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(v0.7.1.9067) honor info

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dr. M.S. (Matthijs) Berends
2019-08-28 17:12:48 +02:00
parent e2b78fa428
commit 34a82d091e
34 changed files with 314 additions and 314 deletions
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4
R/first_isolate.R
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@ -496,7 +496,7 @@ first_isolate <- function(x,
big.mark <- ifelse(decimal.mark != ",", ",", ".")
# handle empty microorganisms
if (any(all_first$newvar_mo == "UNKNOWN", na.rm = TRUE)) {
if (any(all_first$newvar_mo == "UNKNOWN", na.rm = TRUE) & info == TRUE) {
if (include_unknown == TRUE) {
message(blue(paste0("NOTE: Included ", format(sum(all_first$newvar_mo == "UNKNOWN"),
decimal.mark = decimal.mark, big.mark = big.mark),
@ -511,7 +511,7 @@ first_isolate <- function(x,
all_first[which(all_first$newvar_mo == "UNKNOWN"), 'real_first_isolate'] <- include_unknown
# exclude all NAs
if (any(is.na(all_first$newvar_mo))) {
if (any(is.na(all_first$newvar_mo)) & info == TRUE) {
message(blue(paste0("NOTE: Excluded ", format(sum(is.na(all_first$newvar_mo)),
decimal.mark = decimal.mark, big.mark = big.mark),
' isolates with a microbial ID "NA" (column `', bold(col_mo), '`).')))