diff --git a/DESCRIPTION b/DESCRIPTION index 01f679750..ab1b15bf0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9142 +Version: 2.1.1.9143 Date: 2025-02-07 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index ab670e3d7..cb7e07030 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9142 +# AMR 2.1.1.9143 *(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).)* diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index 07d00dadb..f146f9511 100644 --- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO +++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 2.2 Name: AMR -Version: 2.1.1.9142 +Version: 2.1.1.9143 Summary: A Python wrapper for the AMR R package Home-page: https://github.com/msberends/AMR Author: Matthijs Berends diff --git a/PythonPackage/AMR/dist/AMR-2.1.1.9142-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9143-py3-none-any.whl similarity index 85% rename from PythonPackage/AMR/dist/AMR-2.1.1.9142-py3-none-any.whl rename to PythonPackage/AMR/dist/AMR-2.1.1.9143-py3-none-any.whl index e8d2f2843..5e69bbaf9 100644 Binary files a/PythonPackage/AMR/dist/AMR-2.1.1.9142-py3-none-any.whl and b/PythonPackage/AMR/dist/AMR-2.1.1.9143-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9142.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9142.tar.gz deleted file mode 100644 index e6d0a2557..000000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9142.tar.gz and /dev/null differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9143.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9143.tar.gz new file mode 100644 index 000000000..5fbe61593 Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9143.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index 03d90f6e9..1d3ad34b7 100644 --- a/PythonPackage/AMR/setup.py +++ b/PythonPackage/AMR/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages setup( name='AMR', - version='2.1.1.9142', + version='2.1.1.9143', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/R/aa_globals.R b/R/aa_globals.R index 121aed17b..baa388825 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -138,12 +138,15 @@ globalVariables(c( "atc_group1", "atc_group2", "base_ab", + "beta_posterior_1", + "beta_posterior_2", "ci_max", "ci_min", "clinical_breakpoints", "code", "cols", "count", + "coverage", "data", "disk", "dosage", @@ -152,6 +155,7 @@ globalVariables(c( "fullname", "fullname_lower", "g_species", + "gamma_posterior", "genus", "gr", "group", @@ -166,6 +170,7 @@ globalVariables(c( "language", "lookup", "lower", + "lower_ci", "method", "mic ", "mic", @@ -197,9 +202,11 @@ globalVariables(c( "species", "syndromic_group", "total", + "total_rows", "txt", "type", "upper", + "upper_ci", "uti_index", "value", "varname", diff --git a/R/antibiogram.R b/R/antibiogram.R index 9ea996df9..0d2ea5166 100755 --- a/R/antibiogram.R +++ b/R/antibiogram.R @@ -625,7 +625,7 @@ antibiogram.default <- function(x, # simulate pathogen incidence # = Dirichlet (Gamma) parameters - random_incidence <- runif(1, min = 0, max = 1) + random_incidence <- stats::runif(1, min = 0, max = 1) simulated_incidence <- stats::qgamma( p = random_incidence, shape = priors$gamma_posterior, @@ -636,7 +636,7 @@ antibiogram.default <- function(x, # simulate susceptibility # = Beta parameters - random_susceptibity <- runif(1, min = 0, max = 1) + random_susceptibity <- stats::runif(1, min = 0, max = 1) simulated_susceptibility <- stats::qbeta( p = random_susceptibity, shape1 = priors$beta_posterior_1, @@ -1009,7 +1009,7 @@ wisca <- function(x, } #' @export -#' @param wisca_model the outcome of [wisca()] or [antibiogram(..., wisca = TRUE)] +#' @param wisca_model the outcome of [wisca()] or [`antibiogram(..., wisca = TRUE)`][antibiogram()] #' @rdname antibiogram retrieve_wisca_parameters <- function(wisca_model, ...) { stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use `wisca()` or `antibiogram(..., wisca = TRUE)` to create a WISCA model.") diff --git a/data-raw/gpt_training_text_v2.1.1.9142.txt b/data-raw/gpt_training_text_v2.1.1.9143.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9142.txt rename to data-raw/gpt_training_text_v2.1.1.9143.txt index f09d09aab..35564233e 100644 --- a/data-raw/gpt_training_text_v2.1.1.9142.txt +++ b/data-raw/gpt_training_text_v2.1.1.9143.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 2.1.1.9142. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9143. 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. ---------------------------------------------------------------------------------------------------- @@ -1708,7 +1708,7 @@ retrieve_wisca_parameters(wisca_model, ...) \item{info}{a \link{logical} to indicate info should be printed - the default is \code{TRUE} only in interactive mode} -\item{wisca_model}{the outcome of \code{\link[=wisca]{wisca()}} or \link{antibiogram(..., wisca = TRUE)}} +\item{wisca_model}{the outcome of \code{\link[=wisca]{wisca()}} or \code{\link[=antibiogram]{antibiogram(..., wisca = TRUE)}}} \item{...}{when used in \link[knitr:kable]{R Markdown or Quarto}: arguments passed on to \code{\link[knitr:kable]{knitr::kable()}} (otherwise, has no use)} diff --git a/man/antibiogram.Rd b/man/antibiogram.Rd index 463d8da99..570b3aec7 100644 --- a/man/antibiogram.Rd +++ b/man/antibiogram.Rd @@ -83,7 +83,7 @@ retrieve_wisca_parameters(wisca_model, ...) \item{info}{a \link{logical} to indicate info should be printed - the default is \code{TRUE} only in interactive mode} -\item{wisca_model}{the outcome of \code{\link[=wisca]{wisca()}} or \link{antibiogram(..., wisca = TRUE)}} +\item{wisca_model}{the outcome of \code{\link[=wisca]{wisca()}} or \code{\link[=antibiogram]{antibiogram(..., wisca = TRUE)}}} \item{...}{when used in \link[knitr:kable]{R Markdown or Quarto}: arguments passed on to \code{\link[knitr:kable]{knitr::kable()}} (otherwise, has no use)}