update intro logo

.github/prehooks/commit-msg

@@ -36,7 +36,9 @@
 # check the commit message
 COMMIT_MSG=$(cat "$1")
 if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
-  echo "Not running pre-commit checks; commit message contains '(no-check)', '(no-checks)', or '(no-verify)."
+  echo "Not running pre-commit checks:"
+  echo "Commit message contains '(no-check)', '(no-checks)', or '(no-verify)."
+  echo ""
   exit 0
 fi
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9022
+Version: 2.1.1.9025
-Date: 2024-04-23
+Date: 2024-04-24
 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

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9022
+# AMR 2.1.1.9025
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
 
@@ -29,6 +29,8 @@ This package now supports not only tools for AMR data analysis in clinical setti
 * Greatly improved `vctrs` integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as `dplyr`'s `bind_rows()`, `rowwise()` and `c_across()` are now supported for e.g. columns of class `mic`. Despite this, this `AMR` package is still zero-dependent on any other package, including `dplyr` and `vctrs`.
 * Updated all ATC codes from WHOCC
 * Updated all antibiotic DDDs from WHOCC
+* Fix for using a manual value for `mo_transform` in `antibiogram()`
+* Fix for mapping 'high level' antibiotics in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
 
 ## Other
 * Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input

R/ab.R

@@ -645,6 +645,8 @@ generalise_antibiotic_name <- function(x) {
   x <- gsub("_(MIC|RSI|SIR|DIS[CK])$", "", x, perl = TRUE)
   # remove disk concentrations, like LVX_NM -> LVX
   x <- gsub("_[A-Z]{2}[0-9_.]{0,3}$", "", x, perl = TRUE)
+  # correct for 'high level' antibiotics
+  x <- gsub("([^A-Z0-9]+)?(HIGH(.?LEVEL)?|H[^A-Z0-9]?L)([^A-Z0-9]+)?", "-HIGH", x, perl = TRUE)
   # remove part between brackets if that's followed by another string
   x <- gsub("(.*)+ [(].*[)]", "\\1", x)
   # keep only max 1 space

inst/tinytest/test-ab.R

@@ -79,6 +79,16 @@ expect_equal(
 # based on Levenshtein distance
 expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")
 
+expect_identical(as.character(as.ab(c("gentamicine High Level",
+                                      "gentamicine High",
+                                      "gentamicine (High Level)",
+                                      "gentamicine (High)",
+                                      "gentamicine HL",
+                                      "gentamicine H-L",
+                                      "gentamicine (HL)",
+                                      "gentamicine (H-L)"))),
+                 rep("GEH", 8))
+
 # assigning and subsetting
 x <- antibiotics$ab
 expect_inherits(x[1], "ab")