diff --git a/.github/prehooks/pre-commit b/.github/prehooks/pre-commit index 06d47307..983a25d5 100755 --- a/.github/prehooks/pre-commit +++ b/.github/prehooks/pre-commit @@ -11,7 +11,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/.github/workflows/check-old.yaml b/.github/workflows/check-old.yaml index 1f9f2994..ebda1699 100644 --- a/.github/workflows/check-old.yaml +++ b/.github/workflows/check-old.yaml @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # 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! # 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). - - {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: '3.3', allowfail: false} - {os: ubuntu-latest, r: '3.2', allowfail: false} diff --git a/.github/workflows/check-recent.yaml b/.github/workflows/check-recent.yaml index 960e7926..62fb1949 100644 --- a/.github/workflows/check-recent.yaml +++ b/.github/workflows/check-recent.yaml @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index efbd917a..24d1b1ce 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index 12f2e71d..9c618da8 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/.github/workflows/website.yaml b/.github/workflows/website.yaml index 76755456..86d68b60 100644 --- a/.github/workflows/website.yaml +++ b/.github/workflows/website.yaml @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/DESCRIPTION b/DESCRIPTION index 31f683ab..d3bab689 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.0.0.9022 -Date: 2023-05-26 +Version: 2.0.0.9023 +Date: 2023-05-27 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index 98569bda..b06932a4 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.0.0.9022 +# AMR 2.0.0.9023 ## Changed * Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set diff --git a/R/aa_amr-package.R b/R/aa_amr-package.R index 7747627a..0422f869 100755 --- a/R/aa_amr-package.R +++ b/R/aa_amr-package.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/aa_globals.R b/R/aa_globals.R index 32eed3f0..cd8b4f79 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 2d5e83a7..2d457dde 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/aa_helper_pm_functions.R b/R/aa_helper_pm_functions.R index 800976ab..a2e396b9 100755 --- a/R/aa_helper_pm_functions.R +++ b/R/aa_helper_pm_functions.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/aa_options.R b/R/aa_options.R index 94dd79b5..a006ee50 100755 --- a/R/aa_options.R +++ b/R/aa_options.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/ab.R b/R/ab.R index c3d35ae5..d02569a7 100755 --- a/R/ab.R +++ b/R/ab.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/ab_from_text.R b/R/ab_from_text.R index e279519e..db3604e4 100755 --- a/R/ab_from_text.R +++ b/R/ab_from_text.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/ab_property.R b/R/ab_property.R index fb5eba44..66eb33a5 100755 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/ab_selectors.R b/R/ab_selectors.R index 3efc4635..ed9327a8 100755 --- a/R/ab_selectors.R +++ b/R/ab_selectors.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/age.R b/R/age.R index dbbb57b8..3f00b6a1 100755 --- a/R/age.R +++ b/R/age.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/antibiogram.R b/R/antibiogram.R index 4cac33c1..ee5613f2 100755 --- a/R/antibiogram.R +++ b/R/antibiogram.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/atc_online.R b/R/atc_online.R index e2350ac2..bc7c6f36 100755 --- a/R/atc_online.R +++ b/R/atc_online.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/av.R b/R/av.R index 26f53338..2e9d764d 100755 --- a/R/av.R +++ b/R/av.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/av_from_text.R b/R/av_from_text.R index fbf4a9ff..addaf096 100755 --- a/R/av_from_text.R +++ b/R/av_from_text.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/av_property.R b/R/av_property.R index b3a8cb63..670cffa0 100755 --- a/R/av_property.R +++ b/R/av_property.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/availability.R b/R/availability.R index 8dc0b382..137f596d 100755 --- a/R/availability.R +++ b/R/availability.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index 3b38842c..98fb6dc7 100755 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/count.R b/R/count.R index cce82d1d..89c552e7 100755 --- a/R/count.R +++ b/R/count.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/custom_antimicrobials.R b/R/custom_antimicrobials.R index c233ffbc..74f9e967 100755 --- a/R/custom_antimicrobials.R +++ b/R/custom_antimicrobials.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R index b02c6a42..551f07e7 100755 --- a/R/custom_eucast_rules.R +++ b/R/custom_eucast_rules.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/custom_microorganisms.R b/R/custom_microorganisms.R index 5c1b82dd..55145194 100755 --- a/R/custom_microorganisms.R +++ b/R/custom_microorganisms.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/data.R b/R/data.R index 2743d765..b02e7ff9 100755 --- a/R/data.R +++ b/R/data.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # @@ -164,6 +164,15 @@ #' @seealso [as.mo()] [microorganisms] #' @examples #' 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" #' Data Set with `r format(nrow(example_isolates), big.mark = " ")` Example Isolates diff --git a/R/disk.R b/R/disk.R index 5278ab3b..7672f0b7 100755 --- a/R/disk.R +++ b/R/disk.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 7ce81629..9fd66966 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/first_isolate.R b/R/first_isolate.R index 5a4aae73..5e3c1daa 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/g.test.R b/R/g.test.R index 21deef6a..7d7eb8cb 100755 --- a/R/g.test.R +++ b/R/g.test.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/get_episode.R b/R/get_episode.R index a0c807b8..a73f3113 100755 --- a/R/get_episode.R +++ b/R/get_episode.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/ggplot_pca.R b/R/ggplot_pca.R index 4bd1767c..585d4b1a 100755 --- a/R/ggplot_pca.R +++ b/R/ggplot_pca.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/ggplot_sir.R b/R/ggplot_sir.R index cacbeb63..71750d43 100755 --- a/R/ggplot_sir.R +++ b/R/ggplot_sir.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R index f09d8236..8de5a2c3 100755 --- a/R/guess_ab_col.R +++ b/R/guess_ab_col.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/italicise_taxonomy.R b/R/italicise_taxonomy.R index 5acb8d73..d8bae268 100755 --- a/R/italicise_taxonomy.R +++ b/R/italicise_taxonomy.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R index 9f8532df..fe79ca56 100755 --- a/R/join_microorganisms.R +++ b/R/join_microorganisms.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/key_antimicrobials.R b/R/key_antimicrobials.R index de75e913..a2182a5b 100755 --- a/R/key_antimicrobials.R +++ b/R/key_antimicrobials.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/kurtosis.R b/R/kurtosis.R index 03996fd0..84e312d9 100755 --- a/R/kurtosis.R +++ b/R/kurtosis.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/like.R b/R/like.R index fed26c22..cc183221 100755 --- a/R/like.R +++ b/R/like.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/mdro.R b/R/mdro.R index 57cef7d2..4abce1ff 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/mean_amr_distance.R b/R/mean_amr_distance.R index 596c18ea..5dd0b2f1 100755 --- a/R/mean_amr_distance.R +++ b/R/mean_amr_distance.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/mic.R b/R/mic.R index 7223f462..af695139 100755 --- a/R/mic.R +++ b/R/mic.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/mo.R b/R/mo.R index 574c3c1b..624f49d3 100755 --- a/R/mo.R +++ b/R/mo.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/mo_matching_score.R b/R/mo_matching_score.R index 67ac2071..27fdb364 100755 --- a/R/mo_matching_score.R +++ b/R/mo_matching_score.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/mo_property.R b/R/mo_property.R index f9094f31..7ebdc6dc 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/mo_source.R b/R/mo_source.R index b743e863..c0d57e24 100755 --- a/R/mo_source.R +++ b/R/mo_source.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/pca.R b/R/pca.R index e8b42368..c94e39eb 100755 --- a/R/pca.R +++ b/R/pca.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/plot.R b/R/plot.R index 176bd284..ca55a013 100755 --- a/R/plot.R +++ b/R/plot.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/proportion.R b/R/proportion.R index 3492b4ae..f97cb966 100755 --- a/R/proportion.R +++ b/R/proportion.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/random.R b/R/random.R index 54f09baf..fd15cb61 100755 --- a/R/random.R +++ b/R/random.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/resistance_predict.R b/R/resistance_predict.R index f8c2ad5f..f8e41846 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/sir.R b/R/sir.R index aaafd029..f79f4694 100755 --- a/R/sir.R +++ b/R/sir.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/sir_calc.R b/R/sir_calc.R index 24f0fd1e..8b66bafb 100755 --- a/R/sir_calc.R +++ b/R/sir_calc.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/sir_df.R b/R/sir_df.R index 4dca351a..6ed7be0e 100755 --- a/R/sir_df.R +++ b/R/sir_df.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/skewness.R b/R/skewness.R index 44b9b770..1d509b9e 100755 --- a/R/skewness.R +++ b/R/skewness.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/translate.R b/R/translate.R index 1861ec0a..23753095 100755 --- a/R/translate.R +++ b/R/translate.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/vctrs.R b/R/vctrs.R index 10578379..3f07d5cb 100755 --- a/R/vctrs.R +++ b/R/vctrs.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/whocc.R b/R/whocc.R index bfbf3260..92869137 100755 --- a/R/whocc.R +++ b/R/whocc.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/zz_deprecated.R b/R/zz_deprecated.R index 6ae0adad..2cdd6536 100755 --- a/R/zz_deprecated.R +++ b/R/zz_deprecated.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/R/zzz.R b/R/zzz.R index d1dc62a1..68d444f5 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/_pkgdown.yml b/_pkgdown.yml index 085f5215..56b6291f 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # @@ -116,19 +116,19 @@ navbar: icon: "fa-capsules" href: "reference/av_property.html" # reference instead of an article - text: "With other pkgs" - icon: "fa-layer-plus" + icon: "fa-layer-group" menu: - text: "AMR & dplyr/tidyverse" - icon: "fa-layer-plus" + icon: "fa-layer-group" href: "articles/other_pkg.html" - text: "AMR & data.table" - icon: "fa-layer-plus" + icon: "fa-layer-group" href: "articles/other_pkg.html" - text: "AMR & tidymodels" - icon: "fa-layer-plus" + icon: "fa-layer-group" href: "articles/other_pkg.html" - text: "AMR & base R" - icon: "fa-layer-plus" + icon: "fa-layer-group" href: "articles/other_pkg.html" - text: "Manual" icon: "fa-book-open" diff --git a/codecov.yml b/codecov.yml index 4651d9a1..0bd76cc5 100644 --- a/codecov.yml +++ b/codecov.yml @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/_language_update.R b/data-raw/_language_update.R index 6e55afe8..fe94ac00 100644 --- a/data-raw/_language_update.R +++ b/data-raw/_language_update.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/_pre_commit_hook.R b/data-raw/_pre_commit_hook.R index 5789d723..8e21862d 100644 --- a/data-raw/_pre_commit_hook.R +++ b/data-raw/_pre_commit_hook.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/loinc.R b/data-raw/loinc.R index 59681712..7b1725a9 100644 --- a/data-raw/loinc.R +++ b/data-raw/loinc.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/poorman_prepend.R b/data-raw/poorman_prepend.R index ec8bf91d..832467e9 100644 --- a/data-raw/poorman_prepend.R +++ b/data-raw/poorman_prepend.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/read_EUCAST.R b/data-raw/read_EUCAST.R index a52d3153..d6c31283 100644 --- a/data-raw/read_EUCAST.R +++ b/data-raw/read_EUCAST.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index df66f943..0044faab 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_antibiotics.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/reproduction_of_antivirals.R b/data-raw/reproduction_of_antivirals.R index 6287870a..3bf25577 100644 --- a/data-raw/reproduction_of_antivirals.R +++ b/data-raw/reproduction_of_antivirals.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/reproduction_of_clinical_breakpoints.R b/data-raw/reproduction_of_clinical_breakpoints.R index 73c3b25c..1f4f0c3d 100644 --- a/data-raw/reproduction_of_clinical_breakpoints.R +++ b/data-raw/reproduction_of_clinical_breakpoints.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/reproduction_of_dosage.R b/data-raw/reproduction_of_dosage.R index 177c3445..b2c42097 100644 --- a/data-raw/reproduction_of_dosage.R +++ b/data-raw/reproduction_of_dosage.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/reproduction_of_example_isolates_unclean.R b/data-raw/reproduction_of_example_isolates_unclean.R index 5be7426a..a2edfccd 100644 --- a/data-raw/reproduction_of_example_isolates_unclean.R +++ b/data-raw/reproduction_of_example_isolates_unclean.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/reproduction_of_intrinsic_resistant.R b/data-raw/reproduction_of_intrinsic_resistant.R index 8c0afb61..9e88cd86 100644 --- a/data-raw/reproduction_of_intrinsic_resistant.R +++ b/data-raw/reproduction_of_intrinsic_resistant.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/reproduction_of_microorganisms.R b/data-raw/reproduction_of_microorganisms.R index eaabbf8a..7f736f79 100644 --- a/data-raw/reproduction_of_microorganisms.R +++ b/data-raw/reproduction_of_microorganisms.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/salmonellae.R b/data-raw/salmonellae.R index 6a5b1cae..17d61d95 100644 --- a/data-raw/salmonellae.R +++ b/data-raw/salmonellae.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/data-raw/tinytest_1.3.1.tar.gz b/data-raw/tinytest_1.3.1.tar.gz deleted file mode 100644 index e8729b32..00000000 Binary files a/data-raw/tinytest_1.3.1.tar.gz and /dev/null differ diff --git a/inst/tinytest/test-_deprecated.R b/inst/tinytest/test-_deprecated.R index 6fc2e4ae..4dbc0055 100644 --- a/inst/tinytest/test-_deprecated.R +++ b/inst/tinytest/test-_deprecated.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-_misc.R b/inst/tinytest/test-_misc.R index 3313633b..9c999b51 100755 --- a/inst/tinytest/test-_misc.R +++ b/inst/tinytest/test-_misc.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-ab.R b/inst/tinytest/test-ab.R index 588fb74a..d01dc56c 100755 --- a/inst/tinytest/test-ab.R +++ b/inst/tinytest/test-ab.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-ab_from_text.R b/inst/tinytest/test-ab_from_text.R index ec322ae4..8ba20d55 100644 --- a/inst/tinytest/test-ab_from_text.R +++ b/inst/tinytest/test-ab_from_text.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-ab_property.R b/inst/tinytest/test-ab_property.R index aabfb17a..e9c9927a 100644 --- a/inst/tinytest/test-ab_property.R +++ b/inst/tinytest/test-ab_property.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-ab_selectors.R b/inst/tinytest/test-ab_selectors.R index 5a74e545..9a85a1e2 100644 --- a/inst/tinytest/test-ab_selectors.R +++ b/inst/tinytest/test-ab_selectors.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-age.R b/inst/tinytest/test-age.R index 5e8bf005..3f48436e 100644 --- a/inst/tinytest/test-age.R +++ b/inst/tinytest/test-age.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-antibiogram.R b/inst/tinytest/test-antibiogram.R index f551d28f..a74f1bd1 100644 --- a/inst/tinytest/test-antibiogram.R +++ b/inst/tinytest/test-antibiogram.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-atc_online.R b/inst/tinytest/test-atc_online.R index ca9d3e98..b434ddb6 100644 --- a/inst/tinytest/test-atc_online.R +++ b/inst/tinytest/test-atc_online.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-av.R b/inst/tinytest/test-av.R index 68bad76b..b521eca8 100755 --- a/inst/tinytest/test-av.R +++ b/inst/tinytest/test-av.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-av_from_text.R b/inst/tinytest/test-av_from_text.R index 5e720732..897ba184 100644 --- a/inst/tinytest/test-av_from_text.R +++ b/inst/tinytest/test-av_from_text.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-av_property.R b/inst/tinytest/test-av_property.R index d8070f20..2695ec7f 100644 --- a/inst/tinytest/test-av_property.R +++ b/inst/tinytest/test-av_property.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-availability.R b/inst/tinytest/test-availability.R index 83928299..70143087 100644 --- a/inst/tinytest/test-availability.R +++ b/inst/tinytest/test-availability.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-bug_drug_combinations.R b/inst/tinytest/test-bug_drug_combinations.R index 79dab75e..87c31ee6 100644 --- a/inst/tinytest/test-bug_drug_combinations.R +++ b/inst/tinytest/test-bug_drug_combinations.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-count.R b/inst/tinytest/test-count.R index ee86eeb5..ded43407 100644 --- a/inst/tinytest/test-count.R +++ b/inst/tinytest/test-count.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-custom_antimicrobials.R b/inst/tinytest/test-custom_antimicrobials.R index 7c8b53c5..c1ccf0ed 100644 --- a/inst/tinytest/test-custom_antimicrobials.R +++ b/inst/tinytest/test-custom_antimicrobials.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-custom_microorganisms.R b/inst/tinytest/test-custom_microorganisms.R index 3aaa0b56..c79d7e1c 100644 --- a/inst/tinytest/test-custom_microorganisms.R +++ b/inst/tinytest/test-custom_microorganisms.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-data.R b/inst/tinytest/test-data.R index f20fba76..1cd2db65 100644 --- a/inst/tinytest/test-data.R +++ b/inst/tinytest/test-data.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-disk.R b/inst/tinytest/test-disk.R index 105630e3..5763cccf 100755 --- a/inst/tinytest/test-disk.R +++ b/inst/tinytest/test-disk.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-eucast_rules.R b/inst/tinytest/test-eucast_rules.R index 4743c16d..ba5b13b8 100755 --- a/inst/tinytest/test-eucast_rules.R +++ b/inst/tinytest/test-eucast_rules.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-first_isolate.R b/inst/tinytest/test-first_isolate.R index 7a5b2c17..5228f6ce 100755 --- a/inst/tinytest/test-first_isolate.R +++ b/inst/tinytest/test-first_isolate.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-g.test.R b/inst/tinytest/test-g.test.R index f3fb0af8..234e4e7f 100644 --- a/inst/tinytest/test-g.test.R +++ b/inst/tinytest/test-g.test.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-get_episode.R b/inst/tinytest/test-get_episode.R index d1516122..759f8a29 100644 --- a/inst/tinytest/test-get_episode.R +++ b/inst/tinytest/test-get_episode.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-ggplot_rsi.R b/inst/tinytest/test-ggplot_rsi.R index a4c116a9..ab00ea19 100644 --- a/inst/tinytest/test-ggplot_rsi.R +++ b/inst/tinytest/test-ggplot_rsi.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-guess_ab_col.R b/inst/tinytest/test-guess_ab_col.R index c3a537dd..fd9fef82 100644 --- a/inst/tinytest/test-guess_ab_col.R +++ b/inst/tinytest/test-guess_ab_col.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-italicise_taxonomy.R b/inst/tinytest/test-italicise_taxonomy.R index ff6321e8..a133b3e6 100644 --- a/inst/tinytest/test-italicise_taxonomy.R +++ b/inst/tinytest/test-italicise_taxonomy.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-join_microorganisms.R b/inst/tinytest/test-join_microorganisms.R index 40d50012..54dcc44d 100755 --- a/inst/tinytest/test-join_microorganisms.R +++ b/inst/tinytest/test-join_microorganisms.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-key_antimicrobials.R b/inst/tinytest/test-key_antimicrobials.R index 5c9f563a..5d5dda21 100644 --- a/inst/tinytest/test-key_antimicrobials.R +++ b/inst/tinytest/test-key_antimicrobials.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-kurtosis.R b/inst/tinytest/test-kurtosis.R index 65da50c5..1448a8bb 100644 --- a/inst/tinytest/test-kurtosis.R +++ b/inst/tinytest/test-kurtosis.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-like.R b/inst/tinytest/test-like.R index 2b345551..3a456736 100644 --- a/inst/tinytest/test-like.R +++ b/inst/tinytest/test-like.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-mdro.R b/inst/tinytest/test-mdro.R index d1a8e0fe..6643e021 100755 --- a/inst/tinytest/test-mdro.R +++ b/inst/tinytest/test-mdro.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-mean_amr_distance.R b/inst/tinytest/test-mean_amr_distance.R index 25e151af..0a23a52b 100644 --- a/inst/tinytest/test-mean_amr_distance.R +++ b/inst/tinytest/test-mean_amr_distance.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-mic.R b/inst/tinytest/test-mic.R index e4b1bbe7..0632b60d 100755 --- a/inst/tinytest/test-mic.R +++ b/inst/tinytest/test-mic.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-mo.R b/inst/tinytest/test-mo.R index 9878ccdf..95b80a38 100644 --- a/inst/tinytest/test-mo.R +++ b/inst/tinytest/test-mo.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-mo_property.R b/inst/tinytest/test-mo_property.R index e04fd6a2..40d7d2d9 100644 --- a/inst/tinytest/test-mo_property.R +++ b/inst/tinytest/test-mo_property.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-pca.R b/inst/tinytest/test-pca.R index 6df1f08d..f0d51433 100644 --- a/inst/tinytest/test-pca.R +++ b/inst/tinytest/test-pca.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-proportion.R b/inst/tinytest/test-proportion.R index 62a2926f..83f7a237 100755 --- a/inst/tinytest/test-proportion.R +++ b/inst/tinytest/test-proportion.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-random.R b/inst/tinytest/test-random.R index 4d427cc7..aa6ef23d 100644 --- a/inst/tinytest/test-random.R +++ b/inst/tinytest/test-random.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-resistance_predict.R b/inst/tinytest/test-resistance_predict.R index 53228ccb..9670999d 100644 --- a/inst/tinytest/test-resistance_predict.R +++ b/inst/tinytest/test-resistance_predict.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-rsi.R b/inst/tinytest/test-rsi.R index d85e01d4..5a993f91 100644 --- a/inst/tinytest/test-rsi.R +++ b/inst/tinytest/test-rsi.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-skewness.R b/inst/tinytest/test-skewness.R index e5b5f1ce..1414b714 100644 --- a/inst/tinytest/test-skewness.R +++ b/inst/tinytest/test-skewness.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-translate.R b/inst/tinytest/test-translate.R index 59b89bdc..e5e47202 100644 --- a/inst/tinytest/test-translate.R +++ b/inst/tinytest/test-translate.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-vctrs.R b/inst/tinytest/test-vctrs.R index 4d07482c..ddb339ed 100755 --- a/inst/tinytest/test-vctrs.R +++ b/inst/tinytest/test-vctrs.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/inst/tinytest/test-zzz.R b/inst/tinytest/test-zzz.R index d04d7189..7b35ebad 100644 --- a/inst/tinytest/test-zzz.R +++ b/inst/tinytest/test-zzz.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index b7adeb6b..d2ec271a 100644 --- a/man/microorganisms.codes.Rd +++ b/man/microorganisms.codes.Rd @@ -22,6 +22,15 @@ Like all data sets in this package, this data set is publicly available for down } \examples{ 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") } \seealso{ \code{\link[=as.mo]{as.mo()}} \link{microorganisms} diff --git a/pkgdown/extra.css b/pkgdown/extra.css index 695e4d78..819146a5 100644 --- a/pkgdown/extra.css +++ b/pkgdown/extra.css @@ -10,7 +10,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/pkgdown/extra.js b/pkgdown/extra.js index d3ab8d7e..8ec8be52 100644 --- a/pkgdown/extra.js +++ b/pkgdown/extra.js @@ -10,7 +10,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # diff --git a/tests/tinytest.R b/tests/tinytest.R index f68d81dc..500409de 100644 --- a/tests/tinytest.R +++ b/tests/tinytest.R @@ -9,7 +9,7 @@ # 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 # +# https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many #