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new MOs, cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-09-01 21:19:46 +02:00
parent 5965d3c794
commit 75fe4d401f
20 changed files with 166 additions and 179 deletions
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6
R/first_isolate.R
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@ -178,7 +178,7 @@ first_isolate <- function(tbl,
if (!is.na(col_mo)) {
if (!tbl %>% pull(col_mo) %>% is.mo()) {
warning("Improve integrity of the `", col_mo, "` column by transforming it with 'as.mo'.")
tbl[, col_mo] <- as.mo(tbl[, col_mo])
}
# join to microorganisms data set
tbl <- tbl %>% left_join_microorganisms(by = col_mo)
@ -311,7 +311,7 @@ first_isolate <- function(tbl,
if (info == TRUE) {
message('No isolates found.')
}
# NA's where genus is unavailable
# NAs where genus is unavailable
tbl <- tbl %>%
mutate(real_first_isolate = if_else(genus == '', NA, FALSE))
if (output_logical == FALSE) {
@ -406,7 +406,7 @@ first_isolate <- function(tbl,
all_first[which(all_first[, col_icu] == TRUE), 'real_first_isolate'] <- FALSE
}
# NA's where genus is unavailable
# NAs where genus is unavailable
all_first <- all_first %>%
mutate(real_first_isolate = if_else(genus %in% c('', '(no MO)', NA), NA, real_first_isolate))