P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-01-21 00:44:50 +01:00
Code Releases Activity

(v3.0.1.9018) fixes #249

Browse Source 
updates AB groups
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-01-16 10:57:03 +01:00
parent fd50c51543
commit 2df2911cf4
35 changed files with 104 additions and 90 deletions
Download Patch File Download Diff File Expand all files Collapse all files

38
data-raw/_pre_commit_checks.R
View File

@@ -449,14 +449,14 @@ pre_commit_lst$AB_STREPTOGRAMINS <- antimicrobials %>%
filter(atc_group2 %like% "streptogramin") %>%
pull(ab)
pre_commit_lst$AB_TETRACYCLINES <- antimicrobials %>%
filter(group %like% "tetracycline") %>%
filter(atc_group1 %like% "tetracycline" | atc_group2 %like% "tetracycline" | name %like% "chlortetracycline|cetocycline|demeclocycline|doxycycline|eravacycline|lymecycline|meclocycline|meth?acycline|minocycline|omadacycline|oxytetracycline|rolitetracycline|sarecycline|tetracycline|tigecycline") %>%
pull(ab)
pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"]
pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>%
filter(group %like% "trimethoprim") %>%
filter(atc_group1 %like% "trimethoprim" | atc_group2 %like% "trimethoprim" | name %like% "trimethoprim|ormetroprim|iclaprim") %>%
pull(ab)
pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>%
filter(group %like% "trimethoprim" & name %unlike% "trimethoprim") %>%
filter(name %like% "(^|/)sulf[oai]") %>%
pull(ab)
pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
pre_commit_lst$AB_BETALACTAMS <- sort(c(
@@ -500,7 +500,7 @@ for (i in seq_along(group_map)) {
if (is.null(group_map[[i]])) {
group_map[[i]] <- "Other"
if (antimicrobials$group[i] %unlike% "other") {
print(paste0(i, ": ", antimicrobials$group[i], " (", antimicrobials$ab[i], ", ", antimicrobials$name[i], ")"))
usethis::ui_warn("AB had a group but not anymore: ", antimicrobials$name[i], " (", antimicrobials$ab[i], "), was ", toString(antimicrobials$group[i]))
}
}
group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))]
@@ -550,7 +550,6 @@ for (i in seq_along(group_map)) {
}
antimicrobials$group <- unname(group_map)
usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")
rm(antimicrobials)
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(antimicrobials)
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(antivirals)
@@ -738,7 +737,33 @@ files_changed <- function(paths = "^(R|data)/") {
# Update URLs -------------------------------------------------------------
if (files_changed()) {
usethis::ui_info("Checking URLs for redirects")
invisible(urlchecker::url_update("."))
# Step 1: Get sources from tools (excluding man/)
sources <- tools:::url_db_from_package_sources(".")
sources <- sources[!grepl("^man/", sources$Parent), ]
# Step 2: Get URLs from .R files in R/
r_files <- list.files("R", pattern = "\\.R$", full.names = TRUE)
# Function to extract URLs from a file
extract_urls_from_file <- function(file_path) {
lines <- readLines(file_path, warn = FALSE)
urls <- stringr::str_extract_all(lines, "https?://[^\\s)\"'>]+")
urls <- unlist(urls)
if (length(urls) == 0) {
return(NULL)
}
# Remove trailing punctuation (e.g., .,), etc.)
urls <- stringr::str_replace(urls, "[\\.,;)]+$", "")
data.frame(
URL = urls,
Parent = gsub("^\\./", "", file_path),
stringsAsFactors = FALSE
)
}
r_file_urls <- do.call(rbind, lapply(r_files, extract_urls_from_file))
# Step 3: Combine the two sources
total <- rbind(sources, r_file_urls)
# Step 4: Check URLs and update
results <- urlchecker::url_check(db = total)
invisible(urlchecker::url_update(results = results))
}
# Style pkg ---------------------------------------------------------------
@@ -771,5 +796,6 @@ if (files_changed("README.Rmd") ||
}
# Finished ----------------------------------------------------------------
rm(antimicrobials)
usethis::ui_done("All done")
suppressMessages(reset_AMR_locale())