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add strep groups to ABCG
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10
R/sir.R
10
R/sir.R
@ -941,7 +941,7 @@ as_sir_method <- function(method_short,
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mo_current <- df_unique[i, "mo", drop = TRUE]
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uti_current <- df_unique[i, "uti", drop = TRUE]
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if (is.na(uti_current)) {
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# preference, so no filter on UTIs
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# no preference, so no filter on UTIs
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rows <- which(df$mo == mo_current)
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} else {
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rows <- which(df$mo == mo_current & df$uti == uti_current)
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@ -957,10 +957,10 @@ as_sir_method <- function(method_short,
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mo_current_rank <- AMR_env$MO_lookup$rank[match(mo_current, AMR_env$MO_lookup$mo)]
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mo_current_name <- AMR_env$MO_lookup$fullname[match(mo_current, AMR_env$MO_lookup$mo)]
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if (mo_current %in% AMR::microorganisms.groups$mo) {
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# get the species group
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mo_current_species_group <- AMR::microorganisms.groups$mo_group[match(mo_current, AMR::microorganisms.groups$mo)]
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# get the species group (might be more than 1 entry)
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mo_current_species_group <- AMR::microorganisms.groups$mo_group[which(AMR::microorganisms.groups$mo == mo_current)]
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} else {
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mo_current_species_group <- mo_current
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mo_current_species_group <- NULL
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}
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mo_current_other <- structure("UNKNOWN", class = c("mo", "character"))
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# formatted for notes
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@ -977,7 +977,7 @@ as_sir_method <- function(method_short,
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# (this will prefer species breakpoints over order breakpoints)
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breakpoints_current <- breakpoints %pm>%
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subset(mo %in% c(
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mo_current_genus, mo_current_family,
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mo_current, mo_current_genus, mo_current_family,
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mo_current_order, mo_current_class,
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mo_current_species_group,
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mo_current_other
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