P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 00:43:00 +02:00
Code Releases Activity

use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
R/mic.R
View File

@ -219,14 +219,14 @@ as.mic <- function(x, na.rm = FALSE) {
## previously unempty values now empty - should return a warning later on
x[x.bak != "" & x == ""] <- "invalid"
na_before <- x[is.na(x) | x == ""] %pm>% length()
na_before <- x[is.na(x) | x == ""] %>% length()
x[!x %in% valid_mic_levels] <- NA
na_after <- x[is.na(x) | x == ""] %pm>% length()
na_after <- x[is.na(x) | x == ""] %>% length()
if (na_before != na_after) {
list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
unique() %pm>%
sort() %pm>%
list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %>%
unique() %>%
sort() %>%
vector_and(quotes = TRUE)
cur_col <- get_current_column()
warning_("in `as.mic()`: ", na_after - na_before, " result",