diff --git a/.github/prehooks/commit-msg b/.github/prehooks/commit-msg index 4eaf79e26..10906f01f 100755 --- a/.github/prehooks/commit-msg +++ b/.github/prehooks/commit-msg @@ -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 # # ==================================================================== # # Path to the commit message file diff --git a/.github/prehooks/pre-commit b/.github/prehooks/pre-commit index c029d6ddf..36739503c 100755 --- a/.github/prehooks/pre-commit +++ b/.github/prehooks/pre-commit @@ -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 # # ==================================================================== # # Check if commit should skip checks diff --git a/.github/workflows/check-current-testthat.yaml b/.github/workflows/check-current-testthat.yaml index c4ad533c9..961b79e9d 100644 --- a/.github/workflows/check-current-testthat.yaml +++ b/.github/workflows/check-current-testthat.yaml @@ -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 # # ==================================================================== # on: diff --git a/.github/workflows/check-old-tinytest.yaml b/.github/workflows/check-old-tinytest.yaml index 5758bce62..52e43ed10 100644 --- a/.github/workflows/check-old-tinytest.yaml +++ b/.github/workflows/check-old-tinytest.yaml @@ -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 # # ==================================================================== # on: diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 8810b4efd..f618bad32 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -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 # # ==================================================================== # on: diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index 3b70efee9..4f648e09f 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -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 # # ==================================================================== # on: diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index ad1a0b873..f5a81a2a7 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -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 # # ==================================================================== # on: diff --git a/.github/workflows/website.yaml b/.github/workflows/website.yaml index 0891f7359..4bb06b9b8 100644 --- a/.github/workflows/website.yaml +++ b/.github/workflows/website.yaml @@ -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 # # ==================================================================== # # Create a website from the R documentation using pkgdown diff --git a/DESCRIPTION b/DESCRIPTION index 9e59ec047..b9bc62aed 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ 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 diff --git a/NEWS.md b/NEWS.md index 67b03759e..6252de510 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ -# 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. diff --git a/R/aa_amr-package.R b/R/aa_amr-package.R index 8f5cb23dd..57e355b79 100755 --- a/R/aa_amr-package.R +++ b/R/aa_amr-package.R @@ -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 # # ==================================================================== # #' The `AMR` Package diff --git a/R/aa_globals.R b/R/aa_globals.R index 30a8e07f8..de04e4c24 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -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 new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 1ac5444cc..34c500242 100644 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -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 # # ==================================================================== # # faster implementation of left_join than using merge() by poorman - we use match(): diff --git a/R/aa_helper_pm_functions.R b/R/aa_helper_pm_functions.R index 317d8fad6..6d822b18d 100755 --- a/R/aa_helper_pm_functions.R +++ b/R/aa_helper_pm_functions.R @@ -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 # # ==================================================================== # # ------------------------------------------------ diff --git a/R/aa_options.R b/R/aa_options.R index 24d06367e..6e5386c17 100755 --- a/R/aa_options.R +++ b/R/aa_options.R @@ -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 # # ==================================================================== # #' Options for the AMR package diff --git a/R/ab.R b/R/ab.R index b68a010bf..2bf778cf6 100755 --- a/R/ab.R +++ b/R/ab.R @@ -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 # # ==================================================================== # #' Transform Input to an Antibiotic ID diff --git a/R/ab_from_text.R b/R/ab_from_text.R index dfbcef3ef..1b0e77efa 100755 --- a/R/ab_from_text.R +++ b/R/ab_from_text.R @@ -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 # # ==================================================================== # #' Retrieve Antimicrobial Drug Names and Doses from Clinical Text diff --git a/R/ab_property.R b/R/ab_property.R index 5f7d94bdf..0f41c290d 100755 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -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 # # ==================================================================== # #' Get Properties of an Antibiotic diff --git a/R/age.R b/R/age.R index c6a2958d8..66f4a7823 100755 --- a/R/age.R +++ b/R/age.R @@ -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 # # ==================================================================== # #' Age in Years of Individuals diff --git a/R/amr_selectors.R b/R/amr_selectors.R index cf3c57e41..c42dbf1ea 100755 --- a/R/amr_selectors.R +++ b/R/amr_selectors.R @@ -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 # # ==================================================================== # #' Antimicrobial Selectors diff --git a/R/antibiogram.R b/R/antibiogram.R index f15ed057f..446660786 100755 --- a/R/antibiogram.R +++ b/R/antibiogram.R @@ -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 # # ==================================================================== # #' Generate Traditional, Combination, Syndromic, or WISCA Antibiograms diff --git a/R/atc_online.R b/R/atc_online.R index 68653ac71..6cfed0b82 100755 --- a/R/atc_online.R +++ b/R/atc_online.R @@ -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 # # ==================================================================== # #' Get ATC Properties from WHOCC Website diff --git a/R/av.R b/R/av.R index fc7cc7855..8655adf7f 100755 --- a/R/av.R +++ b/R/av.R @@ -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 # # ==================================================================== # #' Transform Input to an Antiviral Drug ID diff --git a/R/av_from_text.R b/R/av_from_text.R index 0a8a32761..3d9da809f 100755 --- a/R/av_from_text.R +++ b/R/av_from_text.R @@ -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 # # ==================================================================== # #' Retrieve Antiviral Drug Names and Doses from Clinical Text diff --git a/R/av_property.R b/R/av_property.R index 0fa219157..9a7e85683 100755 --- a/R/av_property.R +++ b/R/av_property.R @@ -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 # # ==================================================================== # #' Get Properties of an Antiviral Drug diff --git a/R/availability.R b/R/availability.R index 4e18f47bb..f14aefb8c 100755 --- a/R/availability.R +++ b/R/availability.R @@ -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 # # ==================================================================== # #' Check Availability of Columns diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index 84abf442a..9d2679cda 100755 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -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 Bug-Drug Combinations diff --git a/R/count.R b/R/count.R index 90941f66d..81b9b08fd 100755 --- a/R/count.R +++ b/R/count.R @@ -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 # # ==================================================================== # #' Count Available Isolates diff --git a/R/custom_antimicrobials.R b/R/custom_antimicrobials.R index b1d0264d0..48714d420 100755 --- a/R/custom_antimicrobials.R +++ b/R/custom_antimicrobials.R @@ -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 Custom Antimicrobials diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R index aca6aea06..fed97e773 100755 --- a/R/custom_eucast_rules.R +++ b/R/custom_eucast_rules.R @@ -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 # # ==================================================================== # #' Define Custom EUCAST Rules diff --git a/R/custom_microorganisms.R b/R/custom_microorganisms.R index f7c4c1457..be37a348b 100755 --- a/R/custom_microorganisms.R +++ b/R/custom_microorganisms.R @@ -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 Custom Microorganisms diff --git a/R/data.R b/R/data.R index 9af610c64..868d5c288 100755 --- a/R/data.R +++ b/R/data.R @@ -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 # # ==================================================================== # #' Data Sets with `r format(nrow(antimicrobials) + nrow(antivirals), big.mark = " ")` Antimicrobial Drugs diff --git a/R/disk.R b/R/disk.R index d531d2ddf..8cacfc97c 100755 --- a/R/disk.R +++ b/R/disk.R @@ -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 # # ==================================================================== # #' Transform Input to Disk Diffusion Diameters diff --git a/R/eucast_rules.R b/R/eucast_rules.R index b1a522e42..a9290faaa 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -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 # # ==================================================================== # # ====================================================== # @@ -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?" ) diff --git a/R/export_biosample.R b/R/export_biosample.R index bc9b6dc04..32056f4da 100755 --- a/R/export_biosample.R +++ b/R/export_biosample.R @@ -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 diff --git a/R/first_isolate.R b/R/first_isolate.R index 14b59c230..8a3aa58b1 100644 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -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 First Isolates diff --git a/R/g.test.R b/R/g.test.R index 82ce7b718..983b1bd15 100755 --- a/R/g.test.R +++ b/R/g.test.R @@ -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 # # ==================================================================== # #' *G*-test for Count Data diff --git a/R/get_episode.R b/R/get_episode.R index c71586844..1fb33f292 100644 --- a/R/get_episode.R +++ b/R/get_episode.R @@ -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 Clinical or Epidemic Episodes diff --git a/R/ggplot_pca.R b/R/ggplot_pca.R index 032762cf7..2651d1155 100755 --- a/R/ggplot_pca.R +++ b/R/ggplot_pca.R @@ -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` diff --git a/R/ggplot_sir.R b/R/ggplot_sir.R index 3cfa65a6d..8956ada4b 100755 --- a/R/ggplot_sir.R +++ b/R/ggplot_sir.R @@ -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` diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R index ffae1f118..9d6240a19 100755 --- a/R/guess_ab_col.R +++ b/R/guess_ab_col.R @@ -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 diff --git a/R/italicise_taxonomy.R b/R/italicise_taxonomy.R index e271f5400..c47ac82ff 100755 --- a/R/italicise_taxonomy.R +++ b/R/italicise_taxonomy.R @@ -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 diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R index 84eefc3de..c5d54cc38 100755 --- a/R/join_microorganisms.R +++ b/R/join_microorganisms.R @@ -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 # # ==================================================================== # #' Join [microorganisms] to a Data Set diff --git a/R/key_antimicrobials.R b/R/key_antimicrobials.R index a138103a9..0e3af1f4f 100755 --- a/R/key_antimicrobials.R +++ b/R/key_antimicrobials.R @@ -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 diff --git a/R/kurtosis.R b/R/kurtosis.R index f2b17d37d..167320b47 100755 --- a/R/kurtosis.R +++ b/R/kurtosis.R @@ -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 diff --git a/R/like.R b/R/like.R index 37313b63b..62f52300c 100755 --- a/R/like.R +++ b/R/like.R @@ -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 diff --git a/R/mdro.R b/R/mdro.R index 352c948a7..da1da65bb 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -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) diff --git a/R/mean_amr_distance.R b/R/mean_amr_distance.R index bc487e4af..96b9c99cd 100755 --- a/R/mean_amr_distance.R +++ b/R/mean_amr_distance.R @@ -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 diff --git a/R/mic.R b/R/mic.R index 870d51f58..bce332504 100644 --- a/R/mic.R +++ b/R/mic.R @@ -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 diff --git a/R/mo.R b/R/mo.R index 331db639b..4886960d6 100755 --- a/R/mo.R +++ b/R/mo.R @@ -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 # # ==================================================================== # #' Transform Arbitrary Input to Valid Microbial Taxonomy diff --git a/R/mo_matching_score.R b/R/mo_matching_score.R index a8151cefc..78cd1f663 100755 --- a/R/mo_matching_score.R +++ b/R/mo_matching_score.R @@ -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 Matching Score for Microorganisms diff --git a/R/mo_property.R b/R/mo_property.R index 87e182ff1..d8ba8b6fb 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -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 # # ==================================================================== # #' Get Properties of a Microorganism diff --git a/R/mo_source.R b/R/mo_source.R index 9a727bd78..3a932db05 100755 --- a/R/mo_source.R +++ b/R/mo_source.R @@ -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 diff --git a/R/pca.R b/R/pca.R index 490de18bc..481303e09 100755 --- a/R/pca.R +++ b/R/pca.R @@ -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) diff --git a/R/plotting.R b/R/plotting.R index 608ad22df..feca9b519 100755 --- a/R/plotting.R +++ b/R/plotting.R @@ -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 diff --git a/R/proportion.R b/R/proportion.R index 775a22381..88bbf3992 100644 --- a/R/proportion.R +++ b/R/proportion.R @@ -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 diff --git a/R/random.R b/R/random.R index 585ca6e33..bb99599f7 100755 --- a/R/random.R +++ b/R/random.R @@ -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 diff --git a/R/resistance_predict.R b/R/resistance_predict.R index 7dfdd181d..7b4b7049b 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -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 diff --git a/R/sir.R b/R/sir.R index e068b10ad..107eab4f2 100755 --- a/R/sir.R +++ b/R/sir.R @@ -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 diff --git a/R/sir_calc.R b/R/sir_calc.R index 4fd4fb921..ababf3f7a 100755 --- a/R/sir_calc.R +++ b/R/sir_calc.R @@ -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 } diff --git a/R/sir_df.R b/R/sir_df.R index 1a695fe66..14027cd6a 100755 --- a/R/sir_df.R +++ b/R/sir_df.R @@ -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 diff --git a/R/skewness.R b/R/skewness.R index a30ac4afd..9c6955bb5 100755 --- a/R/skewness.R +++ b/R/skewness.R @@ -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 diff --git a/R/top_n_microorganisms.R b/R/top_n_microorganisms.R index 0e08257ef..c03af630d 100755 --- a/R/top_n_microorganisms.R +++ b/R/top_n_microorganisms.R @@ -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 diff --git a/R/translate.R b/R/translate.R index 20d8500be..fe711d8d9 100755 --- a/R/translate.R +++ b/R/translate.R @@ -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 diff --git a/R/vctrs.R b/R/vctrs.R index 33c37d2e1..ae1bdca48 100755 --- a/R/vctrs.R +++ b/R/vctrs.R @@ -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, diff --git a/R/whocc.R b/R/whocc.R index 86fe0f48b..5f970fe30 100755 --- a/R/whocc.R +++ b/R/whocc.R @@ -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 diff --git a/R/zz_deprecated.R b/R/zz_deprecated.R index 1135d587e..49b094921 100755 --- a/R/zz_deprecated.R +++ b/R/zz_deprecated.R @@ -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 diff --git a/R/zzz.R b/R/zzz.R index fa7cb8aeb..c13fce61b 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -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 diff --git a/README.md b/README.md index e2b0cb749..c7a19f000 100755 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # The `AMR` Package for R +Please visit our comprehensive package website 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 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") ``` ---- -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. diff --git a/_pkgdown.yml b/_pkgdown.yml index 4cb564b27..a067cedca 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -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)" diff --git a/codecov.yml b/codecov.yml index 74e4c9835..d02dc544e 100644 --- a/codecov.yml +++ b/codecov.yml @@ -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: diff --git a/data-raw/_generate_python_wrapper.sh b/data-raw/_generate_python_wrapper.sh index 1f41683ca..eb2a3ccdd 100644 --- a/data-raw/_generate_python_wrapper.sh +++ b/data-raw/_generate_python_wrapper.sh @@ -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 diff --git a/data-raw/_language_update.R b/data-raw/_language_update.R index c219e30dd..f727bf2b4 100644 --- a/data-raw/_language_update.R +++ b/data-raw/_language_update.R @@ -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: diff --git a/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index 9ba128c67..51b209096 100644 --- a/data-raw/_pre_commit_checks.R +++ b/data-raw/_pre_commit_checks.R @@ -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: diff --git a/data-raw/_reproduction scripts/reproduction_of_antimicrobials.R b/data-raw/_reproduction scripts/reproduction_of_antimicrobials.R index 9bd3e170a..fce0d02cb 100644 --- a/data-raw/_reproduction scripts/reproduction_of_antimicrobials.R +++ b/data-raw/_reproduction scripts/reproduction_of_antimicrobials.R @@ -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) diff --git a/data-raw/_reproduction scripts/reproduction_of_antivirals.R b/data-raw/_reproduction scripts/reproduction_of_antivirals.R index 1c366a30e..2a9a2e7bf 100644 --- a/data-raw/_reproduction scripts/reproduction_of_antivirals.R +++ b/data-raw/_reproduction scripts/reproduction_of_antivirals.R @@ -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) diff --git a/data-raw/_reproduction scripts/reproduction_of_clinical_breakpoints.R b/data-raw/_reproduction scripts/reproduction_of_clinical_breakpoints.R index abb0be531..a5856cdf8 100644 --- a/data-raw/_reproduction scripts/reproduction_of_clinical_breakpoints.R +++ b/data-raw/_reproduction scripts/reproduction_of_clinical_breakpoints.R @@ -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! diff --git a/data-raw/_reproduction scripts/reproduction_of_dosage.R b/data-raw/_reproduction scripts/reproduction_of_dosage.R index b62268804..b86b33e06 100644 --- a/data-raw/_reproduction scripts/reproduction_of_dosage.R +++ b/data-raw/_reproduction scripts/reproduction_of_dosage.R @@ -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) diff --git a/data-raw/_reproduction scripts/reproduction_of_example_isolates_unclean.R b/data-raw/_reproduction scripts/reproduction_of_example_isolates_unclean.R index 0ffe283f7..a612ff289 100644 --- a/data-raw/_reproduction scripts/reproduction_of_example_isolates_unclean.R +++ b/data-raw/_reproduction scripts/reproduction_of_example_isolates_unclean.R @@ -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)) diff --git a/data-raw/_reproduction scripts/reproduction_of_intrinsic_resistant.R b/data-raw/_reproduction scripts/reproduction_of_intrinsic_resistant.R index e0e1b6e52..8c9932429 100644 --- a/data-raw/_reproduction scripts/reproduction_of_intrinsic_resistant.R +++ b/data-raw/_reproduction scripts/reproduction_of_intrinsic_resistant.R @@ -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) diff --git a/data-raw/_reproduction scripts/reproduction_of_microorganisms.R b/data-raw/_reproduction scripts/reproduction_of_microorganisms.R index 47ee9d0a9..25c182eb8 100644 --- a/data-raw/_reproduction scripts/reproduction_of_microorganisms.R +++ b/data-raw/_reproduction scripts/reproduction_of_microorganisms.R @@ -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 ! diff --git a/data-raw/_reproduction scripts/reproduction_of_microorganisms.groups.R b/data-raw/_reproduction scripts/reproduction_of_microorganisms.groups.R index 24ad3509d..1506c8ec1 100644 --- a/data-raw/_reproduction scripts/reproduction_of_microorganisms.groups.R +++ b/data-raw/_reproduction scripts/reproduction_of_microorganisms.groups.R @@ -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(). diff --git a/data-raw/gpt_training_text_v2.1.1.9235.txt b/data-raw/gpt_training_text_v2.1.1.9236.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9235.txt rename to data-raw/gpt_training_text_v2.1.1.9236.txt index 378ffcf2f..c2989e82d 100644 --- a/data-raw/gpt_training_text_v2.1.1.9235.txt +++ b/data-raw/gpt_training_text_v2.1.1.9236.txt @@ -1,6 +1,6 @@ This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse. -First and foremost, you are trained on version 2.1.1.9235. 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, ``` - + #### 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 Install. -**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: . +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: . ---- -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. ---- -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. diff --git a/data-raw/loinc.R b/data-raw/loinc.R index e2255ba35..26ddc72e1 100644 --- a/data-raw/loinc.R +++ b/data-raw/loinc.R @@ -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 diff --git a/data-raw/poorman_prepend.R b/data-raw/poorman_prepend.R index 0b7e24298..072e5f06c 100644 --- a/data-raw/poorman_prepend.R +++ b/data-raw/poorman_prepend.R @@ -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 # # ==================================================================== # # ------------------------------------------------ diff --git a/data-raw/read_EUCAST.R b/data-raw/read_EUCAST.R index 4f8b18c4a..318658dc0 100644 --- a/data-raw/read_EUCAST.R +++ b/data-raw/read_EUCAST.R @@ -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) diff --git a/data-raw/salmonellae.R b/data-raw/salmonellae.R index 3f238e9be..fe890b1ca 100644 --- a/data-raw/salmonellae.R +++ b/data-raw/salmonellae.R @@ -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 # # ==================================================================== # diff --git a/index.md b/index.md index d110dad4d..c6856fd37 100644 --- a/index.md +++ b/index.md @@ -162,7 +162,7 @@ ggplot(data.frame(mic = some_mic_values, ``` - + #### 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 Install. -**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 diff --git a/man/AMR.Rd b/man/AMR.Rd index 69eb613a5..4dc6837df 100644 --- a/man/AMR.Rd +++ b/man/AMR.Rd @@ -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} } diff --git a/pkgdown/extra.css b/pkgdown/extra.css index 4a815e4f9..16b453753 100644 --- a/pkgdown/extra.css +++ b/pkgdown/extra.css @@ -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 # # ==================================================================== # */ diff --git a/pkgdown/extra.js b/pkgdown/extra.js index 5a7f71a16..58d559c72 100644 --- a/pkgdown/extra.js +++ b/pkgdown/extra.js @@ -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"); diff --git a/tests/testthat.R b/tests/testthat.R index 30363ec57..b1039f04e 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -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) diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R index ae4f39a1a..721b99819 100644 --- a/tests/testthat/helper-functions.R +++ b/tests/testthat/helper-functions.R @@ -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) diff --git a/tests/testthat/test-_deprecated.R b/tests/testthat/test-_deprecated.R index e6082b219..bf08e57f7 100644 --- a/tests/testthat/test-_deprecated.R +++ b/tests/testthat/test-_deprecated.R @@ -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", { diff --git a/tests/testthat/test-_misc.R b/tests/testthat/test-_misc.R index 14ff47078..25565ae08 100755 --- a/tests/testthat/test-_misc.R +++ b/tests/testthat/test-_misc.R @@ -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", { diff --git a/tests/testthat/test-ab.R b/tests/testthat/test-ab.R index 883c8ba74..1ae43fac4 100755 --- a/tests/testthat/test-ab.R +++ b/tests/testthat/test-ab.R @@ -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", { diff --git a/tests/testthat/test-ab_from_text.R b/tests/testthat/test-ab_from_text.R index 2f5eaf5b8..37d5c77b7 100644 --- a/tests/testthat/test-ab_from_text.R +++ b/tests/testthat/test-ab_from_text.R @@ -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", { diff --git a/tests/testthat/test-ab_property.R b/tests/testthat/test-ab_property.R index 534b830c2..0cd165cad 100644 --- a/tests/testthat/test-ab_property.R +++ b/tests/testthat/test-ab_property.R @@ -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", { diff --git a/tests/testthat/test-age.R b/tests/testthat/test-age.R index e7eaab61a..530c950e5 100644 --- a/tests/testthat/test-age.R +++ b/tests/testthat/test-age.R @@ -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", { diff --git a/tests/testthat/test-amr_selectors.R b/tests/testthat/test-amr_selectors.R index 5a63b2713..186748a58 100644 --- a/tests/testthat/test-amr_selectors.R +++ b/tests/testthat/test-amr_selectors.R @@ -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", { diff --git a/tests/testthat/test-antibiogram.R b/tests/testthat/test-antibiogram.R index 83eeb6df9..18bc5b426 100644 --- a/tests/testthat/test-antibiogram.R +++ b/tests/testthat/test-antibiogram.R @@ -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-antibiogram.R", { diff --git a/tests/testthat/test-atc_online.R b/tests/testthat/test-atc_online.R index 3114994f8..d35ee9ddc 100644 --- a/tests/testthat/test-atc_online.R +++ b/tests/testthat/test-atc_online.R @@ -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-atc_online.R", { diff --git a/tests/testthat/test-av.R b/tests/testthat/test-av.R index f5762ffe1..f0151d9a1 100755 --- a/tests/testthat/test-av.R +++ b/tests/testthat/test-av.R @@ -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-av.R", { diff --git a/tests/testthat/test-av_from_text.R b/tests/testthat/test-av_from_text.R index dde0ad0ab..a8dd28472 100644 --- a/tests/testthat/test-av_from_text.R +++ b/tests/testthat/test-av_from_text.R @@ -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-av_from_text.R", { diff --git a/tests/testthat/test-av_property.R b/tests/testthat/test-av_property.R index f568822c0..a389ad053 100644 --- a/tests/testthat/test-av_property.R +++ b/tests/testthat/test-av_property.R @@ -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", { diff --git a/tests/testthat/test-availability.R b/tests/testthat/test-availability.R index 66a571d49..36cad8f5a 100644 --- a/tests/testthat/test-availability.R +++ b/tests/testthat/test-availability.R @@ -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-availibility.R", { diff --git a/tests/testthat/test-bug_drug_combinations.R b/tests/testthat/test-bug_drug_combinations.R index f708df031..f60e00623 100644 --- a/tests/testthat/test-bug_drug_combinations.R +++ b/tests/testthat/test-bug_drug_combinations.R @@ -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-bug/drug.R", { diff --git a/tests/testthat/test-count.R b/tests/testthat/test-count.R index 25710c37b..e27555d0a 100644 --- a/tests/testthat/test-count.R +++ b/tests/testthat/test-count.R @@ -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-count.R", { diff --git a/tests/testthat/test-custom_antimicrobials.R b/tests/testthat/test-custom_antimicrobials.R index 66b3c2e2f..9de11489f 100644 --- a/tests/testthat/test-custom_antimicrobials.R +++ b/tests/testthat/test-custom_antimicrobials.R @@ -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-custom ab.R", { diff --git a/tests/testthat/test-custom_microorganisms.R b/tests/testthat/test-custom_microorganisms.R index 794f7dca5..491c91fa3 100644 --- a/tests/testthat/test-custom_microorganisms.R +++ b/tests/testthat/test-custom_microorganisms.R @@ -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 # # ==================================================================== # diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R index ecc1bea82..181bfc8f5 100644 --- a/tests/testthat/test-data.R +++ b/tests/testthat/test-data.R @@ -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-data.R", { diff --git a/tests/testthat/test-disk.R b/tests/testthat/test-disk.R index 183b8f488..8e74abef4 100755 --- a/tests/testthat/test-disk.R +++ b/tests/testthat/test-disk.R @@ -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-disk.R", { diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R index 46ec81d39..8f4a55bb7 100755 --- a/tests/testthat/test-eucast_rules.R +++ b/tests/testthat/test-eucast_rules.R @@ -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-eucast_rules.R", { diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R index 4a3ff154a..e47fe2320 100755 --- a/tests/testthat/test-first_isolate.R +++ b/tests/testthat/test-first_isolate.R @@ -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-first_isolate.R", { diff --git a/tests/testthat/test-g.test.R b/tests/testthat/test-g.test.R index 6bdd264c9..2b8c22a4d 100644 --- a/tests/testthat/test-g.test.R +++ b/tests/testthat/test-g.test.R @@ -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-g.test.R", { diff --git a/tests/testthat/test-get_episode.R b/tests/testthat/test-get_episode.R index d3ff4cfd8..32a1088e3 100644 --- a/tests/testthat/test-get_episode.R +++ b/tests/testthat/test-get_episode.R @@ -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-get_episode.R", { diff --git a/tests/testthat/test-ggplot_sir.R b/tests/testthat/test-ggplot_sir.R index 77746c622..3eed98bbd 100644 --- a/tests/testthat/test-ggplot_sir.R +++ b/tests/testthat/test-ggplot_sir.R @@ -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-ggplot_sir.R", { diff --git a/tests/testthat/test-guess_ab_col.R b/tests/testthat/test-guess_ab_col.R index 6d8f7f742..5ef8e3954 100644 --- a/tests/testthat/test-guess_ab_col.R +++ b/tests/testthat/test-guess_ab_col.R @@ -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-guess_ab_col.R", { diff --git a/tests/testthat/test-italicise_taxonomy.R b/tests/testthat/test-italicise_taxonomy.R index fb9c63dc0..17862407d 100644 --- a/tests/testthat/test-italicise_taxonomy.R +++ b/tests/testthat/test-italicise_taxonomy.R @@ -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-italicise_taxonomy.R", { diff --git a/tests/testthat/test-join_microorganisms.R b/tests/testthat/test-join_microorganisms.R index fab3dd864..106d70eca 100755 --- a/tests/testthat/test-join_microorganisms.R +++ b/tests/testthat/test-join_microorganisms.R @@ -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-join_microorganisms.R", { diff --git a/tests/testthat/test-key_antimicrobials.R b/tests/testthat/test-key_antimicrobials.R index 687051ca5..6907c261a 100644 --- a/tests/testthat/test-key_antimicrobials.R +++ b/tests/testthat/test-key_antimicrobials.R @@ -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-key_antimicrobials.R", { diff --git a/tests/testthat/test-kurtosis.R b/tests/testthat/test-kurtosis.R index f71ee61cb..cd89e6262 100644 --- a/tests/testthat/test-kurtosis.R +++ b/tests/testthat/test-kurtosis.R @@ -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-kurtosis.R", { diff --git a/tests/testthat/test-like.R b/tests/testthat/test-like.R index c301ae6ac..c4b957ace 100644 --- a/tests/testthat/test-like.R +++ b/tests/testthat/test-like.R @@ -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-like.R", { diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R index c74c6c64c..71aa9cb44 100755 --- a/tests/testthat/test-mdro.R +++ b/tests/testthat/test-mdro.R @@ -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-mdro.R", { diff --git a/tests/testthat/test-mean_amr_distance.R b/tests/testthat/test-mean_amr_distance.R index a0bc72eb7..e69846d60 100644 --- a/tests/testthat/test-mean_amr_distance.R +++ b/tests/testthat/test-mean_amr_distance.R @@ -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-mean_amr_distance.R", { diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R index 04b1abc8c..dee4f9e82 100755 --- a/tests/testthat/test-mic.R +++ b/tests/testthat/test-mic.R @@ -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-mic.R", { diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index 20938a985..d9a76f108 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -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-mo.R", { diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R index 38bc04142..34c77b3c7 100644 --- a/tests/testthat/test-mo_property.R +++ b/tests/testthat/test-mo_property.R @@ -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-mo_property.R", { diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R index fd1415566..99c7637b7 100644 --- a/tests/testthat/test-pca.R +++ b/tests/testthat/test-pca.R @@ -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-pca.R", { diff --git a/tests/testthat/test-plotting.R b/tests/testthat/test-plotting.R index 943f543ec..fc4a04143 100644 --- a/tests/testthat/test-plotting.R +++ b/tests/testthat/test-plotting.R @@ -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-plotting.R", { diff --git a/tests/testthat/test-proportion.R b/tests/testthat/test-proportion.R index 97eff33b8..bce5c78c7 100755 --- a/tests/testthat/test-proportion.R +++ b/tests/testthat/test-proportion.R @@ -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-proportion.R", { diff --git a/tests/testthat/test-random.R b/tests/testthat/test-random.R index ad99b5faf..5f403bf50 100644 --- a/tests/testthat/test-random.R +++ b/tests/testthat/test-random.R @@ -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-random.R", { diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R index f5158e67b..662860c20 100644 --- a/tests/testthat/test-resistance_predict.R +++ b/tests/testthat/test-resistance_predict.R @@ -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-resistance_predict.R", { diff --git a/tests/testthat/test-sir.R b/tests/testthat/test-sir.R index 38003ed39..259abbc65 100644 --- a/tests/testthat/test-sir.R +++ b/tests/testthat/test-sir.R @@ -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-sir.R", { diff --git a/tests/testthat/test-skewness.R b/tests/testthat/test-skewness.R index 78f45ea18..e06508dd1 100644 --- a/tests/testthat/test-skewness.R +++ b/tests/testthat/test-skewness.R @@ -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-skewness.R", { diff --git a/tests/testthat/test-top_n_microorganisms.R b/tests/testthat/test-top_n_microorganisms.R index f769e030a..ce1326a32 100644 --- a/tests/testthat/test-top_n_microorganisms.R +++ b/tests/testthat/test-top_n_microorganisms.R @@ -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-top_n_microorganisms.R", { diff --git a/tests/testthat/test-translate.R b/tests/testthat/test-translate.R index 518806c44..28dae6721 100644 --- a/tests/testthat/test-translate.R +++ b/tests/testthat/test-translate.R @@ -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-translate.R", { diff --git a/tests/testthat/test-vctrs.R b/tests/testthat/test-vctrs.R index 713934c2d..480c631a7 100755 --- a/tests/testthat/test-vctrs.R +++ b/tests/testthat/test-vctrs.R @@ -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-vctrs.R", { diff --git a/tests/testthat/test-zzz.R b/tests/testthat/test-zzz.R index 47bce0b97..819d34d4a 100644 --- a/tests/testthat/test-zzz.R +++ b/tests/testthat/test-zzz.R @@ -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-zzz.R", { diff --git a/tests/tinytest.R.old b/tests/tinytest.R.old index c406de4b7..0de80677b 100644 --- a/tests/tinytest.R.old +++ b/tests/tinytest.R.old @@ -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 # # ==================================================================== # # we use {tinytest} for older R versions to allow unit testing in R >= 3.0.0. diff --git a/vignettes/welcome_to_AMR.Rmd b/vignettes/welcome_to_AMR.Rmd index b3bf50b1c..5461a00d2 100644 --- a/vignettes/welcome_to_AMR.Rmd +++ b/vignettes/welcome_to_AMR.Rmd @@ -22,11 +22,11 @@ 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: . +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: . ---- -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)). @@ -55,12 +55,12 @@ 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. ---- -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.