P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 09:51:48 +02:00
Code Releases Activity

revert back to pre-antibiogram

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-09 13:07:39 +01:00
parent aa48c6bf53
commit 1a0dc4bf46
53 changed files with 984 additions and 1996 deletions
Download Patch File Download Diff File Expand all files Collapse all files

11
R/join_microorganisms.R
View File

@ -159,9 +159,14 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
by <- stats::setNames("mo", by)
}
# 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"))
# 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"))
}
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, ...)