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move object assignment to AMR_env

This commit is contained in:
2022-10-14 13:02:50 +02:00
parent dfae4c7e7d
commit 76bcd3528c
18 changed files with 116 additions and 127 deletions

View File

@ -145,7 +145,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
}
message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # message same as dplyr::join functions
}
if (!all(x[, by, drop = TRUE] %in% MO_lookup$mo, na.rm = TRUE)) {
if (!all(x[, by, drop = TRUE] %in% AMR_env$MO_lookup$mo, na.rm = TRUE)) {
x$join.mo <- as.mo(x[, by, drop = TRUE])
by <- c("join.mo" = "mo")
} else {