AMR/data-raw/loinc.R

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# ==================================================================== #
# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
# SOURCE #
# https://github.com/msberends/AMR #
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# #
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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 and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
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# #
# 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/ #
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# ==================================================================== #
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# last updated: 30 October 2022 - Loinc_2.73
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# Steps to reproduce:
# 1. Create a fake account at https://loinc.org (sad you have to create one...)
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# 2. Download the CSV from https://loinc.org/download/loinc-complete/ (Loinc_2.67_Text_2.67.zip)
# 3. Read Loinc.csv that's in zip folder LoincTable
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loinc_df <- read.csv("data-raw/Loinc.csv",
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row.names = NULL,
stringsAsFactors = FALSE
)
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# 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")
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ab_names <- antibiotics %>%
pull(name) %>%
paste0(collapse = "|") %>%
paste0("(", ., ")")
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antibiotics$loinc <- as.list(rep(NA_character_, nrow(antibiotics)))
for (i in seq_len(nrow(antibiotics))) {
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message(i)
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loinc_ab <- loinc_df %>%
filter(COMPONENT %like% paste0("^", antibiotics$name[i])) %>%
pull(LOINC_NUM)
if (length(loinc_ab) > 0) {
antibiotics$loinc[i] <- list(loinc_ab)
}
}
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# 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(loinc[!loinc == ""]) == 0, list(""), list(loinc))
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}
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# remember to update R/aa_globals.R for the documentation
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dim(antibiotics) # for R/data.R
usethis::use_data(antibiotics, overwrite = TRUE)
rm(antibiotics)