diff --git a/.github/prehooks/commit-msg b/.github/prehooks/commit-msg index 6f4ce0753..4eaf79e26 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://msberends.github.io/AMR/ # +# 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 0999c4948..c029d6ddf 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://msberends.github.io/AMR/ # +# 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 a33ddb311..c4ad533c9 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://msberends.github.io/AMR/ # +# 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 4f90f2606..5758bce62 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://msberends.github.io/AMR/ # +# 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 927d867c1..8810b4efd 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://msberends.github.io/AMR/ # +# 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 cceb37261..3b70efee9 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://msberends.github.io/AMR/ # +# 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 de3f52fdf..ad1a0b873 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://msberends.github.io/AMR/ # +# 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 dff226cf3..0891f7359 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://msberends.github.io/AMR/ # +# 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 beb4e53fa..9e59ec047 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9234 -Date: 2025-04-07 +Version: 2.1.1.9235 +Date: 2025-04-08 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by @@ -62,7 +62,7 @@ Suggests: vctrs, xml2 VignetteBuilder: knitr,rmarkdown -URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR +URL: https://www.amr-for-r.org/, https://github.com/msberends/AMR BugReports: https://github.com/msberends/AMR/issues License: GPL-2 | file LICENSE Encoding: UTF-8 diff --git a/NEWS.md b/NEWS.md index ff3903579..67b03759e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ -# AMR 2.1.1.9234 +# AMR 2.1.1.9235 -*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)* +*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://www.amr-for-r.org/).)* #### A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental) This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island's Atlantic Veterinary College](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change. @@ -8,12 +8,12 @@ This package now supports not only tools for AMR data analysis in clinical setti ## Breaking * Dataset `antibiotics` has been renamed to `antimicrobials` as the data set contains more than just antibiotics. Using `antibiotics` will still work, but now returns a warning. * Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over two years ago. -* Function `resistance_predict()` is now deprecated and will be removed in a future version. Use the `tidymodels` framework instead, for which we [wrote a basic introduction](https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html). +* Function `resistance_predict()` is now deprecated and will be removed in a future version. Use the `tidymodels` framework instead, for which we [wrote a basic introduction](https://www.amr-for-r.org/articles/AMR_with_tidymodels.html). ## New * **One Health implementation** * Function `as.sir()` now has extensive support for veterinary breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names. - * The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html). + * The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://www.amr-for-r.org/articles/datasets.html). * The (new) `antimicrobials` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well. * `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q") * `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages @@ -38,7 +38,7 @@ This package now supports not only tools for AMR data analysis in clinical setti * **Support for Python** * While using R for the heavy lifting, [our 'AMR' Python Package](https://pypi.org/project/AMR/) was developed to run the AMR R package natively in Python. The Python package will always have the same version number as the R package, as it is built automatically with every code change. * **Support for `tidymodels`** - * All antimicrobial selectors (such as `aminoglycosides()` and `betalactams()`) are now supported in `tidymodels` packages such as `recipe` and `parsnip`. See for more info [our tutorial](https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html) on using these AMR functions for predictive modelling. + * All antimicrobial selectors (such as `aminoglycosides()` and `betalactams()`) are now supported in `tidymodels` packages such as `recipe` and `parsnip`. See for more info [our tutorial](https://www.amr-for-r.org/articles/AMR_with_tidymodels.html) on using these AMR functions for predictive modelling. * **Other** * New function `top_n_microorganisms()` to filter a data set to the top *n* of any taxonomic property, e.g., filter to the top 3 species, filter to any species in the top 5 genera, or filter to the top 3 species in each of the top 5 genera * New function `mo_group_members()` to retrieve the member microorganisms of a microorganism group. For example, `mo_group_members("Strep group C")` returns a vector of all microorganisms that belong to that group. diff --git a/R/aa_amr-package.R b/R/aa_amr-package.R index be12c0188..8f5cb23dd 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # #' The `AMR` Package @@ -32,11 +32,11 @@ #' @description #' Welcome to the `AMR` package. #' -#' The `AMR` package is a [free and open-source](https://msberends.github.io/AMR/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project! +#' The `AMR` package is a [free and open-source](https://amr-for-r.org/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://amr-for-r.org/authors.html) from around the globe are continually helping us to make this a successful and durable project! #' #' This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}). #' -#' After installing this package, R knows [**`r format_included_data_number(AMR::microorganisms)` microorganisms**](https://msberends.github.io/AMR/reference/microorganisms.html) (updated `r format(TAXONOMY_VERSION$GBIF$accessed_date, "%B %Y")`) and all [**`r format_included_data_number(nrow(AMR::antimicrobials) + nrow(AMR::antivirals))` antibiotic, antimycotic and antiviral drugs**](https://msberends.github.io/AMR/reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). +#' After installing this package, R knows [**`r format_included_data_number(AMR::microorganisms)` microorganisms**](https://amr-for-r.org/reference/microorganisms.html) (updated `r format(TAXONOMY_VERSION$GBIF$accessed_date, "%B %Y")`) and all [**`r format_included_data_number(nrow(AMR::antimicrobials) + nrow(AMR::antivirals))` antibiotic, antimycotic and antiviral drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). #' #' The `AMR` package is available in `r vector_and(vapply(FUN.VALUE = character(1), LANGUAGES_SUPPORTED_NAMES, function(x) x$exonym), quotes = FALSE, sort = FALSE)`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages. #' @section Download Our Reference Data: @@ -44,7 +44,7 @@ #' #' For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. #' -#' Visit [our website for direct download links](https://msberends.github.io/AMR/articles/datasets.html), or explore the actual files in [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw). +#' Visit [our website for direct download links](https://amr-for-r.org/articles/datasets.html), or explore the actual files in [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw). #' @source #' To cite AMR in publications use: #' diff --git a/R/aa_globals.R b/R/aa_globals.R index cf3e6a9ab..30a8e07f8 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index f340fc0d6..1ac5444cc 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # faster implementation of left_join than using merge() by poorman - we use match(): diff --git a/R/aa_helper_pm_functions.R b/R/aa_helper_pm_functions.R index 1df2a2d44..317d8fad6 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # ------------------------------------------------ diff --git a/R/aa_options.R b/R/aa_options.R index 1713ae2f9..24d06367e 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://msberends.github.io/AMR/ # +# 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 54b60dc86..b68a010bf 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://msberends.github.io/AMR/ # +# 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 58a65d0a9..dfbcef3ef 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://msberends.github.io/AMR/ # +# 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 ff5a97f58..5f7d94bdf 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://msberends.github.io/AMR/ # +# 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 3797f0a90..c6a2958d8 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://msberends.github.io/AMR/ # +# 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 fb3cea76f..cf3c57e41 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # #' Antimicrobial Selectors @@ -47,7 +47,7 @@ #' @details #' These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and `data.table`. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but are not limited to `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*. #' -#' All selectors can also be used in `tidymodels` packages such as `recipe` and `parsnip`. See for more info [our tutorial](https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html) on using antimicrobial selectors for predictive modelling. +#' All selectors can also be used in `tidymodels` packages such as `recipe` and `parsnip`. See for more info [our tutorial](https://amr-for-r.org/articles/AMR_with_tidymodels.html) on using antimicrobial selectors for predictive modelling. #' #' All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antimicrobials] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. #' diff --git a/R/antibiogram.R b/R/antibiogram.R index af26aea03..f15ed057f 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://msberends.github.io/AMR/ # +# 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 f18be0438..68653ac71 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://msberends.github.io/AMR/ # +# 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 7831dd431..fc7cc7855 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://msberends.github.io/AMR/ # +# 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 abd1f9697..0a8a32761 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://msberends.github.io/AMR/ # +# 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 c9382340d..0fa219157 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://msberends.github.io/AMR/ # +# 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 b50cd1ba2..4e18f47bb 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://msberends.github.io/AMR/ # +# 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 746a7db54..84abf442a 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://msberends.github.io/AMR/ # +# 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 9652764b2..90941f66d 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://msberends.github.io/AMR/ # +# 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 bb0743084..b1d0264d0 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://msberends.github.io/AMR/ # +# 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 8e8eee0e0..aca6aea06 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://msberends.github.io/AMR/ # +# 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 d86d30d9b..f7c4c1457 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://msberends.github.io/AMR/ # +# 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 15647a7db..9af610c64 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # #' Data Sets with `r format(nrow(antimicrobials) + nrow(antivirals), big.mark = " ")` Antimicrobial Drugs @@ -200,7 +200,7 @@ #' Data Set with `r format(nrow(example_isolates), big.mark = " ")` Example Isolates #' -#' A data set containing `r format(nrow(example_isolates), big.mark = " ")` microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read [the tutorial on our website](https://msberends.github.io/AMR/articles/AMR.html). +#' A data set containing `r format(nrow(example_isolates), big.mark = " ")` microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read [the tutorial on our website](https://amr-for-r.org/articles/AMR.html). #' @format A [tibble][tibble::tibble] with `r format(nrow(example_isolates), big.mark = " ")` observations and `r ncol(example_isolates)` variables: #' - `date`\cr Date of receipt at the laboratory #' - `patient`\cr ID of the patient diff --git a/R/disk.R b/R/disk.R index 565a0db5a..d531d2ddf 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://msberends.github.io/AMR/ # +# 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 ced1c56b1..b1a522e42 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # ====================================================== # diff --git a/R/export_biosample.R b/R/export_biosample.R index a28e1b0f8..bc9b6dc04 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://msberends.github.io/AMR/ # +# 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 bd33bf546..14b59c230 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://msberends.github.io/AMR/ # +# 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 eb5e4a705..82ce7b718 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://msberends.github.io/AMR/ # +# 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 4cff831f0..c71586844 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://msberends.github.io/AMR/ # +# 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 0321cf53d..032762cf7 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://msberends.github.io/AMR/ # +# 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 4afbd2839..3cfa65a6d 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://msberends.github.io/AMR/ # +# 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 2cc333286..ffae1f118 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://msberends.github.io/AMR/ # +# 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 a3ef771aa..e271f5400 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://msberends.github.io/AMR/ # +# 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 90c808c94..84eefc3de 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://msberends.github.io/AMR/ # +# 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 991c49c67..a138103a9 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://msberends.github.io/AMR/ # +# 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 85c5b010b..f2b17d37d 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://msberends.github.io/AMR/ # +# 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 9429b5b1e..37313b63b 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://msberends.github.io/AMR/ # +# 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 3edae343b..352c948a7 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://msberends.github.io/AMR/ # +# 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 843849476..bc487e4af 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://msberends.github.io/AMR/ # +# 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 28f231f29..870d51f58 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # these are allowed MIC values and will become factor levels diff --git a/R/mo.R b/R/mo.R index 2c354dc26..331db639b 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://msberends.github.io/AMR/ # +# 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 a398581b2..a8151cefc 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://msberends.github.io/AMR/ # +# 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 5257dbd7d..87e182ff1 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://msberends.github.io/AMR/ # +# 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 55b6aa7a8..9a727bd78 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://msberends.github.io/AMR/ # +# 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 8343c3321..490de18bc 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://msberends.github.io/AMR/ # +# 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 7957815ea..608ad22df 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://msberends.github.io/AMR/ # +# 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 f79a48896..775a22381 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://msberends.github.io/AMR/ # +# 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 83e6ba26d..585ca6e33 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://msberends.github.io/AMR/ # +# 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 f0ec70c8a..7dfdd181d 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # #' Predict Antimicrobial Resistance @@ -133,7 +133,7 @@ resistance_predict <- function(x, deprecation_warning( old = "resistance_predict", is_function = TRUE, - extra_msg = paste0("Use the tidymodels framework instead, for which we have written a basic and short introduction on our website: ", font_url("https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html", txt = font_bold("AMR with tidymodels"))) + extra_msg = paste0("Use the tidymodels framework instead, for which we have written a basic and short introduction on our website: ", font_url("https://amr-for-r.org/articles/AMR_with_tidymodels.html", txt = font_bold("AMR with tidymodels"))) ) stop_if(is.null(model), 'choose a regression model with the `model` argument, e.g. resistance_predict(..., model = "binomial")') diff --git a/R/sir.R b/R/sir.R index a09ed5392..e068b10ad 100755 --- a/R/sir.R +++ b/R/sir.R @@ -24,10 +24,10 @@ # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # -# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # -#' Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data +#' Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data #' #' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor] containing the levels `S`, `SDD`, `I`, `R`, `NI`. #' @@ -167,7 +167,7 @@ #' - **CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). . ###### TODO - **CLSI VET09: Understanding Susceptibility Test Data as a Component of Antimicrobial Stewardship in Veterinary Settings**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). . #' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). . -#' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. . +#' - **WHONET** as a source for machine-reading the clinical breakpoints ([read more here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)), 1989-`r max(as.integer(gsub("[^0-9]", "", AMR::clinical_breakpoints$guideline)))`, *WHO Collaborating Centre for Surveillance of Antimicrobial Resistance*. . #' #' @inheritSection AMR Download Our Reference Data #' @examples diff --git a/R/sir_calc.R b/R/sir_calc.R index e6042d32a..4fd4fb921 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # dots2vars <- function(...) { diff --git a/R/sir_df.R b/R/sir_df.R index 4d64e3de6..1a695fe66 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # #' @rdname proportion diff --git a/R/skewness.R b/R/skewness.R index f12badd3f..a30ac4afd 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://msberends.github.io/AMR/ # +# 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 d3238a706..0e08257ef 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://msberends.github.io/AMR/ # +# 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 d1c67e35f..20d8500be 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://msberends.github.io/AMR/ # +# 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 ce864e391..33c37d2e1 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://msberends.github.io/AMR/ # +# 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 39e734d8b..86fe0f48b 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://msberends.github.io/AMR/ # +# 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 558bb72e4..1135d587e 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # #' Deprecated Functions diff --git a/R/zzz.R b/R/zzz.R index d0c99c64c..fa7cb8aeb 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://msberends.github.io/AMR/ # +# 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 3fa0864e1..e2b0cb749 100755 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ Overview: ---- -Please visit our extensive website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package, including many examples and tutorials. +Please visit our extensive website to read more about this package, including many examples and tutorials. ### How to get this package @@ -27,14 +27,14 @@ To install the latest 'release' version from CRAN: install.packages("AMR") ``` -To install the latest 'beta' version from GitHub: +To install the latest 'beta' version: ```r -remotes::install_github("msberends/AMR") +install.packages("AMR", repos = "beta.amr-for-r.org") ``` ---- -This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://msberends.github.io/AMR/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package. +This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://www.amr-for-r.org//LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package. diff --git a/_pkgdown.yml b/_pkgdown.yml index a33ea9097..4cb564b27 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -24,11 +24,11 @@ # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # -# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # title: "AMR (for R)" -url: "https://msberends.github.io/AMR/" +url: "https://amr-for-r.org/" template: bootstrap: 5 diff --git a/codecov.yml b/codecov.yml index 2b31d3239..74e4c9835 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # codecov: diff --git a/data-raw/AMRforRGPT.pdf b/data-raw/AMRforRGPT.pdf index 801dccdb8..c58492577 100644 Binary files a/data-raw/AMRforRGPT.pdf and b/data-raw/AMRforRGPT.pdf differ diff --git a/data-raw/AMRforRGPT.pptx b/data-raw/AMRforRGPT.pptx index f905a0c05..29c36c939 100644 Binary files a/data-raw/AMRforRGPT.pptx and b/data-raw/AMRforRGPT.pptx differ diff --git a/data-raw/AMRforRGPT.svg b/data-raw/AMRforRGPT.svg index 7202662aa..df6df486d 100644 --- a/data-raw/AMRforRGPT.svg +++ b/data-raw/AMRforRGPT.svg @@ -1,2307 +1,443 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/data-raw/AMRforRGPT_python.pdf b/data-raw/AMRforRGPT_python.pdf index ef0dec955..4c5376976 100644 Binary files a/data-raw/AMRforRGPT_python.pdf and b/data-raw/AMRforRGPT_python.pdf differ diff --git a/data-raw/AMRforRGPT_python.pptx b/data-raw/AMRforRGPT_python.pptx index e5d710718..4febbae45 100644 Binary files a/data-raw/AMRforRGPT_python.pptx and b/data-raw/AMRforRGPT_python.pptx differ diff --git a/data-raw/AMRforRGPT_python.svg b/data-raw/AMRforRGPT_python.svg new file mode 100644 index 000000000..ce82b81b0 --- /dev/null +++ b/data-raw/AMRforRGPT_python.svg @@ -0,0 +1,443 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/data-raw/_generate_python_wrapper.sh b/data-raw/_generate_python_wrapper.sh index 3d9fc8b9b..1f41683ca 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # Clean up @@ -71,7 +71,7 @@ base._libPaths(r_lib_path) # Check if the AMR package is installed in R if not isinstalled('AMR', lib_loc=r_lib_path): print(f"AMR: Installing latest AMR R package to {r_lib_path}...", flush=True) - utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True) + utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True) # # Retrieve Python AMR version # try: @@ -87,7 +87,7 @@ if not isinstalled('AMR', lib_loc=r_lib_path): # if r_amr_version != python_amr_version: # try: # print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True) -# utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True) +# utils.install_packages('AMR', repos='beta.amr-for-r.org', quiet=True) # except Exception as e: # print(f"AMR: Could not update: {e}", flush=True) @@ -248,7 +248,7 @@ for rd_file in "$rd_dir"/*.Rd; do # Write the Python function definition to the output file print "def " func_name_py "(" func_args "):" >> "'"$functions_file"'" - print " \"\"\"See our website of the R package for the manual: https://msberends.github.io/AMR/index.html\"\"\"" >> "'"$functions_file"'" + print " \"\"\"See our website of the R package for the manual: https://amr-for-r.org/index.html\"\"\"" >> "'"$functions_file"'" print " return convert_to_python(amr_r." func_name_py "(" func_args "))" >> "'"$functions_file"'" print "from .functions import " func_name_py >> "'"$init_file"'" diff --git a/data-raw/_language_update.R b/data-raw/_language_update.R index 8277d616f..c219e30dd 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # Run this file to update the languages used in the packages: diff --git a/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index c90b6aa04..9ba128c67 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://msberends.github.io/AMR/ # +# 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 b012a510a..9bd3e170a 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://msberends.github.io/AMR/ # +# 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 aa9f43789..1c366a30e 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://msberends.github.io/AMR/ # +# 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 84bf6e3dd..abb0be531 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # This script runs in 20-30 minutes and renews all guidelines of CLSI and EUCAST! diff --git a/data-raw/_reproduction scripts/reproduction_of_dosage.R b/data-raw/_reproduction scripts/reproduction_of_dosage.R index 171cf02d9..b62268804 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://msberends.github.io/AMR/ # +# 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 ef4731e2e..0ffe283f7 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://msberends.github.io/AMR/ # +# 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 d927d8fd0..e0e1b6e52 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://msberends.github.io/AMR/ # +# 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 70691454a..47ee9d0a9 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://msberends.github.io/AMR/ # +# 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 17596ec1a..24ad3509d 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # # This data set is being used in the clinical_breakpoints data set, and thus by as.sir(). diff --git a/data-raw/gpt_training_text_v2.1.1.9234.txt b/data-raw/gpt_training_text_v2.1.1.9235.txt similarity index 98% rename from data-raw/gpt_training_text_v2.1.1.9234.txt rename to data-raw/gpt_training_text_v2.1.1.9235.txt index 0edaec92c..378ffcf2f 100644 --- a/data-raw/gpt_training_text_v2.1.1.9234.txt +++ b/data-raw/gpt_training_text_v2.1.1.9235.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 2.1.1.9234. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9235. Remember this whenever someone asks which AMR package version you’re at. Below are the contents of the NAMESPACE file, the index.md file, and all the man/*.Rd files (documentation) in the package. Every file content is split using 100 hypens. ---------------------------------------------------------------------------------------------------- @@ -395,7 +395,7 @@ importFrom(stats,var) THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'index.md': -# The `AMR` Package for R +# The `AMR` Package for R * Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach * Used in over 175 countries, available in 20 languages @@ -409,7 +409,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'index.md': > Now available for Python too! [Click here](./articles/AMR_for_Python.html) to read more. @@ -437,7 +437,7 @@ With the help of contributors from all corners of the world, the `AMR` package i #### Filtering and selecting data -One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial selectors](https://msberends.github.io/AMR/reference/antimicrobial_selectors.html), which work in base R, `dplyr` and `data.table`. +One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial selectors](https://amr-for-r.org/reference/antimicrobial_selectors.html), which work in base R, `dplyr` and `data.table`. ```r # AMR works great with dplyr, but it's not required or neccesary @@ -583,7 +583,7 @@ example_isolates %>% |ICU | 0.2902655 | 0.253-0.33 | 0.4004739 | 0.353-0.449 | |Outpatient | 0.2000000 | 0.131-0.285 | 0.3676471 | 0.254-0.493 | -Or use [antimicrobial selectors](https://msberends.github.io/AMR/reference/antimicrobial_selectors.html) to select a series of antibiotic columns: +Or use [antimicrobial selectors](https://amr-for-r.org/reference/antimicrobial_selectors.html) to select a series of antibiotic columns: ```r library(AMR) @@ -673,15 +673,15 @@ It will be downloaded and installed automatically. For RStudio, click on the men Please read our [Developer Guideline here](https://github.com/msberends/AMR/wiki/Developer-Guideline). -The latest and unpublished development version can be installed from the [rOpenSci R-universe platform](https://msberends.r-universe.dev/AMR): +To install the latest and unpublished development version: ```r -install.packages("AMR", repos = "https://msberends.r-universe.dev") +install.packages("AMR", repos = "beta.amr-for-r.org") ``` ### Get started -To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://msberends.github.io/AMR/articles/). +To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://amr-for-r.org/articles/). ### Partners @@ -851,11 +851,11 @@ A BibTeX entry for LaTeX users is: \description{ Welcome to the \code{AMR} package. -The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://msberends.github.io/AMR/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project! +The \code{AMR} package is a \href{https://amr-for-r.org/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://amr-for-r.org/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project! This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}). -After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}. +After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}. The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages. } @@ -865,13 +865,13 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \seealso{ Useful links: \itemize{ - \item \url{https://msberends.github.io/AMR/} + \item \url{https://www.amr-for-r.org/} \item \url{https://github.com/msberends/AMR} \item Report bugs at \url{https://github.com/msberends/AMR/issues} } @@ -1007,7 +1007,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -1227,7 +1227,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -2313,7 +2313,7 @@ my_data_with_all_these_columns \%>\% \details{ These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and \code{data.table}. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but are not limited to \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}. -All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling. +All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling. All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antimicrobials} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. @@ -2369,7 +2369,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -2622,7 +2622,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \section{WHOCC}{ @@ -2725,7 +2725,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -2838,7 +2838,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -3313,7 +3313,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -3386,7 +3386,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/as.sir.Rd': \alias{as.sir.disk} \alias{as.sir.data.frame} \alias{sir_interpretation_history} -\title{Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data} +\title{Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data} \source{ For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters: \itemize{ @@ -3394,7 +3394,7 @@ For interpretations of minimum inhibitory concentration (MIC) values and disk di \item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}. \item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}. \item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2024, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}. -\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}. +\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}. } } \usage{ @@ -3621,7 +3621,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -4056,7 +4056,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -4297,7 +4297,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -4698,7 +4698,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -4825,7 +4825,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -4898,7 +4898,7 @@ A \link[tibble:tibble]{tibble} with 2 000 observations and 46 variables: example_isolates } \description{ -A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read \href{https://msberends.github.io/AMR/articles/AMR.html}{the tutorial on our website}. +A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read \href{https://amr-for-r.org/articles/AMR.html}{the tutorial on our website}. } \section{Download Our Reference Data}{ @@ -4906,7 +4906,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -4948,7 +4948,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -5941,7 +5941,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -6766,7 +6766,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -6808,7 +6808,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -6861,7 +6861,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -6945,7 +6945,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -7201,7 +7201,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ @@ -9986,7 +9986,7 @@ library(readxl) data <- read_excel(path = "path/to/your/file.xlsx") ``` -This package comes with an [example data set `WHONET`](https://msberends.github.io/AMR/reference/WHONET.html). We will use it for this analysis. +This package comes with an [example data set `WHONET`](https://amr-for-r.org/reference/WHONET.html). We will use it for this analysis. ### Preparation @@ -10001,7 +10001,7 @@ library(cleaner) # to create frequency tables We will have to transform some variables to simplify and automate the analysis: -* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms. +* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://amr-for-r.org/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms. * Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.sir()` function is for. ```{r} @@ -10100,7 +10100,7 @@ download_txt <- function(filename) { msg <- paste0( "It was last updated on ", trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")), - ". Find more info about the contents, (scientific) source, and structure of this [data set here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n" + ". Find more info about the contents, (scientific) source, and structure of this [data set here](https://amr-for-r.org/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n" ) github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/datasets/" local_filename <- paste0("../data-raw/datasets/", filename) @@ -10170,7 +10170,7 @@ print_df <- function(x, rows = 6) { All reference data (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. -> If you are working in Python, be sure to use our [AMR for Python](https://msberends.github.io/AMR/articles/AMR_for_Python.html) package. It allows all relevant AMR data sets to be natively available in Python. +> If you are working in Python, be sure to use our [AMR for Python](https://amr-for-r.org/articles/AMR_for_Python.html) package. It allows all relevant AMR data sets to be natively available in Python. ## `microorganisms`: Full Microbial Taxonomy @@ -10392,11 +10392,11 @@ knitr::opts_chunk$set( ) ``` -Note: to keep the package size as small as possible, we only include this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST and CLSI breakpoints, and much more: . +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://msberends.github.io/AMR/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project! +The `AMR` package is a [free and open-source](https://www.amr-for-r.org/) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://www.amr-for-r.org/authors.html) from around the globe are continually helping us to make this a successful and durable project! This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)). @@ -10425,14 +10425,14 @@ This package can be used for: * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to SIR * Principal component analysis for AMR -All reference data sets (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change. +All reference data sets (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://www.amr-for-r.org/articles/datasets.html), which is automatically updated with every code change. -This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](https://msberends.github.io/AMR/news/) by two public healthcare organisations in the Netherlands. +This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](https://www.amr-for-r.org/news/) by two public healthcare organisations in the Netherlands. ---- -This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://msberends.github.io/AMR/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package. +This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://www.amr-for-r.org/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package. diff --git a/data-raw/loinc.R b/data-raw/loinc.R index 4633a80d3..e2255ba35 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://msberends.github.io/AMR/ # +# 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 d498ce36b..0b7e24298 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://msberends.github.io/AMR/ # +# 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 05994bd1e..4f8b18c4a 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://msberends.github.io/AMR/ # +# 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 e0aa51306..3f238e9be 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # diff --git a/data-raw/~$v_14.0_Breakpoint_Tables.xlsx b/data-raw/~$v_14.0_Breakpoint_Tables.xlsx deleted file mode 100644 index 767eb740c..000000000 Binary files a/data-raw/~$v_14.0_Breakpoint_Tables.xlsx and /dev/null differ diff --git a/index.md b/index.md index ea89af6d9..d110dad4d 100644 --- a/index.md +++ b/index.md @@ -1,4 +1,4 @@ -# The `AMR` Package for R +# The `AMR` Package for R * Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach * Used in over 175 countries, available in 20 languages @@ -12,7 +12,7 @@ > Now available for Python too! [Click here](./articles/AMR_for_Python.html) to read more. @@ -40,7 +40,7 @@ With the help of contributors from all corners of the world, the `AMR` package i #### Filtering and selecting data -One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial selectors](https://msberends.github.io/AMR/reference/antimicrobial_selectors.html), which work in base R, `dplyr` and `data.table`. +One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial selectors](https://amr-for-r.org/reference/antimicrobial_selectors.html), which work in base R, `dplyr` and `data.table`. ```r # AMR works great with dplyr, but it's not required or neccesary @@ -186,7 +186,7 @@ example_isolates %>% |ICU | 0.2902655 | 0.253-0.33 | 0.4004739 | 0.353-0.449 | |Outpatient | 0.2000000 | 0.131-0.285 | 0.3676471 | 0.254-0.493 | -Or use [antimicrobial selectors](https://msberends.github.io/AMR/reference/antimicrobial_selectors.html) to select a series of antibiotic columns: +Or use [antimicrobial selectors](https://amr-for-r.org/reference/antimicrobial_selectors.html) to select a series of antibiotic columns: ```r library(AMR) @@ -276,15 +276,15 @@ It will be downloaded and installed automatically. For RStudio, click on the men Please read our [Developer Guideline here](https://github.com/msberends/AMR/wiki/Developer-Guideline). -The latest and unpublished development version can be installed from the [rOpenSci R-universe platform](https://msberends.r-universe.dev/AMR): +To install the latest and unpublished development version: ```r -install.packages("AMR", repos = "https://msberends.r-universe.dev") +install.packages("AMR", repos = "beta.amr-for-r.org") ``` ### Get started -To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://msberends.github.io/AMR/articles/). +To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://amr-for-r.org/articles/). ### Partners diff --git a/man/AMR.Rd b/man/AMR.Rd index 61a5a8d80..69eb613a5 100644 --- a/man/AMR.Rd +++ b/man/AMR.Rd @@ -28,11 +28,11 @@ A BibTeX entry for LaTeX users is: \description{ Welcome to the \code{AMR} package. -The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://msberends.github.io/AMR/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project! +The \code{AMR} package is a \href{https://amr-for-r.org/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://amr-for-r.org/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project! This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}). -After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}. +After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}. The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages. } @@ -42,13 +42,13 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \seealso{ Useful links: \itemize{ - \item \url{https://msberends.github.io/AMR/} + \item \url{https://www.amr-for-r.org/} \item \url{https://github.com/msberends/AMR} \item Report bugs at \url{https://github.com/msberends/AMR/issues} } diff --git a/man/WHONET.Rd b/man/WHONET.Rd index 2881ee8bb..8ebfcd480 100644 --- a/man/WHONET.Rd +++ b/man/WHONET.Rd @@ -47,7 +47,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/ab_property.Rd b/man/ab_property.Rd index 3562ebc5e..ad79afee7 100644 --- a/man/ab_property.Rd +++ b/man/ab_property.Rd @@ -103,7 +103,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/antimicrobial_selectors.Rd b/man/antimicrobial_selectors.Rd index 914453a6a..19c75e0b1 100644 --- a/man/antimicrobial_selectors.Rd +++ b/man/antimicrobial_selectors.Rd @@ -163,7 +163,7 @@ my_data_with_all_these_columns \%>\% \details{ These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and \code{data.table}. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but are not limited to \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}. -All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling. +All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling. All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antimicrobials} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. @@ -219,7 +219,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/antimicrobials.Rd b/man/antimicrobials.Rd index af268c7cd..7e3eece77 100644 --- a/man/antimicrobials.Rd +++ b/man/antimicrobials.Rd @@ -69,7 +69,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \section{WHOCC}{ diff --git a/man/as.ab.Rd b/man/as.ab.Rd index c8aeeb4d0..8a2573625 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -72,7 +72,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/as.av.Rd b/man/as.av.Rd index a2fa7143a..99d8f2fcf 100644 --- a/man/as.av.Rd +++ b/man/as.av.Rd @@ -64,7 +64,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/as.mo.Rd b/man/as.mo.Rd index fb7b54ae4..01eb17ab9 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -208,7 +208,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/as.sir.Rd b/man/as.sir.Rd index 6bc17239e..8cd91005d 100644 --- a/man/as.sir.Rd +++ b/man/as.sir.Rd @@ -12,7 +12,7 @@ \alias{as.sir.disk} \alias{as.sir.data.frame} \alias{sir_interpretation_history} -\title{Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data} +\title{Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data} \source{ For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters: \itemize{ @@ -20,7 +20,7 @@ For interpretations of minimum inhibitory concentration (MIC) values and disk di \item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}. \item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}. \item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2024, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}. -\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}. +\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}. } } \usage{ @@ -247,7 +247,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/av_property.Rd b/man/av_property.Rd index 034c371cf..6d09acff8 100644 --- a/man/av_property.Rd +++ b/man/av_property.Rd @@ -83,7 +83,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/clinical_breakpoints.Rd b/man/clinical_breakpoints.Rd index 29aac21e0..6756e14da 100644 --- a/man/clinical_breakpoints.Rd +++ b/man/clinical_breakpoints.Rd @@ -69,7 +69,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/dosage.Rd b/man/dosage.Rd index b329d4b1d..8bebc0217 100644 --- a/man/dosage.Rd +++ b/man/dosage.Rd @@ -30,7 +30,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index 2f718c5c1..f00f7f618 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -111,7 +111,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/example_isolates.Rd b/man/example_isolates.Rd index 2ce7f112c..f025cc0e1 100644 --- a/man/example_isolates.Rd +++ b/man/example_isolates.Rd @@ -20,7 +20,7 @@ A \link[tibble:tibble]{tibble} with 2 000 observations and 46 variables: example_isolates } \description{ -A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read \href{https://msberends.github.io/AMR/articles/AMR.html}{the tutorial on our website}. +A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read \href{https://amr-for-r.org/articles/AMR.html}{the tutorial on our website}. } \section{Download Our Reference Data}{ @@ -28,7 +28,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/example_isolates_unclean.Rd b/man/example_isolates_unclean.Rd index 45296a6a5..bd4f9c85d 100644 --- a/man/example_isolates_unclean.Rd +++ b/man/example_isolates_unclean.Rd @@ -26,7 +26,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/intrinsic_resistant.Rd b/man/intrinsic_resistant.Rd index f183c5fe2..54dacfa0e 100644 --- a/man/intrinsic_resistant.Rd +++ b/man/intrinsic_resistant.Rd @@ -32,7 +32,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index 8097ea7a5..46b4a2fb9 100644 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -96,7 +96,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index 864baea80..4fc95d15f 100644 --- a/man/microorganisms.codes.Rd +++ b/man/microorganisms.codes.Rd @@ -23,7 +23,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/microorganisms.groups.Rd b/man/microorganisms.groups.Rd index 22894f2d5..f1aae9fa8 100644 --- a/man/microorganisms.groups.Rd +++ b/man/microorganisms.groups.Rd @@ -25,7 +25,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/mo_matching_score.Rd b/man/mo_matching_score.Rd index f6140b68e..0ac347e13 100644 --- a/man/mo_matching_score.Rd +++ b/man/mo_matching_score.Rd @@ -62,7 +62,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/man/mo_property.Rd b/man/mo_property.Rd index cdc70fbd4..0f2738503 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -233,7 +233,7 @@ All reference data sets in the AMR package - including information on microorgan For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems. -Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. +Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}. } \examples{ diff --git a/pkgdown/assets/AMRforRGPT.svg b/pkgdown/assets/AMRforRGPT.svg index 7202662aa..df6df486d 100644 --- a/pkgdown/assets/AMRforRGPT.svg +++ b/pkgdown/assets/AMRforRGPT.svg @@ -1,2307 +1,443 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + - - + + + + + + + + - - + + + - - + + + - - + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/pkgdown/extra.css b/pkgdown/extra.css index 683a800f9..4a815e4f9 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # */ diff --git a/pkgdown/extra.js b/pkgdown/extra.js index f70a7b71c..5a7f71a16 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://msberends.github.io/AMR/ # +# how to conduct AMR data analysis: https://amr-for-r.org/ # # ==================================================================== # */ @@ -146,4 +146,4 @@ $(document).ready(function() { $(".developers a[href='authors.html']").text("All contributors..."); }); -$('head').append(" "); +$('head').append(" "); diff --git a/tests/testthat.R b/tests/testthat.R index 0acf02312..30363ec57 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://msberends.github.io/AMR/ # +# 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 352ef38d5..ae4f39a1a 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://msberends.github.io/AMR/ # +# 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 feec4ed5f..e6082b219 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://msberends.github.io/AMR/ # +# 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 6c3aa51fa..14ff47078 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://msberends.github.io/AMR/ # +# 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 84b39e8d8..883c8ba74 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://msberends.github.io/AMR/ # +# 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 cbb5a4fba..2f5eaf5b8 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://msberends.github.io/AMR/ # +# 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 78430fabd..534b830c2 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://msberends.github.io/AMR/ # +# 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 8e20ca932..e7eaab61a 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://msberends.github.io/AMR/ # +# 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 8b834ae79..5a63b2713 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://msberends.github.io/AMR/ # +# 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 4f622dd0d..83eeb6df9 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://msberends.github.io/AMR/ # +# 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 24ece9e51..3114994f8 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://msberends.github.io/AMR/ # +# 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 4555f3571..f5762ffe1 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://msberends.github.io/AMR/ # +# 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 dd753e461..dde0ad0ab 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://msberends.github.io/AMR/ # +# 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 b7bce56f8..f568822c0 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://msberends.github.io/AMR/ # +# 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 c6d11ebfa..66a571d49 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://msberends.github.io/AMR/ # +# 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 b35a2b90b..f708df031 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://msberends.github.io/AMR/ # +# 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 d651601e3..25710c37b 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://msberends.github.io/AMR/ # +# 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 2607055a8..66b3c2e2f 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://msberends.github.io/AMR/ # +# 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 65036cbe1..794f7dca5 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://msberends.github.io/AMR/ # +# 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 f4054faff..ecc1bea82 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://msberends.github.io/AMR/ # +# 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 bf50ab93f..183b8f488 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://msberends.github.io/AMR/ # +# 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 ab82a59c5..46ec81d39 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://msberends.github.io/AMR/ # +# 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 7fad41447..4a3ff154a 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://msberends.github.io/AMR/ # +# 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 ea17ec8b5..6bdd264c9 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://msberends.github.io/AMR/ # +# 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 6c3d9d400..d3ff4cfd8 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://msberends.github.io/AMR/ # +# 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 0cf2390a3..77746c622 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://msberends.github.io/AMR/ # +# 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 b64bfa2c1..6d8f7f742 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://msberends.github.io/AMR/ # +# 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 06d43f51b..fb9c63dc0 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://msberends.github.io/AMR/ # +# 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 5f38602a7..fab3dd864 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://msberends.github.io/AMR/ # +# 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 4359099f4..687051ca5 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://msberends.github.io/AMR/ # +# 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 ff6b450e0..f71ee61cb 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://msberends.github.io/AMR/ # +# 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 2a35245cb..c301ae6ac 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://msberends.github.io/AMR/ # +# 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 6543a59d3..c74c6c64c 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://msberends.github.io/AMR/ # +# 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 df1852715..a0bc72eb7 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://msberends.github.io/AMR/ # +# 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 536786f27..04b1abc8c 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://msberends.github.io/AMR/ # +# 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 de97df2ec..20938a985 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://msberends.github.io/AMR/ # +# 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 b4d701af4..38bc04142 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://msberends.github.io/AMR/ # +# 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 bc9eb1c83..fd1415566 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://msberends.github.io/AMR/ # +# 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 6ba1d625b..943f543ec 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://msberends.github.io/AMR/ # +# 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 dd363c741..97eff33b8 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://msberends.github.io/AMR/ # +# 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 d464cc3c7..ad99b5faf 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://msberends.github.io/AMR/ # +# 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 e3136b406..f5158e67b 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://msberends.github.io/AMR/ # +# 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 a30dea303..38003ed39 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://msberends.github.io/AMR/ # +# 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 b141bfdc9..78f45ea18 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://msberends.github.io/AMR/ # +# 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 6000406ce..f769e030a 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://msberends.github.io/AMR/ # +# 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 813d482a6..518806c44 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://msberends.github.io/AMR/ # +# 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 0f982a4ba..713934c2d 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://msberends.github.io/AMR/ # +# 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 deaef7167..47bce0b97 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://msberends.github.io/AMR/ # +# 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 dd815bc2b..c406de4b7 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://msberends.github.io/AMR/ # +# 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/WHONET.Rmd b/vignettes/WHONET.Rmd index ef67392cd..1aca7e582 100644 --- a/vignettes/WHONET.Rmd +++ b/vignettes/WHONET.Rmd @@ -32,7 +32,7 @@ library(readxl) data <- read_excel(path = "path/to/your/file.xlsx") ``` -This package comes with an [example data set `WHONET`](https://msberends.github.io/AMR/reference/WHONET.html). We will use it for this analysis. +This package comes with an [example data set `WHONET`](https://amr-for-r.org/reference/WHONET.html). We will use it for this analysis. ### Preparation @@ -47,7 +47,7 @@ library(cleaner) # to create frequency tables We will have to transform some variables to simplify and automate the analysis: -* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms. +* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://amr-for-r.org/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms. * Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.sir()` function is for. ```{r} diff --git a/vignettes/datasets.Rmd b/vignettes/datasets.Rmd index c2e077abd..ce7adf92b 100644 --- a/vignettes/datasets.Rmd +++ b/vignettes/datasets.Rmd @@ -40,7 +40,7 @@ download_txt <- function(filename) { msg <- paste0( "It was last updated on ", trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")), - ". Find more info about the contents, (scientific) source, and structure of this [data set here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n" + ". Find more info about the contents, (scientific) source, and structure of this [data set here](https://amr-for-r.org/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n" ) github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/datasets/" local_filename <- paste0("../data-raw/datasets/", filename) @@ -110,7 +110,7 @@ print_df <- function(x, rows = 6) { All reference data (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. -> If you are working in Python, be sure to use our [AMR for Python](https://msberends.github.io/AMR/articles/AMR_for_Python.html) package. It allows all relevant AMR data sets to be natively available in Python. +> If you are working in Python, be sure to use our [AMR for Python](https://amr-for-r.org/articles/AMR_for_Python.html) package. It allows all relevant AMR data sets to be natively available in Python. ## `microorganisms`: Full Microbial Taxonomy diff --git a/vignettes/welcome_to_AMR.Rmd b/vignettes/welcome_to_AMR.Rmd index 49cd25c07..b3bf50b1c 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://msberends.github.io/AMR/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project! +The `AMR` package is a [free and open-source](https://www.amr-for-r.org/) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://www.amr-for-r.org/authors.html) from around the globe are continually helping us to make this a successful and durable project! This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)). @@ -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://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change. +All reference data sets (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://www.amr-for-r.org/articles/datasets.html), which is automatically updated with every code change. -This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](https://msberends.github.io/AMR/news/) by two public healthcare organisations in the Netherlands. +This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl), and is being [actively and durably maintained](https://www.amr-for-r.org/news/) by two public healthcare organisations in the Netherlands. ---- -This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://msberends.github.io/AMR/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package. +This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://www.amr-for-r.org/LICENSE-text.html). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.