P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-12-14 20:30:19 +01:00
Code Releases Activity

(v2.1.1.9195) add BTL-S, fix ranks in unknown microorganisms

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-13 14:30:14 +01:00
parent a7ef22a21e
commit 9aab129ea6
48 changed files with 1789 additions and 1710 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
data-raw/reproduction_of_clinical_breakpoints.R
View File

@@ -346,14 +346,14 @@ breakpoints_new$mo[breakpoints_new$mo == "B_STPHY" & breakpoints_new$ab == "NIT"
# determine rank again now that some changes were made on taxonomic level (genus -> species)
breakpoints_new <- breakpoints_new %>%
mutate(rank_index = case_when(
is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
mo_rank(mo, keep_synonyms = TRUE) == "species group" ~ 2.5,
mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
TRUE ~ 6
mo != "UNKNOWN" ~ 6, # for B_ANAER, etc.
TRUE ~ 7
))
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales: