(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() …

…and fixed Python wrapper

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9125
-Date: 2025-01-17
+Version: 2.1.1.9126
+Date: 2025-01-26
 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
@@ -59,4 +59,4 @@ License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
-Roxygen: list(markdown = TRUE)
+Roxygen: list(markdown = TRUE, old_usage = TRUE)

NAMESPACE

@@ -32,6 +32,8 @@ S3method(Ops,mic)
 S3method(Summary,mic)
 S3method(all,amr_selector)
 S3method(all,amr_selector_any_all)
+S3method(antibiogram,default)
+S3method(antibiogram,grouped_df)
 S3method(any,amr_selector)
 S3method(any,amr_selector_any_all)
 S3method(as.data.frame,ab)
@@ -219,6 +221,7 @@ export(g.test)
 export(geom_sir)
 export(get_AMR_locale)
 export(get_episode)
+export(get_long_numeric_format)
 export(get_mo_source)
 export(ggplot_pca)
 export(ggplot_sir)
@@ -335,9 +338,11 @@ export(streptogramins)
 export(susceptibility)
 export(tetracyclines)
 export(theme_sir)
+export(top_n_microorganisms)
 export(translate_AMR)
 export(trimethoprims)
 export(ureidopenicillins)
+export(wisca)
 importFrom(graphics,arrows)
 importFrom(graphics,axis)
 importFrom(graphics,barplot)

NEWS.md

@@ -1,12 +1,12 @@
-# AMR 2.1.1.9125
+# AMR 2.1.1.9126
 
 *(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).)*
 
 #### A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
 This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island's Atlantic Veterinary College](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
 
 ## Breaking
-* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
+* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents two years ago
 
 ## New
 * **One Health implementation**
@@ -16,6 +16,8 @@ This package now supports not only tools for AMR data analysis in clinical setti
   * The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
   * `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
   * `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
+* Support for WISCA antibiograms**  
+  * The `antibiogram()` function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in datasets with sparse data. A dedicated `wisca()` function is also available for easy usage.
 * **Major update to fungal taxonomy and tools for mycologists**
   * MycoBank has now been integrated as the primary taxonomic source for fungi. The `microorganisms` data set has been enriched with new columns (`mycobank`, `mycobank_parent`, and `mycobank_renamed_to`) that provide detailed information for fungal species.
   * A remarkable addition of over 20,000 new fungal records
@@ -33,7 +35,9 @@ This package now supports not only tools for AMR data analysis in clinical setti
 * **Support for `tidymodels`**
   * All antimicrobial selectors (such as `aminoglycosides()` and `betalactams()`) are now supported in `tidymodels` packages such as `recipe` and `parsnip`. See for more info [our tutorial](https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html) on using these AMR functions for predictive modelling.
 * **Other**
+  * New function `top_n_microorganisms()` to filter a data set to the top *n* of any taxonomic property, e.g., filter to the top 3 species, filter to any species in the top 5 genera, or filter to the top 3 species in each of the top 5 genera
   * New function `mo_group_members()` to retrieve the member microorganisms of a microorganism group. For example, `mo_group_members("Strep group C")` returns a vector of all microorganisms that belong to that group.
+
 
 ## Changed
 * SIR interpretation
@@ -68,12 +72,12 @@ This package now supports not only tools for AMR data analysis in clinical setti
 * Updated all antibiotic DDDs from WHOCC
 * Added over 1,500 trade names for antibiotics
 * 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.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
-* Fixed a bug for when `antibiogram()` returns an empty data set
 * Fixed a bug for `sir_confidence_interval()` when there are no isolates available
 * Updated the prevalence calculation to include genera from the World Health Organization's (WHO) Priority Pathogen List
 * Improved algorithm of `first_isolate()` when using the phenotype-based method, to prioritise records with the highest availability of SIR values
@@ -83,14 +87,15 @@ This package now supports not only tools for AMR data analysis in clinical setti
   * Added arguments `esbl`, `carbapenemase`, `mecA`, `mecC`, `vanA`, `vanB` to denote column names or logical values indicating presence of these genes (or production of their proteins)
 
 ## Other
+* Added Dr. Larisse Bolton as contributor for her fantastic implementation of WISCA in a mathematically solid way
+* Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
 * 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 updated and expanded documentation
-* Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
 * Stopped support for SAS (`.xpt`) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
 
 ## Older Versions
 
-This changelog only contains changes from AMR v3.0 (October 2024) and later.
+This changelog only contains changes from AMR v3.0 (February 2025) and later.
 
 * For prior v2 versions, please see [our v2 archive](https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md).
 * For prior v1 versions, please see [our v1 archive](https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md).

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9125
+Version: 2.1.1.9126
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/AMR/__init__.py

@@ -26,6 +26,7 @@
 from .functions import age
 from .functions import age_groups
 from .functions import antibiogram
+from .functions import wisca
 from .functions import amr_class
 from .functions import amr_selector
 from .functions import aminoglycosides
@@ -201,5 +202,6 @@
 from .functions import sir_predict
 from .functions import ggplot_sir_predict
 from .functions import skewness
+from .functions import top_n_microorganisms
 from .functions import reset_AMR_locale
 from .functions import translate_AMR

PythonPackage/AMR/AMR/datasets.py

@@ -3,14 +3,15 @@
 RESET = '\033[0m'
 
 import os
+import sys
 from rpy2 import robjects
 from rpy2.robjects import pandas2ri
 from rpy2.robjects.packages import importr, isinstalled
 import pandas as pd
 import importlib.metadata as metadata
 
 # Get the path to the virtual environment
-venv_path = os.getenv('VIRTUAL_ENV')  # Path to the active virtual environment
+venv_path = sys.prefix
 
 # Define R library path within the venv
 r_lib_path = os.path.join(venv_path, "R_libs")
@@ -19,10 +20,12 @@
 # Set the R library path in .libPaths
 base = importr('base')
 base._libPaths(r_lib_path)
+r_amr_lib_path = base._libPaths()[0]
 
 # Check if the AMR package is installed in R
-if not isinstalled('AMR'):
+if not isinstalled('AMR', lib_loc = r_amr_lib_path):
     utils = importr('utils')
+    print(f"{BLUE}AMR:{RESET} Installing AMR package to {BLUE}{r_amr_lib_path}/{RESET}...", flush=True)
     utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
 
 # Python package version of AMR
@@ -37,7 +40,7 @@
 # Compare R and Python package versions
 if r_amr_version != python_amr_version:
     try:
-        print(f"{BLUE}AMR:{RESET} Updating package version{RESET}", flush=True)
+        print(f"{BLUE}AMR:{RESET} Updating AMR package in {BLUE}{r_amr_lib_path}/{RESET}...", flush=True)
         utils = importr('utils')
         utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
     except Exception as e: