P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-02-22 18:30:07 +01:00
Code Releases Activity

(v2.1.1.9143) unit tests

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2025-02-07 19:18:55 +01:00
parent cc2bb151ab
commit 2171f05951
No known key found for this signature in database
11 changed files with 17 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
DESCRIPTION
View File

@ -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)

2
NEWS.md
View File

@ -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).)*

2
PythonPackage/AMR/AMR.egg-info/PKG-INFO
View File

@ -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

BIN
PythonPackage/AMR/dist/AMR-2.1.1.9142-py3-none-any.whl → PythonPackage/AMR/dist/AMR-2.1.1.9143-py3-none-any.whl vendored
View File

Binary file not shown.

BIN
PythonPackage/AMR/dist/amr-2.1.1.9142.tar.gz vendored
View File

Binary file not shown.

BIN
PythonPackage/AMR/dist/amr-2.1.1.9143.tar.gz vendored Normal file
View File

Binary file not shown.

2
PythonPackage/AMR/setup.py
View File

@ -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',

7
R/aa_globals.R
View File

@ -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",

6
R/antibiogram.R
View File

@ -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.")

4
data-raw/gpt_training_text_v2.1.1.9142.txt → data-raw/gpt_training_text_v2.1.1.9143.txt
View File

@ -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)}

2
man/antibiogram.Rd
View File

@ -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)}