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add strep groups to ABCG

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-07-12 11:41:25 +01:00
parent 66eeeb4b88
commit 7cd9ca274c
7 changed files with 12 additions and 39 deletions
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10
R/sir.R
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@ -941,7 +941,7 @@ as_sir_method <- function(method_short,
mo_current <- df_unique[i, "mo", drop = TRUE]
uti_current <- df_unique[i, "uti", drop = TRUE]
if (is.na(uti_current)) {
# preference, so no filter on UTIs
# no preference, so no filter on UTIs
rows <- which(df$mo == mo_current)
} else {
rows <- which(df$mo == mo_current & df$uti == uti_current)
@ -957,10 +957,10 @@ as_sir_method <- function(method_short,
mo_current_rank <- AMR_env$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$mo)]
if (mo_current %in% AMR::microorganisms.groups$mo) {
# get the species group
mo_current_species_group <- AMR::microorganisms.groups$mo_group[match(mo_current, AMR::microorganisms.groups$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 <- mo_current
mo_current_species_group <- NULL
}
mo_current_other <- structure("UNKNOWN", class = c("mo", "character"))
# formatted for notes
@ -977,7 +977,7 @@ as_sir_method <- function(method_short,
# (this will prefer species breakpoints over order breakpoints)
breakpoints_current <- breakpoints %pm>%
subset(mo %in% c(
mo_current_genus, mo_current_family,
mo_current, mo_current_genus, mo_current_family,
mo_current_order, mo_current_class,
mo_current_species_group,
mo_current_other