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use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

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dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
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11
R/join_microorganisms.R
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@ -159,14 +159,9 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
by <- stats::setNames("mo", by)
}
# use dplyr if available - it's much faster than poorman alternatives
dplyr_join <- import_fn(name = type, pkg = "dplyr", error_on_fail = FALSE)
if (!is.null(dplyr_join)) {
join_fn <- dplyr_join
} else {
# otherwise use poorman, see R/aa_helper_pm_functions.R
join_fn <- get(paste0("pm_", type), envir = asNamespace("AMR"))
}
# this will use dplyr if available, and the slower poorman otherwise, see R/aaa_helper_pm_functions.R
join_fn <- get(type, envir = asNamespace("AMR"))
MO_df <- AMR_env$MO_lookup[, colnames(AMR::microorganisms), drop = FALSE]
if (type %like% "full|left|right|inner") {
joined <- join_fn(x = x, y = MO_df, by = by, suffix = suffix, ...)