P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 22:21:52 +02:00
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

17
R/sir.R
View File

@ -1270,10 +1270,13 @@ as_sir_method <- function(method_short,
}
}
mo_grams <- suppressWarnings(suppressMessages(mo_gramstain(df_unique$mo, language = NULL, keep_synonyms = FALSE)))
# run the rules (df_unique is a row combination per mo/ab/uti/host) ----
for (i in seq_len(nrow(df_unique))) {
p$tick()
mo_current <- df_unique[i, "mo", drop = TRUE]
mo_gram_current <- mo_grams[i]
ab_current <- df_unique[i, "ab", drop = TRUE]
host_current <- df_unique[i, "host", drop = TRUE]
uti_current <- df_unique[i, "uti", drop = TRUE]
@ -1300,12 +1303,25 @@ as_sir_method <- function(method_short,
mo_current_class <- AMR_env$MO_lookup$mo[match(AMR_env$MO_lookup$class[match(mo_current, AMR_env$MO_lookup$mo)], AMR_env$MO_lookup$fullname)]
mo_current_rank <- AMR_env$MO_lookup$rank[match(mo_current, AMR_env$MO_lookup$mo)]
mo_current_name <- AMR_env$MO_lookup$fullname[match(mo_current, AMR_env$MO_lookup$mo)]
mo_current_oxygen_tolerance <- AMR_env$MO_lookup$oxygen_tolerance[match(mo_current, AMR_env$MO_lookup$mo)]
if (mo_current %in% AMR::microorganisms.groups$mo) {
# get the species group (might be more than 1 entry)
mo_current_species_group <- AMR::microorganisms.groups$mo_group[which(AMR::microorganisms.groups$mo == mo_current)]
} else {
mo_current_species_group <- NULL
}
mo_current_gram <- structure(character(0), class = c("mo", "character"))
if (identical(mo_gram_current, "Gram-negative")) {
mo_current_gram <- c(mo_current_gram, "B_GRAMN")
if (identical(mo_current_oxygen_tolerance, "anaerobe")) {
mo_current_gram <- c(mo_current_gram, "B_ANAER", "B_ANAER-NEG")
}
} else if (identical(mo_gram_current, "Gram-positive")) {
mo_current_gram <- c(mo_current_gram, "B_GRAMP")
if (identical(mo_current_oxygen_tolerance, "anaerobe")) {
mo_current_gram <- c(mo_current_gram, "B_ANAER", "B_ANAER-POS")
}
}
mo_current_other <- structure("UNKNOWN", class = c("mo", "character"))
# formatted for notes
mo_formatted <- mo_current_name
@ -1325,6 +1341,7 @@ as_sir_method <- function(method_short,
mo_current, mo_current_genus, mo_current_family,
mo_current_order, mo_current_class,
mo_current_species_group,
mo_current_gram,
mo_current_other
))