P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-04-17 19:10:38 +02:00
Code Releases Activity

(v2.1.1.9235) New website!

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2025-04-08 15:54:30 +01:00
parent a905303296
commit 36fd99e1f4
No known key found for this signature in database
172 changed files with 2003 additions and 5522 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.github/prehooks/commit-msg vendored
View File

@ -26,7 +26,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# Path to the commit message file

2
.github/prehooks/pre-commit vendored
View File

@ -26,7 +26,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# Check if commit should skip checks

2
.github/workflows/check-current-testthat.yaml vendored
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
on:

2
.github/workflows/check-old-tinytest.yaml vendored
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
on:

2
.github/workflows/codecovr.yaml vendored
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
on:

2
.github/workflows/lintr.yaml vendored
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
on:

2
.github/workflows/publish-to-pypi.yml vendored
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
on:

2
.github/workflows/website.yaml vendored
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# Create a website from the R documentation using pkgdown

6
DESCRIPTION
View File

@ -1,6 +1,6 @@
Package: AMR
Version: 2.1.1.9234
Date: 2025-04-07
Version: 2.1.1.9235
Date: 2025-04-08
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
@ -62,7 +62,7 @@ Suggests:
vctrs,
xml2
VignetteBuilder: knitr,rmarkdown
URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
URL: https://www.amr-for-r.org/, https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8

10
NEWS.md
View File

@ -1,6 +1,6 @@
# AMR 2.1.1.9234
# AMR 2.1.1.9235
*(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).)*
*(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://www.amr-for-r.org/).)*
#### 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.
@ -8,12 +8,12 @@ This package now supports not only tools for AMR data analysis in clinical setti
## Breaking
* Dataset `antibiotics` has been renamed to `antimicrobials` as the data set contains more than just antibiotics. Using `antibiotics` will still work, but now returns a warning.
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over two years ago.
* Function `resistance_predict()` is now deprecated and will be removed in a future version. Use the `tidymodels` framework instead, for which we [wrote a basic introduction](https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html).
* Function `resistance_predict()` is now deprecated and will be removed in a future version. Use the `tidymodels` framework instead, for which we [wrote a basic introduction](https://www.amr-for-r.org/articles/AMR_with_tidymodels.html).
## New
* **One Health implementation**
* Function `as.sir()` now has extensive support for veterinary breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://www.amr-for-r.org/articles/datasets.html).
* The (new) `antimicrobials` 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
@ -38,7 +38,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* **Support for Python**
* While using R for the heavy lifting, [our 'AMR' Python Package](https://pypi.org/project/AMR/) was developed to run the AMR R package natively in Python. The Python package will always have the same version number as the R package, as it is built automatically with every code change.
* **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.
* 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://www.amr-for-r.org/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.

8
R/aa_amr-package.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' The `AMR` Package
@ -32,11 +32,11 @@
#' @description
#' Welcome to the `AMR` package.
#'
#' The `AMR` package is a [free and open-source](https://msberends.github.io/AMR/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project!
#' The `AMR` package is a [free and open-source](https://amr-for-r.org/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://amr-for-r.org/authors.html) from around the globe are continually helping us to make this a successful and durable project!
#'
#' This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
#'
#' After installing this package, R knows [**`r format_included_data_number(AMR::microorganisms)` microorganisms**](https://msberends.github.io/AMR/reference/microorganisms.html) (updated `r format(TAXONOMY_VERSION$GBIF$accessed_date, "%B %Y")`) and all [**`r format_included_data_number(nrow(AMR::antimicrobials) + nrow(AMR::antivirals))` antibiotic, antimycotic and antiviral drugs**](https://msberends.github.io/AMR/reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl).
#' After installing this package, R knows [**`r format_included_data_number(AMR::microorganisms)` microorganisms**](https://amr-for-r.org/reference/microorganisms.html) (updated `r format(TAXONOMY_VERSION$GBIF$accessed_date, "%B %Y")`) and all [**`r format_included_data_number(nrow(AMR::antimicrobials) + nrow(AMR::antivirals))` antibiotic, antimycotic and antiviral drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl).
#'
#' The `AMR` package is available in `r vector_and(vapply(FUN.VALUE = character(1), LANGUAGES_SUPPORTED_NAMES, function(x) x$exonym), quotes = FALSE, sort = FALSE)`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
#' @section Download Our Reference Data:
@ -44,7 +44,7 @@
#'
#' For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
#'
#' Visit [our website for direct download links](https://msberends.github.io/AMR/articles/datasets.html), or explore the actual files in [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' Visit [our website for direct download links](https://amr-for-r.org/articles/datasets.html), or explore the actual files in [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @source
#' To cite AMR in publications use:
#'

2
R/aa_globals.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints

2
R/aa_helper_functions.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# faster implementation of left_join than using merge() by poorman - we use match():

2
R/aa_helper_pm_functions.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# ------------------------------------------------

2
R/aa_options.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Options for the AMR package

2
R/ab.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Transform Input to an Antibiotic ID

2
R/ab_from_text.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Retrieve Antimicrobial Drug Names and Doses from Clinical Text

2
R/ab_property.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Get Properties of an Antibiotic

2
R/age.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Age in Years of Individuals

4
R/amr_selectors.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Antimicrobial Selectors
@ -47,7 +47,7 @@
#' @details
#' These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and `data.table`. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but are not limited to `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
#'
#' All selectors can also be used 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 antimicrobial selectors for predictive modelling.
#' All selectors can also be used in `tidymodels` packages such as `recipe` and `parsnip`. See for more info [our tutorial](https://amr-for-r.org/articles/AMR_with_tidymodels.html) on using antimicrobial selectors for predictive modelling.
#'
#' All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antimicrobials] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
#'

2
R/antibiogram.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Generate Traditional, Combination, Syndromic, or WISCA Antibiograms

2
R/atc_online.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Get ATC Properties from WHOCC Website

2
R/av.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Transform Input to an Antiviral Drug ID

2
R/av_from_text.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Retrieve Antiviral Drug Names and Doses from Clinical Text

2
R/av_property.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Get Properties of an Antiviral Drug

2
R/availability.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Check Availability of Columns

2
R/bug_drug_combinations.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Determine Bug-Drug Combinations

2
R/count.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Count Available Isolates

2
R/custom_antimicrobials.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Add Custom Antimicrobials

2
R/custom_eucast_rules.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Define Custom EUCAST Rules

2
R/custom_microorganisms.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Add Custom Microorganisms

4
R/data.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Data Sets with `r format(nrow(antimicrobials) + nrow(antivirals), big.mark = " ")` Antimicrobial Drugs
@ -200,7 +200,7 @@
#' Data Set with `r format(nrow(example_isolates), big.mark = " ")` Example Isolates
#'
#' A data set containing `r format(nrow(example_isolates), big.mark = " ")` microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read [the tutorial on our website](https://msberends.github.io/AMR/articles/AMR.html).
#' A data set containing `r format(nrow(example_isolates), big.mark = " ")` microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read [the tutorial on our website](https://amr-for-r.org/articles/AMR.html).
#' @format A [tibble][tibble::tibble] with `r format(nrow(example_isolates), big.mark = " ")` observations and `r ncol(example_isolates)` variables:
#' - `date`\cr Date of receipt at the laboratory
#' - `patient`\cr ID of the patient

2
R/disk.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Transform Input to Disk Diffusion Diameters

2
R/eucast_rules.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# ====================================================== #

2
R/export_biosample.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Export Data Set as NCBI BioSample Antibiogram

2
R/first_isolate.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Determine First Isolates

2
R/g.test.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' *G*-test for Count Data

2
R/get_episode.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Determine Clinical or Epidemic Episodes

2
R/ggplot_pca.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' PCA Biplot with `ggplot2`

2
R/ggplot_sir.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' AMR Plots with `ggplot2`

2
R/guess_ab_col.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Guess Antibiotic Column

2
R/italicise_taxonomy.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Italicise Taxonomic Families, Genera, Species, Subspecies

2
R/join_microorganisms.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Join [microorganisms] to a Data Set

2
R/key_antimicrobials.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' (Key) Antimicrobials for First Weighted Isolates

2
R/kurtosis.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Kurtosis of the Sample

2
R/like.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Vectorised Pattern Matching with Keyboard Shortcut

2
R/mdro.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Determine Multidrug-Resistant Organisms (MDRO)

2
R/mean_amr_distance.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Calculate the Mean AMR Distance

2
R/mic.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# these are allowed MIC values and will become factor levels

2
R/mo.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Transform Arbitrary Input to Valid Microbial Taxonomy

2
R/mo_matching_score.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Calculate the Matching Score for Microorganisms

2
R/mo_property.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Get Properties of a Microorganism

2
R/mo_source.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' User-Defined Reference Data Set for Microorganisms

2
R/pca.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Principal Component Analysis (for AMR)

2
R/plotting.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Plotting Helpers for AMR Data Analysis

2
R/proportion.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Calculate Antimicrobial Resistance

2
R/random.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Random MIC Values/Disk Zones/SIR Generation

4
R/resistance_predict.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Predict Antimicrobial Resistance
@ -133,7 +133,7 @@ resistance_predict <- function(x,
deprecation_warning(
old = "resistance_predict", is_function = TRUE,
extra_msg = paste0("Use the tidymodels framework instead, for which we have written a basic and short introduction on our website: ", font_url("https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html", txt = font_bold("AMR with tidymodels")))
extra_msg = paste0("Use the tidymodels framework instead, for which we have written a basic and short introduction on our website: ", font_url("https://amr-for-r.org/articles/AMR_with_tidymodels.html", txt = font_bold("AMR with tidymodels")))
)
stop_if(is.null(model), 'choose a regression model with the `model` argument, e.g. resistance_predict(..., model = "binomial")')

6
R/sir.R
View File

@ -24,10 +24,10 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data
#' Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data
#'
#' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor] containing the levels `S`, `SDD`, `I`, `R`, `NI`.
#'
@ -167,7 +167,7 @@
#' - **CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.
###### TODO - **CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet09/>.
#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/clinical_breakpoints>.
#' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. <https://whonet.org/>.
#' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. <https://whonet.org/>.
#'
#' @inheritSection AMR Download Our Reference Data
#' @examples

2
R/sir_calc.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
dots2vars <- function(...) {

2
R/sir_df.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' @rdname proportion

2
R/skewness.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Skewness of the Sample

2
R/top_n_microorganisms.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Filter Top *n* Microorganisms

2
R/translate.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Translate Strings from the AMR Package

2
R/vctrs.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# These are all S3 implementations for the vctrs package,

2
R/whocc.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' WHOCC: WHO Collaborating Centre for Drug Statistics Methodology

2
R/zz_deprecated.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
#' Deprecated Functions

2
R/zzz.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# set up package environment, used by numerous AMR functions

8
README.md
View File

@ -17,7 +17,7 @@ Overview:
----
Please visit our extensive website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package, including many examples and tutorials.
Please visit our extensive website <https://www.amr-for-r.org/> to read more about this package, including many examples and tutorials.
### How to get this package
@ -27,14 +27,14 @@ To install the latest 'release' version from CRAN:
install.packages("AMR")
```
To install the latest 'beta' version from GitHub:
To install the latest 'beta' version:
```r
remotes::install_github("msberends/AMR")
install.packages("AMR", repos = "beta.amr-for-r.org")
```
----
<small>
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://msberends.github.io/AMR/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://www.amr-for-r.org//LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.
</small>

4
_pkgdown.yml
View File

@ -24,11 +24,11 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
title: "AMR (for R)"
url: "https://msberends.github.io/AMR/"
url: "https://amr-for-r.org/"
template:
bootstrap: 5

2
codecov.yml
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
codecov:

BIN
data-raw/AMRforRGPT.pdf
View File

Binary file not shown.

BIN
data-raw/AMRforRGPT.pptx
View File

Binary file not shown.

2746
data-raw/AMRforRGPT.svg
View File

File diff suppressed because one or more lines are too long
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 330 KiB

After

Width:  |  Height:  |  Size: 296 KiB

BIN
data-raw/AMRforRGPT_python.pdf
View File

Binary file not shown.

BIN
data-raw/AMRforRGPT_python.pptx
View File

Binary file not shown.

443
data-raw/AMRforRGPT_python.svg Normal file
View File

File diff suppressed because one or more lines are too long
Side by Side

After

Width:  |  Height:  |  Size: 296 KiB

8
data-raw/_generate_python_wrapper.sh
View File

@ -26,7 +26,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# Clean up
@ -71,7 +71,7 @@ base._libPaths(r_lib_path)
# Check if the AMR package is installed in R
if not isinstalled('AMR', lib_loc=r_lib_path):
print(f"AMR: Installing latest AMR R package to {r_lib_path}...", flush=True)
utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True)
# # Retrieve Python AMR version
# try:
@ -87,7 +87,7 @@ if not isinstalled('AMR', lib_loc=r_lib_path):
# if r_amr_version != python_amr_version:
# try:
# print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True)
# utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
# utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True)
# except Exception as e:
# print(f"AMR: Could not update: {e}", flush=True)
@ -248,7 +248,7 @@ for rd_file in "$rd_dir"/*.Rd; do
# Write the Python function definition to the output file
print "def " func_name_py "(" func_args "):" >> "'"$functions_file"'"
print " \"\"\"See our website of the R package for the manual: https://msberends.github.io/AMR/index.html\"\"\"" >> "'"$functions_file"'"
print " \"\"\"See our website of the R package for the manual: https://amr-for-r.org/index.html\"\"\"" >> "'"$functions_file"'"
print " return convert_to_python(amr_r." func_name_py "(" func_args "))" >> "'"$functions_file"'"
print "from .functions import " func_name_py >> "'"$init_file"'"

2
data-raw/_language_update.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# Run this file to update the languages used in the packages:

2
data-raw/_pre_commit_checks.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# Run this file to update the package using:

2
data-raw/_reproduction scripts/reproduction_of_antimicrobials.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
library(dplyr)

2
data-raw/_reproduction scripts/reproduction_of_antivirals.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
library(dplyr)

2
data-raw/_reproduction scripts/reproduction_of_clinical_breakpoints.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# This script runs in 20-30 minutes and renews all guidelines of CLSI and EUCAST!

2
data-raw/_reproduction scripts/reproduction_of_dosage.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
library(dplyr)

2
data-raw/_reproduction scripts/reproduction_of_example_isolates_unclean.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
patients <- unlist(lapply(LETTERS, paste0, 1:10))

2
data-raw/_reproduction scripts/reproduction_of_intrinsic_resistant.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
library(AMR)

2
data-raw/_reproduction scripts/reproduction_of_microorganisms.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# ! THIS SCRIPT REQUIRES AT LEAST 16 GB RAM !

2
data-raw/_reproduction scripts/reproduction_of_microorganisms.groups.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# This data set is being used in the clinical_breakpoints data set, and thus by as.sir().

90
data-raw/gpt_training_text_v2.1.1.9234.txt → data-raw/gpt_training_text_v2.1.1.9235.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 2.1.1.9234. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9235. Remember this whenever someone asks which AMR package version you’re at.
Below are the contents of the NAMESPACE file, the index.md file, and all the man/*.Rd files (documentation) in the package. Every file content is split using 100 hypens.
----------------------------------------------------------------------------------------------------
@ -395,7 +395,7 @@ importFrom(stats,var)
THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'index.md':
# The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
# The `AMR` Package for R <a href="https://amr-for-r.org/"><img src="./logo.svg" align="right" height="139" /></a>
* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
* Used in over 175 countries, available in 20 languages
@ -409,7 +409,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'index.md':
> Now available for Python too! [Click here](./articles/AMR_for_Python.html) to read more.
<div style="display: flex; font-size: 0.8em;">
<p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
<p style="text-align:left; width: 50%;"><small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small></p>
<p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small></p>
</div>
@ -437,7 +437,7 @@ With the help of contributors from all corners of the world, the `AMR` package i
#### Filtering and selecting data
One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial selectors](https://msberends.github.io/AMR/reference/antimicrobial_selectors.html), which work in base R, `dplyr` and `data.table`.
One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial selectors](https://amr-for-r.org/reference/antimicrobial_selectors.html), which work in base R, `dplyr` and `data.table`.
```r
# AMR works great with dplyr, but it's not required or neccesary
@ -583,7 +583,7 @@ example_isolates %>%
|ICU | 0.2902655 | 0.253-0.33 | 0.4004739 | 0.353-0.449 |
|Outpatient | 0.2000000 | 0.131-0.285 | 0.3676471 | 0.254-0.493 |
Or use [antimicrobial selectors](https://msberends.github.io/AMR/reference/antimicrobial_selectors.html) to select a series of antibiotic columns:
Or use [antimicrobial selectors](https://amr-for-r.org/reference/antimicrobial_selectors.html) to select a series of antibiotic columns:
```r
library(AMR)
@ -673,15 +673,15 @@ It will be downloaded and installed automatically. For RStudio, click on the men
Please read our [Developer Guideline here](https://github.com/msberends/AMR/wiki/Developer-Guideline).
The latest and unpublished development version can be installed from the [rOpenSci R-universe platform](https://msberends.r-universe.dev/AMR):
To install the latest and unpublished development version:
```r
install.packages("AMR", repos = "https://msberends.r-universe.dev")
install.packages("AMR", repos = "beta.amr-for-r.org")
```
### Get started
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://msberends.github.io/AMR/articles/).
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://amr-for-r.org/articles/).
### Partners
@ -851,11 +851,11 @@ A BibTeX entry for LaTeX users is:
\description{
Welcome to the \code{AMR} package.
The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://msberends.github.io/AMR/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
The \code{AMR} package is a \href{https://amr-for-r.org/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://amr-for-r.org/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
}
@ -865,13 +865,13 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\seealso{
Useful links:
\itemize{
\item \url{https://msberends.github.io/AMR/}
\item \url{https://www.amr-for-r.org/}
\item \url{https://github.com/msberends/AMR}
\item Report bugs at \url{https://github.com/msberends/AMR/issues}
}
@ -1007,7 +1007,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -1227,7 +1227,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -2313,7 +2313,7 @@ my_data_with_all_these_columns \%>\%
\details{
These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and \code{data.table}. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but are not limited to \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}.
All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling.
All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling.
All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antimicrobials} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
@ -2369,7 +2369,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -2622,7 +2622,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\section{WHOCC}{
@ -2725,7 +2725,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -2838,7 +2838,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -3313,7 +3313,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -3386,7 +3386,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/as.sir.Rd':
\alias{as.sir.disk}
\alias{as.sir.data.frame}
\alias{sir_interpretation_history}
\title{Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data}
\title{Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data}
\source{
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
\itemize{
@ -3394,7 +3394,7 @@ For interpretations of minimum inhibitory concentration (MIC) values and disk di
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2024, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
}
}
\usage{
@ -3621,7 +3621,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -4056,7 +4056,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -4297,7 +4297,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -4698,7 +4698,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -4825,7 +4825,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -4898,7 +4898,7 @@ A \link[tibble:tibble]{tibble} with 2 000 observations and 46 variables:
example_isolates
}
\description{
A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read \href{https://msberends.github.io/AMR/articles/AMR.html}{the tutorial on our website}.
A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read \href{https://amr-for-r.org/articles/AMR.html}{the tutorial on our website}.
}
\section{Download Our Reference Data}{
@ -4906,7 +4906,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -4948,7 +4948,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -5941,7 +5941,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -6766,7 +6766,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -6808,7 +6808,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -6861,7 +6861,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -6945,7 +6945,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -7201,7 +7201,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{
@ -9986,7 +9986,7 @@ library(readxl)
data <- read_excel(path = "path/to/your/file.xlsx")
```
This package comes with an [example data set `WHONET`](https://msberends.github.io/AMR/reference/WHONET.html). We will use it for this analysis.
This package comes with an [example data set `WHONET`](https://amr-for-r.org/reference/WHONET.html). We will use it for this analysis.
### Preparation
@ -10001,7 +10001,7 @@ library(cleaner) # to create frequency tables
We will have to transform some variables to simplify and automate the analysis:
* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://amr-for-r.org/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.sir()` function is for.
```{r}
@ -10100,7 +10100,7 @@ download_txt <- function(filename) {
msg <- paste0(
"It was last updated on ",
trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
". Find more info about the contents, (scientific) source, and structure of this [data set here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n"
". Find more info about the contents, (scientific) source, and structure of this [data set here](https://amr-for-r.org/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n"
)
github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/datasets/"
local_filename <- paste0("../data-raw/datasets/", filename)
@ -10170,7 +10170,7 @@ print_df <- function(x, rows = 6) {
All reference data (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems.
> If you are working in Python, be sure to use our [AMR for Python](https://msberends.github.io/AMR/articles/AMR_for_Python.html) package. It allows all relevant AMR data sets to be natively available in Python.
> If you are working in Python, be sure to use our [AMR for Python](https://amr-for-r.org/articles/AMR_for_Python.html) package. It allows all relevant AMR data sets to be natively available in Python.
## `microorganisms`: Full Microbial Taxonomy
@ -10392,11 +10392,11 @@ knitr::opts_chunk$set(
)
```
Note: to keep the package size as small as possible, we only include this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST and CLSI breakpoints, and much more: <https://msberends.github.io/AMR/articles/>.
Note: to keep the package size as small as possible, we only include this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST and CLSI breakpoints, and much more: <https://www.amr-for-r.org/articles/>.
----
The `AMR` package is a [free and open-source](https://msberends.github.io/AMR/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project!
The `AMR` package is a [free and open-source](https://www.amr-for-r.org/) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://www.amr-for-r.org/authors.html) from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
@ -10425,14 +10425,14 @@ This package can be used for:
* Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to SIR
* Principal component analysis for AMR
All reference data sets (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change.
All reference data sets (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://www.amr-for-r.org/articles/datasets.html), which is automatically updated with every code change.
This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](https://msberends.github.io/AMR/news/) by two public healthcare organisations in the Netherlands.
This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](https://www.amr-for-r.org/news/) by two public healthcare organisations in the Netherlands.
----
<small>
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://msberends.github.io/AMR/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://www.amr-for-r.org/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.
</small>

2
data-raw/loinc.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# last updated: 30 October 2022 - Loinc_2.73

2
data-raw/poorman_prepend.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
# ------------------------------------------------

2
data-raw/read_EUCAST.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #
library(openxlsx)

2
data-raw/salmonellae.R
View File

@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://amr-for-r.org/ #
# ==================================================================== #

BIN
data-raw/~$v_14.0_Breakpoint_Tables.xlsx
View File

Binary file not shown.

14
index.md
View File

@ -1,4 +1,4 @@
# The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
# The `AMR` Package for R <a href="https://amr-for-r.org/"><img src="./logo.svg" align="right" height="139" /></a>
* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
* Used in over 175 countries, available in 20 languages
@ -12,7 +12,7 @@
> Now available for Python too! [Click here](./articles/AMR_for_Python.html) to read more.
<div style="display: flex; font-size: 0.8em;">
<p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
<p style="text-align:left; width: 50%;"><small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small></p>
<p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small></p>
</div>
@ -40,7 +40,7 @@ With the help of contributors from all corners of the world, the `AMR` package i
#### Filtering and selecting data
One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial selectors](https://msberends.github.io/AMR/reference/antimicrobial_selectors.html), which work in base R, `dplyr` and `data.table`.
One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial selectors](https://amr-for-r.org/reference/antimicrobial_selectors.html), which work in base R, `dplyr` and `data.table`.
```r
# AMR works great with dplyr, but it's not required or neccesary
@ -186,7 +186,7 @@ example_isolates %>%
|ICU | 0.2902655 | 0.253-0.33 | 0.4004739 | 0.353-0.449 |
|Outpatient | 0.2000000 | 0.131-0.285 | 0.3676471 | 0.254-0.493 |
Or use [antimicrobial selectors](https://msberends.github.io/AMR/reference/antimicrobial_selectors.html) to select a series of antibiotic columns:
Or use [antimicrobial selectors](https://amr-for-r.org/reference/antimicrobial_selectors.html) to select a series of antibiotic columns:
```r
library(AMR)
@ -276,15 +276,15 @@ It will be downloaded and installed automatically. For RStudio, click on the men
Please read our [Developer Guideline here](https://github.com/msberends/AMR/wiki/Developer-Guideline).
The latest and unpublished development version can be installed from the [rOpenSci R-universe platform](https://msberends.r-universe.dev/AMR):
To install the latest and unpublished development version:
```r
install.packages("AMR", repos = "https://msberends.r-universe.dev")
install.packages("AMR", repos = "beta.amr-for-r.org")
```
### Get started
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://msberends.github.io/AMR/articles/).
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://amr-for-r.org/articles/).
### Partners

8
man/AMR.Rd
View File

@ -28,11 +28,11 @@ A BibTeX entry for LaTeX users is:
\description{
Welcome to the \code{AMR} package.
The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://msberends.github.io/AMR/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
The \code{AMR} package is a \href{https://amr-for-r.org/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://amr-for-r.org/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
}
@ -42,13 +42,13 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\seealso{
Useful links:
\itemize{
\item \url{https://msberends.github.io/AMR/}
\item \url{https://www.amr-for-r.org/}
\item \url{https://github.com/msberends/AMR}
\item Report bugs at \url{https://github.com/msberends/AMR/issues}
}

2
man/WHONET.Rd
View File

@ -47,7 +47,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

2
man/ab_property.Rd
View File

@ -103,7 +103,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

4
man/antimicrobial_selectors.Rd
View File

@ -163,7 +163,7 @@ my_data_with_all_these_columns \%>\%
\details{
These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and \code{data.table}. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but are not limited to \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}.
All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling.
All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling.
All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antimicrobials} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
@ -219,7 +219,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{

2
man/antimicrobials.Rd
View File

@ -69,7 +69,7 @@ All reference data sets in the AMR package - including information on microorgan
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\section{WHOCC}{

Some files were not shown because too many files have changed in this diff Show More