update reproduction scripts links

data-raw/_reproduction_scripts/reproduction_of_antivirals.R

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+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
+# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
+# Journal of Statistical Software, 104(3), 1-31.                       #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   #
+#                                                                      #
+# 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://amr-for-r.org              #
+# ==================================================================== #
+
+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://atcddd.fhi.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
+  table_title <- downloaded %>%
+    html_nodes(paste0('a[href^="./?code=', atc_group, '&"]')) %>%
+    html_text()
+  table_title <- table_title[tolower(table_title) != "show text from guidelines"][1]
+  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://atcddd.fhi.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]))
+}
+
+# arrange on name, untibble it
+antivirals <- antivirals %>%
+  arrange(name) %>%
+  as.data.frame(stringsAsFactors = FALSE)
+
+# add PubChem Compound ID (cid) and their trade names
+# see `data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R` for get_CID() and get_synonyms()
+CIDs <- get_CID(antivirals$name)
+# these could not be found:
+antivirals[is.na(CIDs), ] %>% View()
+# get brand names from PubChem
+synonyms <- get_synonyms(CIDs)
+synonyms <- lapply(
+  synonyms,
+  function(x) {
+    if (length(x) == 0 | all(is.na(x))) {
+      ""
+    } else {
+      x
+    }
+  }
+)
+
+antivirals <- antivirals %>%
+  transmute(atc,
+    cid = as.double(CIDs),
+    name,
+    atc_group,
+    synonyms = unname(synonyms),
+    oral_ddd,
+    oral_units,
+    iv_ddd,
+    iv_units
+  ) %>%
+  AMR:::dataset_UTF8_to_ASCII()
+
+av_codes <- tibble(name = antivirals$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, run 'data-raw/loinc.R' !
+
+# 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
+
+# save it
+usethis::use_data(antivirals, overwrite = TRUE, internal = FALSE, compress = "xz", version = 2)