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(v2.1.1.9158) updated as.ab

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dr. M.S. (Matthijs) Berends 2025-02-26 13:32:16 +01:00
parent 195dfb4b91
commit 122bca0f95
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9 changed files with 21 additions and 11 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 2.1.1.9157
Version: 2.1.1.9158
Date: 2025-02-26
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

4
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9157
# AMR 2.1.1.9158
*(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! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
@ -80,7 +80,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Fix for using a manual value for `mo_transform` in `antibiogram()`
* Fixed a bug for when `antibiogram()` returns an empty data set
* Fix for mapping 'high level' antibiotics in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
* Improved overall algorithm of `as.ab()` for better performance and accuracy
* Improved overall algorithm of `as.ab()` for better performance and accuracy, including the new function `as_reset_session()` to remove earlier coercions.
* Improved overall algorithm of `as.mo()` for better performance and accuracy. Specifically:
* More weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species
* Genera from the World Health Organization's (WHO) Priority Pathogen List now have the highest prevalence

2
PythonPackage/AMR/AMR.egg-info/PKG-INFO
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@ -1,6 +1,6 @@
Metadata-Version: 2.2
Name: AMR
Version: 2.1.1.9157
Version: 2.1.1.9158
Summary: A Python wrapper for the AMR R package
Home-page: https://github.com/msberends/AMR
Author: Matthijs Berends

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PythonPackage/AMR/dist/amr-2.1.1.9157.tar.gz vendored
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PythonPackage/AMR/dist/amr-2.1.1.9157-py3-none-any.whl → PythonPackage/AMR/dist/amr-2.1.1.9158-py3-none-any.whl vendored
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PythonPackage/AMR/dist/amr-2.1.1.9158.tar.gz vendored Normal file
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PythonPackage/AMR/setup.py
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@ -2,7 +2,7 @@ from setuptools import setup, find_packages
setup(
name='AMR',
version='2.1.1.9157',
version='2.1.1.9158',
packages=find_packages(),
install_requires=[
'rpy2',

20
R/ab.R
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@ -349,6 +349,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), loop_time = loop_time + 2))
if (length(found) > 0 && !is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
}
@ -358,6 +359,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
if (length(found) > 0 && !is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
}
@ -392,6 +394,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
if (length(found_perms) > 0) {
found <- found_perms[order(nchar(found_perms), decreasing = TRUE)][1]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
}
@ -418,6 +421,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 2))
if (!is.na(x_translated_guess)) {
x_new[i] <- x_translated_guess
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -441,6 +445,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 2))
if (!is.na(x_translated_guess)) {
x_new[i] <- x_translated_guess
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -449,6 +454,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i], perl = TRUE), loop_time = loop_time + 2))
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
}
@ -457,6 +463,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -471,6 +478,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -483,6 +491,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(substr(x[i], 1, 7), loop_time = loop_time + 2))
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -495,6 +504,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -507,6 +517,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -519,6 +530,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(x_spelling, loop_time = loop_time + 2, already_regex = TRUE))
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -540,6 +552,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
if (!is.na(found)) {
x_new[i] <- found[1L]
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
} # end of loop_time <= 2
@ -590,11 +603,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# Throw note about uncertainties
if (isTRUE(info) && length(x_uncertain) > 0 && fast_mode == FALSE) {
x_uncertain <- unique(x_uncertain)
if (message_not_thrown_before("as.ab", "uncertainties", x_bak)) {
plural <- c("", "this")
if (length(x_uncertain) > 1) {
plural <- c("s", "these uncertainties")
}
if (length(x_uncertain) <= 3) {
examples <- vector_and(
paste0(
@ -603,7 +613,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
", ", AMR_env$ab_previously_coerced$ab[which(AMR_env$ab_previously_coerced$x_bak %in% x_uncertain)], ")"),
quotes = FALSE)
} else {
examples <- paste0(nr2char(length(x_uncertain)), " antimicrobial", plural[1])
examples <- paste0(nr2char(length(x_uncertain)), " antimicrobials")
}
message_("Antimicrobial translation was uncertain for ", examples,
". If required, use `add_custom_antimicrobials()` to add custom entries.")

2
data-raw/gpt_training_text_v2.1.1.9157.txt → data-raw/gpt_training_text_v2.1.1.9158.txt
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@ -1,6 +1,6 @@
This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
First and foremost, you are trained on version 2.1.1.9157. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9158. Remember this whenever someone asks which AMR package version you’re at.
Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens.
----------------------------------------------------------------------------------------------------