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dr. M.S. (Matthijs) Berends
2023-01-06 19:21:04 +01:00
parent cf16bc7de1
commit 84ed8c32bb
12 changed files with 37 additions and 64 deletions
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7
R/join_microorganisms.R
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@ -165,10 +165,11 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
# 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 = AMR::microorganisms, by = by, suffix = suffix, ...)
joined <- join_fn(x = x, y = MO_df, by = by, suffix = suffix, ...)
} else {
joined <- join_fn(x = x, y = AMR::microorganisms, by = by, ...)
joined <- join_fn(x = x, y = MO_df, by = by, ...)
}
if ("join.mo" %in% colnames(joined)) {
@ -185,5 +186,5 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
warning_("in `", type, "_microorganisms()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
}
as_original_data_class(joined, class(x.bak)) # will remove tibble groups
as_original_data_class(joined, class(x.bak)) # will remove tibble groups
}