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dr. M.S. (Matthijs) Berends 2025-04-12 11:46:42 +02:00
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.github/prehooks/commit-msg vendored
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# Path to the commit message file

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.github/prehooks/pre-commit vendored
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# Check if commit should skip checks

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.github/workflows/check-current-testthat.yaml vendored
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
on:

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.github/workflows/check-old-tinytest.yaml vendored
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
on:

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.github/workflows/codecovr.yaml vendored
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
on:

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.github/workflows/lintr.yaml vendored
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
on:

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.github/workflows/publish-to-pypi.yml vendored
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
on:

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.github/workflows/website.yaml vendored
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# Create a website from the R documentation using pkgdown

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DESCRIPTION
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Package: AMR
Version: 2.1.1.9235
Date: 2025-04-08
Version: 2.1.1.9236
Date: 2025-04-12
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://www.amr-for-r.org/, https://github.com/msberends/AMR
URL: https://amr-for-r.org, https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8

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NEWS.md
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# AMR 2.1.1.9235
# AMR 2.1.1.9236
*(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/).)*
*(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://amr-for-r.org/#get-this-package).)*
#### 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://www.amr-for-r.org/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://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://www.amr-for-r.org/articles/datasets.html).
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://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://www.amr-for-r.org/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://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.

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R/aa_amr-package.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' The `AMR` Package

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R/aa_globals.R
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# 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://amr-for-r.org/ #
# 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

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R/aa_helper_functions.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# faster implementation of left_join than using merge() by poorman - we use match():

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R/aa_helper_pm_functions.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# ------------------------------------------------

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R/aa_options.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Options for the AMR package

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R/ab.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Transform Input to an Antibiotic ID

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R/ab_from_text.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Retrieve Antimicrobial Drug Names and Doses from Clinical Text

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R/ab_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Get Properties of an Antibiotic

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R/age.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Age in Years of Individuals

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R/amr_selectors.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Antimicrobial Selectors

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R/antibiogram.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Generate Traditional, Combination, Syndromic, or WISCA Antibiograms

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R/atc_online.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Get ATC Properties from WHOCC Website

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R/av.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Transform Input to an Antiviral Drug ID

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R/av_from_text.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Retrieve Antiviral Drug Names and Doses from Clinical Text

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R/av_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Get Properties of an Antiviral Drug

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R/availability.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Check Availability of Columns

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R/bug_drug_combinations.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Determine Bug-Drug Combinations

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R/count.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Count Available Isolates

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R/custom_antimicrobials.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Add Custom Antimicrobials

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R/custom_eucast_rules.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Define Custom EUCAST Rules

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R/custom_microorganisms.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Add Custom Microorganisms

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R/data.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Data Sets with `r format(nrow(antimicrobials) + nrow(antivirals), big.mark = " ")` Antimicrobial Drugs

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R/disk.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Transform Input to Disk Diffusion Diameters

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R/eucast_rules.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# ====================================================== #
@ -219,7 +219,7 @@ eucast_rules <- function(x,
if (interactive() && isTRUE(verbose) && isTRUE(info)) {
txt <- paste0(
"WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
"WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with comprehensive info about which rows and columns would be effected and in which way.",
"\n\nThis may overwrite your existing data if you use e.g.:",
"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?"
)

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R/export_biosample.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Export Data Set as NCBI BioSample Antibiogram

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R/first_isolate.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Determine First Isolates

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R/g.test.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' *G*-test for Count Data

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R/get_episode.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Determine Clinical or Epidemic Episodes

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R/ggplot_pca.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' PCA Biplot with `ggplot2`

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R/ggplot_sir.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' AMR Plots with `ggplot2`

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R/guess_ab_col.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Guess Antibiotic Column

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R/italicise_taxonomy.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Italicise Taxonomic Families, Genera, Species, Subspecies

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R/join_microorganisms.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Join [microorganisms] to a Data Set

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R/key_antimicrobials.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' (Key) Antimicrobials for First Weighted Isolates

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R/kurtosis.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Kurtosis of the Sample

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R/like.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Vectorised Pattern Matching with Keyboard Shortcut

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R/mdro.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Determine Multidrug-Resistant Organisms (MDRO)

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R/mean_amr_distance.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Calculate the Mean AMR Distance

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R/mic.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# these are allowed MIC values and will become factor levels

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R/mo.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Transform Arbitrary Input to Valid Microbial Taxonomy

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R/mo_matching_score.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Calculate the Matching Score for Microorganisms

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R/mo_property.R
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# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Get Properties of a Microorganism

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R/mo_source.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' User-Defined Reference Data Set for Microorganisms

2
R/pca.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Principal Component Analysis (for AMR)

2
R/plotting.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Plotting Helpers for AMR Data Analysis

2
R/proportion.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Calculate Antimicrobial Resistance

2
R/random.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Random MIC Values/Disk Zones/SIR Generation

2
R/resistance_predict.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Predict Antimicrobial Resistance

2
R/sir.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data

4
R/sir_calc.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
dots2vars <- function(...) {
@ -217,7 +217,7 @@ sir_calc <- function(...,
}
if (as_percent == TRUE) {
percentage(fraction, digits = 1)
trimws(percentage(fraction, digits = 1))
} else {
fraction
}

2
R/sir_df.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' @rdname proportion

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R/skewness.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Skewness of the Sample

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R/top_n_microorganisms.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Filter Top *n* Microorganisms

2
R/translate.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Translate Strings from the AMR Package

2
R/vctrs.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# These are all S3 implementations for the vctrs package,

2
R/whocc.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' WHOCC: WHO Collaborating Centre for Drug Statistics Methodology

2
R/zz_deprecated.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Deprecated Functions

2
R/zzz.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# set up package environment, used by numerous AMR functions

9
README.md
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@ -1,5 +1,7 @@
# The `AMR` Package for R
Please visit our comprehensive package website <https://amr-for-r.org> to read more about this package, including many examples and tutorials.
----
The `AMR` package is a free and open-source R package with 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. **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.
@ -17,8 +19,6 @@ Overview:
----
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
To install the latest 'release' version from CRAN:
@ -31,10 +31,13 @@ To install the latest 'beta' version:
```r
install.packages("AMR", repos = "beta.amr-for-r.org")
# if this does not work, try to install directly from GitHub using the 'remotes' package:
remotes::install_github("msberends/AMR")
```
----
<small>
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.
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://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
_pkgdown.yml
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
title: "AMR (for R)"

2
codecov.yml
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
codecov:

2
data-raw/_generate_python_wrapper.sh
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# Clean up

2
data-raw/_language_update.R
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@ -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://amr-for-r.org/ #
# 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
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@ -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://amr-for-r.org/ #
# 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
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
library(dplyr)

2
data-raw/_reproduction scripts/reproduction_of_antivirals.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
library(dplyr)

2
data-raw/_reproduction scripts/reproduction_of_clinical_breakpoints.R
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@ -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://amr-for-r.org/ #
# 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://amr-for-r.org/ #
# 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://amr-for-r.org/ #
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
library(AMR)

2
data-raw/_reproduction scripts/reproduction_of_microorganisms.R
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@ -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://amr-for-r.org/ #
# 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://amr-for-r.org/ #
# 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().

27
data-raw/gpt_training_text_v2.1.1.9235.txt → data-raw/gpt_training_text_v2.1.1.9236.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 2.1.1.9235. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9236. 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.
----------------------------------------------------------------------------------------------------
@ -559,7 +559,7 @@ ggplot(data.frame(mic = some_mic_values,
```
<a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis">
<img src="./plot_readme.png" style="max-width: 600px;">
<img src="./plot_readme.png" style="width: 600px; max-width: 100%;">
</a>
#### Calculating resistance per group
@ -662,9 +662,9 @@ install.packages("AMR")
It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
**Note:** Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.
**Note:** Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest beta version.
#### Latest development version
#### Latest beta version
[![check-old](https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml/badge.svg?branch=main)](https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml)
[![check-recent](https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml/badge.svg?branch=main)](https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml)
@ -673,15 +673,18 @@ 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).
To install the latest and unpublished development version:
To install the latest and unpublished beta version:
```r
install.packages("AMR", repos = "beta.amr-for-r.org")
# if this does not work, try to install directly from GitHub using the 'remotes' package:
remotes::install_github("msberends/AMR")
```
### 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://amr-for-r.org/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](./articles/).
### Partners
@ -871,7 +874,7 @@ Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct
\seealso{
Useful links:
\itemize{
\item \url{https://www.amr-for-r.org/}
\item \url{https://amr-for-r.org}
\item \url{https://github.com/msberends/AMR}
\item Report bugs at \url{https://github.com/msberends/AMR/issues}
}
@ -10392,11 +10395,11 @@ 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://www.amr-for-r.org/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://amr-for-r.org/articles/>.
----
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!
The `AMR` package is a [free and open-source](https://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://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 +10428,14 @@ 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://www.amr-for-r.org/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://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://www.amr-for-r.org/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://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://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.
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://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
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@ -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://amr-for-r.org/ #
# 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
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# ------------------------------------------------

2
data-raw/read_EUCAST.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
library(openxlsx)

2
data-raw/salmonellae.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #

13
index.md
View File

@ -162,7 +162,7 @@ ggplot(data.frame(mic = some_mic_values,
```
<a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis">
<img src="./plot_readme.png" style="max-width: 600px;">
<img src="./plot_readme.png" style="width: 600px; max-width: 100%;">
</a>
#### Calculating resistance per group
@ -265,9 +265,9 @@ install.packages("AMR")
It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
**Note:** Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.
**Note:** Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest beta version.
#### Latest development version
#### Latest beta version
[![check-old](https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml/badge.svg?branch=main)](https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml)
[![check-recent](https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml/badge.svg?branch=main)](https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml)
@ -276,15 +276,18 @@ 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).
To install the latest and unpublished development version:
To install the latest and unpublished beta version:
```r
install.packages("AMR", repos = "beta.amr-for-r.org")
# if this does not work, try to install directly from GitHub using the 'remotes' package:
remotes::install_github("msberends/AMR")
```
### 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://amr-for-r.org/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](./articles/).
### Partners

2
man/AMR.Rd
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@ -48,7 +48,7 @@ Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct
\seealso{
Useful links:
\itemize{
\item \url{https://www.amr-for-r.org/}
\item \url{https://amr-for-r.org}
\item \url{https://github.com/msberends/AMR}
\item Report bugs at \url{https://github.com/msberends/AMR/issues}
}

2
pkgdown/extra.css
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@ -25,7 +25,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
*/

6
pkgdown/extra.js
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@ -25,7 +25,7 @@
# 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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
*/
@ -110,9 +110,9 @@ $(document).ready(function() {
// add doctoral titles to authors
function doct_tit(x) {
if (typeof(x) != "undefined") {
x = x.replace(/Author, maintainer/g, "Principal developer");
x = x.replace(/Author, maintainer/g, "Project founder and lead developer");
x = x.replace(/Author, contributor/g, "Package maintainer");
x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor");
x = x.replace(/Thesis advisor/g, "Former doctoral advisor");
// contributors
x = x.replace("Alex", "Prof. Alex");
x = x.replace("Andrew", "Dr. Andrew");

2
tests/testthat.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
library(testthat)

2
tests/testthat/helper-functions.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# add functions from the tinytest package (which we use for older R versions)

2
tests/testthat/test-_deprecated.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-_deprecated.R", {

2
tests/testthat/test-_misc.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-misc.R", {

2
tests/testthat/test-ab.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-ab.R", {

2
tests/testthat/test-ab_from_text.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-ab_from_text.R", {

2
tests/testthat/test-ab_property.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-ab_property.R", {

2
tests/testthat/test-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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-age.R", {

2
tests/testthat/test-amr_selectors.R
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@ -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://amr-for-r.org/ #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
test_that("test-amr selectors.R", {

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