breakpoints fixes

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.0.0.9038
+Version: 2.0.0.9039
 Date: 2023-07-11
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.0.0.9038
+# AMR 2.0.0.9039
 
 ## New
 * Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations

R/mdro.R

@@ -52,7 +52,7 @@
 #'
 #' * `guideline = "CMI2012"` (default)
 #'
-#'   Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) ([link](https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext))
+#'   Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\doi{10.1111/j.1469-0691.2011.03570.x})
 #'
 #' * `guideline = "EUCAST3.3"` (or simply `guideline = "EUCAST"`)
 #'

data-raw/clin_break.md5

@@ -1 +1 @@
-b7b41c57fe7e03f0a6af93737aa139d6
+b0c1c3ddb9f8a23aedff6208e9f8d32a

data-raw/reproduction_of_clinical_breakpoints.R

@@ -313,6 +313,21 @@ clinical_breakpoints <- clinical_breakpoints %>%
 clinical_breakpoints <- clinical_breakpoints %>% filter(mo != as.mo("Achromobacter denitrificans"))
 # WHONET contains gentamicin breakpoints for viridans streptocci, which are intrinsic R - they meant genta-high, which is ALSO in their table, so we just remove gentamicin in viridans streptococci
 clinical_breakpoints <- clinical_breakpoints %>% filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
+# Nitrofurantoin in Staph (EUCAST) only applies to S. saprophyticus, while WHONET has the DISK correct but the MIC on genus level
+clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STPHY" & clinical_breakpoints$ab == "NIT" & clinical_breakpoints$guideline %like% "EUCAST"] <- as.mo("B_STPHY_SPRP")
+# determine rank again
+clinical_breakpoints <- clinical_breakpoints %>% 
+  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
+  ))
+
 
 # WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
 # EUCAST 2022 guideline: S <= 8 and R > 8
@@ -349,6 +364,7 @@ dim(clinical_breakpoints)
 # SAVE TO PACKAGE ----
 
 clinical_breakpoints <- breakpoints_new
+clinical_breakpoints <- clinical_breakpoints %>% dataset_UTF8_to_ASCII()
 usethis::use_data(clinical_breakpoints, overwrite = TRUE, compress = "xz", version = 2)
 rm(clinical_breakpoints)
 devtools::load_all(".")

man/mdro.Rd

@@ -93,7 +93,7 @@ Currently supported guidelines are (case-insensitive):
 \itemize{
 \item \code{guideline = "CMI2012"} (default)
 
-Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link})
+Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\doi{10.1111/j.1469-0691.2011.03570.x})
 \item \code{guideline = "EUCAST3.3"} (or simply \code{guideline = "EUCAST"})
 
 The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{link})