P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 21:01:57 +02:00
Code Releases Activity

(v2.1.1.9095) Python support

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-10-15 17:12:55 +02:00
parent 94501371cd
commit 5c4d8fcd2a
18 changed files with 513 additions and 435 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
R/sir.R
View File

@ -1263,7 +1263,7 @@ as_sir_method <- function(method_short,
if (breakpoint_type == "animal" && !host_current %in% breakpoints_current$host) {
if (guideline_coerced %like% "CLSI") {
# VET09 says that staph/strep/enterococcus BP can be extrapolated to all Gr+ cocci except for intrinsic resistance, so take all Gr+ cocci:
all_gram_pos_genera <- c("B_STPHY", "B_STRPT", "B_ENTRC", "B_PPTST", "B_AERCC", "B_MCRCCC", "B_TRPRL")
all_gram_pos_genera <- c("B_STPHY", "B_STRPT", "B_PPTST", "B_AERCC", "B_MCRCCC", "B_TRPRL")
# HUMAN SUBSTITUTES
if (ab_current == "AZM" && mo_current_genus %in% all_gram_pos_genera && host_current %in% c("dogs", "cats", "horse")) {
@ -1310,9 +1310,9 @@ as_sir_method <- function(method_short,
# vancomycin can take human breakpoints in these hosts
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", ab_formatted, " based on CLSI VET09."))
} else if (host_current %in% c("dogs", "cats") && (mo_current_genus %in% c("B_AMYCS", "B_NOCRD", "B_CMPYL", "B_CRYNB", "B_ENTRC", "B_MYCBC", "B_PSDMN", "B_AERMN") | mo_current_class == "B_[CLS]_BTPRTBCT" | mo_current == "B_LISTR_MNCY")) {
# human breakpoints if no canine/feline
# dog breakpoints if no canine/feline
breakpoints_current <- breakpoints_current %pm>% subset(host == "human")
notes_current <- c(notes_current, paste0("Using ", font_bold("human"), " breakpoints for ", mo_formatted, " based on CLSI VET09."))