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(v2.1.1.9123) add EFF code to antibiotics data set

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dr. M.S. (Matthijs) Berends
2025-01-15 16:14:09 +01:00
parent 2e31ec19c3
commit 08ddbaa930
32 changed files with 522 additions and 461 deletions
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8
R/zzz.R
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@ -200,10 +200,14 @@ AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
if (pkg_is_available("tibble")) {
try(loadNamespace("tibble"), silent = TRUE)
}
# reference data - they have additional data to improve algorithm speed
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
if (NROW(AB_LOOKUP) != NROW(AMR::antibiotics)) {
# antibiotics data set was updated - run create_AB_AV_lookup() again
AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
}
AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
}