])]
antivirals[i, "synonyms"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(syn))
}
antivirals <- antivirals %>% AMR:::dataset_UTF8_to_ASCII()
# check it
antivirals
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# save it
usethis::use_data(antivirals, overwrite = TRUE, internal = FALSE, compress = "xz", version = 2)