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dr. M.S. (Matthijs) Berends 2023-05-27 10:39:22 +02:00
parent e1966503ee
commit 9591688811
128 changed files with 151 additions and 133 deletions
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2
.github/prehooks/pre-commit vendored
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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.github/workflows/check-old.yaml vendored
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #
@ -49,7 +49,7 @@ jobs:
# Test all old versions of R >= 3.0, we support them all! # Test all old versions of R >= 3.0, we support them all!
# For these old versions, dependencies and vignettes will not be checked. # For these old versions, dependencies and vignettes will not be checked.
# For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases). # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases).
- {os: ubuntu-latest, r: '3.5', allowfail: false} - {os: windows-latest, r: '3.5', allowfail: true}
- {os: ubuntu-latest, r: '3.4', allowfail: false} - {os: ubuntu-latest, r: '3.4', allowfail: false}
- {os: ubuntu-latest, r: '3.3', allowfail: false} - {os: ubuntu-latest, r: '3.3', allowfail: false}
- {os: ubuntu-latest, r: '3.2', allowfail: false} - {os: ubuntu-latest, r: '3.2', allowfail: false}

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.github/workflows/check-recent.yaml vendored
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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.github/workflows/codecovr.yaml vendored
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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.github/workflows/lintr.yaml vendored
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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.github/workflows/website.yaml vendored
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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DESCRIPTION
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Package: AMR Package: AMR
Version: 2.0.0.9022 Version: 2.0.0.9023
Date: 2023-05-26 Date: 2023-05-27
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

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NEWS.md
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# AMR 2.0.0.9022 # AMR 2.0.0.9023
## Changed ## Changed
* Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set * Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set

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R/aa_amr-package.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/aa_globals.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/aa_helper_functions.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/aa_helper_pm_functions.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/aa_options.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/ab.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/ab_from_text.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/ab_property.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/ab_selectors.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/age.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/antibiogram.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/atc_online.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/av.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/av_from_text.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/av_property.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/availability.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/bug_drug_combinations.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/count.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/custom_antimicrobials.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/custom_eucast_rules.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/custom_microorganisms.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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R/data.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #
@ -164,6 +164,15 @@
#' @seealso [as.mo()] [microorganisms] #' @seealso [as.mo()] [microorganisms]
#' @examples #' @examples
#' microorganisms.codes #' microorganisms.codes
#'
#' # 'ECO' or 'eco' is the WHONET code for E. coli:
#' microorganisms.codes[microorganisms.codes$code == "ECO", ]
#'
#' # and therefore, 'eco' will be understood as E. coli in this package:
#' mo_info("eco")
#'
#' # works for all AMR functions:
#' mo_is_intrinsic_resistant("eco", ab = "vancomycin")
"microorganisms.codes" "microorganisms.codes"
#' Data Set with `r format(nrow(example_isolates), big.mark = " ")` Example Isolates #' Data Set with `r format(nrow(example_isolates), big.mark = " ")` Example Isolates

2
R/disk.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/eucast_rules.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/first_isolate.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/g.test.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/get_episode.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/ggplot_pca.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/ggplot_sir.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/guess_ab_col.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/italicise_taxonomy.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/join_microorganisms.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/key_antimicrobials.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/kurtosis.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/like.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/mdro.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/mean_amr_distance.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/mic.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/mo.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/mo_matching_score.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/mo_property.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/mo_source.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/pca.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/plot.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/proportion.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/random.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/resistance_predict.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/sir.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/sir_calc.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/sir_df.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/skewness.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/translate.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/vctrs.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/whocc.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/zz_deprecated.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
R/zzz.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

12
_pkgdown.yml
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #
@ -116,19 +116,19 @@ navbar:
icon: "fa-capsules" icon: "fa-capsules"
href: "reference/av_property.html" # reference instead of an article href: "reference/av_property.html" # reference instead of an article
- text: "With other pkgs" - text: "With other pkgs"
icon: "fa-layer-plus" icon: "fa-layer-group"
menu: menu:
- text: "AMR & dplyr/tidyverse" - text: "AMR & dplyr/tidyverse"
icon: "fa-layer-plus" icon: "fa-layer-group"
href: "articles/other_pkg.html" href: "articles/other_pkg.html"
- text: "AMR & data.table" - text: "AMR & data.table"
icon: "fa-layer-plus" icon: "fa-layer-group"
href: "articles/other_pkg.html" href: "articles/other_pkg.html"
- text: "AMR & tidymodels" - text: "AMR & tidymodels"
icon: "fa-layer-plus" icon: "fa-layer-group"
href: "articles/other_pkg.html" href: "articles/other_pkg.html"
- text: "AMR & base R" - text: "AMR & base R"
icon: "fa-layer-plus" icon: "fa-layer-group"
href: "articles/other_pkg.html" href: "articles/other_pkg.html"
- text: "Manual" - text: "Manual"
icon: "fa-book-open" icon: "fa-book-open"

2
codecov.yml
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/_language_update.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/_pre_commit_hook.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/loinc.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/poorman_prepend.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/read_EUCAST.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/reproduction_of_antibiotics.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/reproduction_of_antivirals.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/reproduction_of_clinical_breakpoints.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/reproduction_of_dosage.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/reproduction_of_example_isolates_unclean.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/reproduction_of_intrinsic_resistant.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/reproduction_of_microorganisms.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
data-raw/salmonellae.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

BIN
data-raw/tinytest_1.3.1.tar.gz
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2
inst/tinytest/test-_deprecated.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-_misc.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-ab.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-ab_from_text.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-ab_property.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-ab_selectors.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-age.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-antibiogram.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-atc_online.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-av.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-av_from_text.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-av_property.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-availability.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-bug_drug_combinations.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-count.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-custom_antimicrobials.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-custom_microorganisms.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-data.R
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-disk.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

2
inst/tinytest/test-eucast_rules.R
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@ -9,7 +9,7 @@
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance # # (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. # # Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in The Netherlands, in collaboration with many #

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