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correct for high-level abx

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dr. M.S. (Matthijs) Berends 2024-04-24 09:50:32 +02:00
parent 0d8a91db49
commit 25089e811e
4 changed files with 17 additions and 1 deletions
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4
.github/prehooks/commit-msg vendored
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@ -36,7 +36,9 @@
# check the commit message # check the commit message
COMMIT_MSG=$(cat "$1") COMMIT_MSG=$(cat "$1")
if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then 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 exit 0
fi fi

2
NEWS.md
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@ -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`. * 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 ATC codes from WHOCC
* Updated all antibiotic DDDs 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 ## Other
* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input * Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input

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

10
inst/tinytest/test-ab.R
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@ -79,6 +79,16 @@ expect_equal(
# based on Levenshtein distance # based on Levenshtein distance
expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam") 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 # assigning and subsetting
x <- antibiotics$ab x <- antibiotics$ab
expect_inherits(x[1], "ab") expect_inherits(x[1], "ab")