Make anaerobes more specific than a Gram stain in rank_index

Anaerobes now have rank_index 5.5 (5.6 for a blocking row), and a Gram stain stays at 6. They had the same rank, so the order of sites could make the Gram-negative row with site Parenteral (CLSI Table 2B-5) precede the anaerobe row without a site (CLSI Table 2J), e.g., for ceftriaxone in B. fragilis.

A rebuild changes rank_index in 884 rows and nothing else.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
 Version: 3.1.0.9015
-Date: 2026-11-02
+Date: 2026-11-03
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

R/data.R

@@ -298,7 +298,7 @@
 #' - `method`\cr Testing method, either `r vector_or(clinical_breakpoints$method, documentation = TRUE)`
 #' - `site`\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
 #' - `mo`\cr Microbial ID, see [as.mo()]
-#' - `rank_index`\cr Taxonomic rank index of `mo`, used to choose the most specific breakpoint (the lowest index): 1 for subspecies and infraspecies, 2 for species, 2.5 for species groups (e.g., *Streptococcus* group A), 3 for genus, 4 for family, 5 for order, 6 for other groups (e.g., Gram-negative or anaerobic bacteria), and 7 for non-species related (PK-PD) breakpoints. Blocking rows (see *Details*) have the rank index of their organism + 0.1, e.g., 2.6 for a species group, so that a breakpoint for the same organism always takes precedence.
+#' - `rank_index`\cr Taxonomic rank index of `mo`, used to choose the most specific breakpoint (the lowest index): 1 for subspecies and infraspecies, 2 for species, 2.5 for species groups (e.g., *Streptococcus* group A), 3 for genus, 4 for family, 5 for order, 5.5 for anaerobic bacteria, 6 for other groups (e.g., Gram-negative bacteria), and 7 for non-species related (PK-PD) breakpoints. Blocking rows (see *Details*) have the rank index of their organism + 0.1, e.g., 2.6 for a species group, so that a breakpoint for the same organism always takes precedence.
 #' - `ab`\cr Antimicrobial code as used by this package, EARS-Net and WHONET, see [as.ab()]
 #' - `ref_tbl`\cr Info about where the guideline rule can be found
 #' - `disk_dose`\cr Dose of the used disk diffusion method

data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R

@@ -720,7 +720,8 @@ breakpoints_new <- breakpoints_new |>
     mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
     mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
     mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
-    mo != "UNKNOWN" ~ 6, # for B_ANAER, etc.
+    grepl("^B_ANAER", as.character(mo)) ~ 5.5, # anaerobes are more specific than a Gram stain
+    mo != "UNKNOWN" ~ 6, # for B_GRAMN, etc.
     TRUE ~ 7
   ) +
     # a breakpoint of the same organism always precedes its blocking row

data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R

@@ -2782,7 +2782,8 @@ breakpoints_eucast <- breakpoints_eucast |>
   mutate(
     rank_index = case_when(
       mo == "UNKNOWN" ~ 7, # the PK-PD table, as for the WHONET-based rows
-      is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
+      grepl("^B_ANAER", as.character(mo)) ~ 5.5, # anaerobes are more specific than a Gram stain
+      is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for B_GRAMN, 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,

data-raw/clin_break.md5

@@ -1 +1 @@
-56c3254d6c81a4b3b82d3dc345fdaa68
+8ec8bf482dcbf91277066759fe4f498b

man/clinical_breakpoints.Rd

@@ -13,7 +13,7 @@ A \link[tibble:tibble]{tibble} with 48 382 observations and 15 variables:
 \item \code{method}\cr Testing method, either \code{"DISK"} or \code{"MIC"}
 \item \code{site}\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
 \item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}}
-\item \code{rank_index}\cr Taxonomic rank index of \code{mo}, used to choose the most specific breakpoint (the lowest index): 1 for subspecies and infraspecies, 2 for species, 2.5 for species groups (e.g., \emph{Streptococcus} group A), 3 for genus, 4 for family, 5 for order, 6 for other groups (e.g., Gram-negative or anaerobic bacteria), and 7 for non-species related (PK-PD) breakpoints. Blocking rows (see \emph{Details}) have the rank index of their organism + 0.1, e.g., 2.6 for a species group, so that a breakpoint for the same organism always takes precedence.
+\item \code{rank_index}\cr Taxonomic rank index of \code{mo}, used to choose the most specific breakpoint (the lowest index): 1 for subspecies and infraspecies, 2 for species, 2.5 for species groups (e.g., \emph{Streptococcus} group A), 3 for genus, 4 for family, 5 for order, 5.5 for anaerobic bacteria, 6 for other groups (e.g., Gram-negative bacteria), and 7 for non-species related (PK-PD) breakpoints. Blocking rows (see \emph{Details}) have the rank index of their organism + 0.1, e.g., 2.6 for a species group, so that a breakpoint for the same organism always takes precedence.
 \item \code{ab}\cr Antimicrobial code as used by this package, EARS-Net and WHONET, see \code{\link[=as.ab]{as.ab()}}
 \item \code{ref_tbl}\cr Info about where the guideline rule can be found
 \item \code{disk_dose}\cr Dose of the used disk diffusion method

tests/testthat/test-data.R

@@ -756,6 +756,9 @@ test_that("clinical_breakpoints: consistent and unambiguous", {
   expected <- c("subspecies" = 1, "species" = 2, "species group" = 2.5, "genus" = 3, "family" = 4, "order" = 5)[rank]
   wrong <- which(!is.na(expected) & floor(cb$rank_index * 2) / 2 != expected & cb$rank_index != expected)
   expect_true(length(wrong) == 0, info = paste("rank_index does not match the rank:", describe_mo(unique(cb$mo[wrong]))))
+  # anaerobes are more specific than a Gram stain, with or without the 0.1 of a blocking row
+  expect_true(all(cb$rank_index[grepl("^B_ANAER", cb$mo)] %in% c(5.5, 5.6)))
+  expect_true(all(cb$rank_index[cb$mo %in% c("B_GRAMN", "B_GRAMP")] %in% c(6, 6.1)))
 })
 
 test_that("antimicrobials: unique and well-formed", {

tests/testthat/test-sir.R

@@ -730,6 +730,11 @@ test_that("as.sir() takes the site of a breakpoint into account", {
   expect_true(sir_site_rank("Intravenous, Meningitis") < sir_site_rank("Intravenous, Non-meningitis"))
   expect_true(sir_site_rank("Intravenous, Non-meningitis") < sir_site_rank("Meningitis"))
 
+  # the order of sites does not make a Gram stain precede the more specific anaerobes: CLSI Table 2J, not Table 2B-5
+  expect_identical(sir(as.mic(16), "Bacteroides fragilis", "CRO", guideline = "CLSI 2022"), "S")
+  # and it does make a meningitis breakpoint precede a non-meningitis breakpoint of another taxon of the same rank
+  expect_identical(sir(as.mic(0.25), "Streptococcus agalactiae", "PEN", guideline = "EUCAST 2024"), "R")
+
   # "other" in as.sir(): takes the breakpoint for other infections, or without a site
   expect_identical(sir(as.mic(0.25), "Streptococcus pneumoniae", "PEN", site = "other", guideline = "EUCAST 2012"), "I")
   expect_identical(sir(as.mic(0.25), "Streptococcus pneumoniae", "PEN", site = "meningitis", guideline = "EUCAST 2012"), "R")