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prepare for CRAN

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dr. M.S. (Matthijs) Berends
2023-10-20 14:51:48 +02:00
parent 7dc96794be
commit 7cda9e575b
46 changed files with 7863 additions and 5663 deletions
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55
data-raw/loinc.R
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@ -31,8 +31,8 @@
# 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-complete/ (Loinc_2.67_Text_2.67.zip)
# 3. Read Loinc.csv that's in zip folder LoincTable
# 2. Download the CSV from https://loinc.org/download/loinc-complete/
# 3. Read file LoincTable/Loinc.csv
loinc_df <- read.csv("data-raw/Loinc.csv",
row.names = NULL,
stringsAsFactors = FALSE
@ -42,31 +42,62 @@ loinc_df <- read.csv("data-raw/Loinc.csv",
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("(", ., ")")
# to find the drugs:
loinc_df %>%
filter(COMPONENT %like% "ampicillin|fluconazol|meropenem") %>%
count(CLASS, sort = TRUE)
loinc_df <- loinc_df %>%
filter(CLASS %in% c("DRUG/TOX", "ABXBACT")) %>%
mutate(name = generalise_antibiotic_name(COMPONENT), .before = 1)
# antibiotics
antibiotics$loinc <- as.list(rep(NA_character_, nrow(antibiotics)))
for (i in seq_len(nrow(antibiotics))) {
message(i)
loinc_ab <- loinc_df %>%
filter(COMPONENT %like% paste0("^", antibiotics$name[i])) %>%
filter(name %like% paste0("^", generalise_antibiotic_name(antibiotics$name[i]))) %>%
pull(LOINC_NUM)
if (length(loinc_ab) > 0) {
antibiotics$loinc[i] <- list(loinc_ab)
}
}
# antivirals
antivirals$loinc <- as.list(rep(NA_character_, nrow(antivirals)))
for (i in seq_len(nrow(antivirals))) {
message(i)
loinc_ab <- loinc_df %>%
filter(name %like% paste0("^", generalise_antibiotic_name(antivirals$name[i]))) %>%
pull(LOINC_NUM)
if (length(loinc_ab) > 0) {
antivirals$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(loinc[!loinc == ""]) == 0, list(""), list(loinc))
loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc", drop = TRUE][[1]]))))
loinc <- loinc[loinc != ""]
antibiotics[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc))
}
for (i in 1:nrow(antivirals)) {
loinc <- as.character(sort(unique(tolower(antivirals[i, "loinc", drop = TRUE][[1]]))))
loinc <- loinc[loinc != ""]
antivirals[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc))
}
antibiotics <- dataset_UTF8_to_ASCII(as.data.frame(antibiotics, stringsAsFactors = FALSE))
antibiotics <- dplyr::arrange(antibiotics, name)
antivirals <- dataset_UTF8_to_ASCII(as.data.frame(antivirals, stringsAsFactors = FALSE))
antivirals <- dplyr::arrange(antivirals, name)
# remember to update R/aa_globals.R for the documentation
dim(antibiotics) # for R/data.R
usethis::use_data(antibiotics, overwrite = TRUE)
usethis::use_data(antibiotics, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
rm(antibiotics)
dim(antivirals) # for R/data.R
usethis::use_data(antivirals, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
rm(antivirals)