(v2.1.1.9158) updated as.ab

DESCRIPTION

@@ -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)

NEWS.md

@@ -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

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -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

PythonPackage/AMR/setup.py

@@ -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',

R/ab.R

@@ -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.")

data-raw/gpt_training_text_v2.1.1.9158.txt

@@ -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.
 ----------------------------------------------------------------------------------------------------