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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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R/mo_source.R
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@ -288,9 +288,9 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
return(FALSE)
}
}
if (!all(x$mo %in% c("", AMR::microorganisms$mo, AMR::microorganisms$fullname), na.rm = TRUE)) {
if (!all(x$mo %in% c("", AMR_env$MO_lookup$mo, AMR_env$MO_lookup$fullname), na.rm = TRUE)) {
if (stop_on_error == TRUE) {
invalid <- x[which(!x$mo %in% c("", AMR::microorganisms$mo, AMR::microorganisms$fullname)), , drop = FALSE]
invalid <- x[which(!x$mo %in% c("", AMR_env$MO_lookup$mo, AMR_env$MO_lookup$fullname)), , drop = FALSE]
if (nrow(invalid) > 1) {
plural <- "s"
} else {