mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:06:12 +01:00
107 lines
4.4 KiB
R
107 lines
4.4 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# 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 #
|
|
# #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# 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. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
# 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"))
|
|
table_title <- downloaded %>%
|
|
html_nodes(paste0('a[href="./?code=', atc_group, '"]')) %>%
|
|
html_text()
|
|
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
|
|
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_)
|
|
}
|
|
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", "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)) {
|
|
antivirals <- rbind(antivirals, get_atc_table(atc_groups[i]))
|
|
}
|
|
|
|
# arrange on name, untibble it
|
|
antivirals <- antivirals %>%
|
|
arrange(name) %>%
|
|
as.data.frame(stringsAsFactors = FALSE)
|
|
|
|
# add PubChem Compound ID (cid) and their trade names - functions are in file to create `antibiotics` data set
|
|
CIDs <- get_CID(antivirals$name)
|
|
# these could not be found:
|
|
antivirals[is.na(CIDs), ] %>% View()
|
|
# get brand names from PubChem
|
|
synonyms <- get_synonyms(CIDs)
|
|
synonyms <- lapply(
|
|
synonyms,
|
|
function(x) {
|
|
if (length(x) == 0 | all(is.na(x))) {
|
|
""
|
|
} else {
|
|
x
|
|
}
|
|
}
|
|
)
|
|
|
|
antivirals <- antivirals %>%
|
|
transmute(atc,
|
|
cid = CIDs,
|
|
name,
|
|
atc_group,
|
|
synonyms = unname(synonyms),
|
|
oral_ddd,
|
|
oral_units,
|
|
iv_ddd,
|
|
iv_units
|
|
)
|
|
|
|
# save it
|
|
usethis::use_data(antivirals, overwrite = TRUE)
|