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dr. M.S. (Matthijs) Berends
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R/aa_amr-package.R
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://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:
#'

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R/aa_globals.R
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://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

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R/aa_helper_functions.R
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://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():

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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R/data.R
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://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
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#' 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

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

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

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

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

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

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

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R/ggplot_pca.R
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# useful, but it comes 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`

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

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R/guess_ab_col.R
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# useful, but it comes 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

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

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

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R/key_antimicrobials.R
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# useful, but it comes 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

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

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R/like.R
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# useful, but it comes 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

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

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R/mean_amr_distance.R
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# useful, but it comes 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

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R/mic.R
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://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

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

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

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

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R/mo_source.R
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# useful, but it comes 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

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

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

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

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

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R/resistance_predict.R
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@ -24,7 +24,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://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")')

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

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

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

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

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

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

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

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

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

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