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update beta version to 1.8.2.*, add JSS paper

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dr. M.S. (Matthijs) Berends
2022-10-02 15:31:16 +02:00
parent dfdd7a0968
commit c2b89d541e
120 changed files with 985 additions and 464 deletions
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data-raw/_install_deps.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/_language_update.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/_pre_commit_hook.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/loinc.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/poorman_prepend.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/read_EUCAST.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/reproduction_of_antibiotics.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/reproduction_of_antivirals.R
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/reproduction_of_dosage.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/reproduction_of_example_isolates_unclean.R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/reproduction_of_intrinsic_resistant.R
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

10
data-raw/reproduction_of_microorganisms.R
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

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data-raw/reproduction_of_rsi_translation.R
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #