P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-06-27 11:36:17 +02:00
Code Releases Activity

(v3.0.1.9059) Update taxonomy of microorganisms

Browse Source
This commit is contained in:
Matthijs Berends
2026-06-23 01:38:13 +02:00
committed by GitHub
parent 0af3f84655
commit 3f9f931777
123 changed files with 121928 additions and 94162 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
R/key_antimicrobials.R
View File

@@ -161,11 +161,11 @@ key_antimicrobials <- function(x = NULL,
if (is.null(col_mo)) {
warning_("in {.fun key_antimicrobials}: no column found for {.arg col_mo}, ignoring antibiotics set in {.arg gram_negative} and {.arg gram_positive}, and antimycotics set in {.arg antifungal}")
gramstain <- NA_character_
kingdom <- NA_character_
domain <- NA_character_
} else {
x.mo <- as.mo(x[, col_mo, drop = TRUE])
gramstain <- mo_gramstain(x.mo, language = NULL)
kingdom <- mo_kingdom(x.mo, language = NULL)
domain <- mo_domain(x.mo, language = NULL)
}
AMR_string <- function(x, values, name, filter, cols = cols) {
@@ -219,11 +219,11 @@ key_antimicrobials <- function(x = NULL,
cols = cols
)
key_ab[which(kingdom == "Fungi")] <- AMR_string(
key_ab[which(domain == "Fungi")] <- AMR_string(
x = x,
values = antifungal,
name = "antifungal",
filter = kingdom == "Fungi",
filter = domain == "Fungi",
cols = cols
)