(v0.9.0.9012) Support for LOINC codes

data-raw/loinc.R

@@ -0,0 +1,52 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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 more info: https://msberends.gitlab.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)
+  }
+}
+
+dim(antibiotics) # for R/data.R
+usethis::use_data(antibiotics, overwrite = TRUE)
+rm(antibiotics)