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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# 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/ #
# ==================================================================== #
# last updated: 20 January 2020 - Loinc_2.67
# Steps to reproduce:
# 1. Create a fake account at https://loinc.org (sad you have to create one...)
# 2. Download the CSV from https://loinc.org/download/loinc-table-file-csv/ (Loinc_2.67_Text_2.67.zip)
# 3. Read Loinc.csv that's in this zip file
loinc_df <- read.csv("data-raw/Loinc.csv",
row.names = NULL,
stringsAsFactors = FALSE)
# 4. Clean and add
library(dplyr)
library(cleaner)
library(AMR)
loinc_df %>% freq(CLASS) # to find the drugs
loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
ab_names <- antibiotics %>% pull(name) %>% paste0(collapse = "|") %>% paste0("(", ., ")")
antibiotics$loinc <- as.list(rep(NA_character_, nrow(antibiotics)))
for (i in seq_len(nrow(antibiotics))) {
loinc_ab <- loinc_df %>%
filter(COMPONENT %like% paste0("^", antibiotics$name[i])) %>%
pull(LOINC_NUM)
if (length(loinc_ab) > 0) {
antibiotics$loinc[i] <- list(loinc_ab)
}
}
# sort and fix for empty values
for (i in 1:nrow(antibiotics)) {
loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc"][[1]]))))
antibiotics[i, "loinc"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(loinc))
}
dim(antibiotics) # for R/data.R
usethis::use_data(antibiotics, overwrite = TRUE)
rm(antibiotics)