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(v1.8.0) prerelease 1.8.0

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  1. 2
      .github/workflows/check.yaml
  2. 2
      .github/workflows/codecovr.yaml
  3. 2
      .github/workflows/lintr.yaml
  4. 4
      DESCRIPTION
  5. 4
      NEWS.md
  6. 2
      R/aa_globals.R
  7. 2
      R/aa_helper_functions.R
  8. 2
      R/aa_helper_pm_functions.R
  9. 2
      R/ab.R
  10. 2
      R/ab_from_text.R
  11. 2
      R/ab_property.R
  12. 2
      R/ab_selectors.R
  13. 2
      R/age.R
  14. 2
      R/amr.R
  15. 2
      R/atc_online.R
  16. 2
      R/availability.R
  17. 2
      R/bug_drug_combinations.R
  18. 2
      R/catalogue_of_life.R
  19. 2
      R/count.R
  20. 2
      R/custom_eucast_rules.R
  21. 2
      R/data.R
  22. 2
      R/deprecated.R
  23. 2
      R/disk.R
  24. 2
      R/episode.R
  25. 2
      R/eucast_rules.R
  26. 2
      R/first_isolate.R
  27. 2
      R/g.test.R
  28. 2
      R/ggplot_pca.R
  29. 2
      R/ggplot_rsi.R
  30. 2
      R/guess_ab_col.R
  31. 2
      R/italicise_taxonomy.R
  32. 2
      R/join_microorganisms.R
  33. 2
      R/key_antimicrobials.R
  34. 2
      R/kurtosis.R
  35. 2
      R/lifecycle.R
  36. 2
      R/like.R
  37. 2
      R/mdro.R
  38. 2
      R/mic.R
  39. 2
      R/mo.R
  40. 2
      R/mo_matching_score.R
  41. 2
      R/mo_property.R
  42. 2
      R/mo_source.R
  43. 2
      R/pca.R
  44. 2
      R/plot.R
  45. 2
      R/proportion.R
  46. 2
      R/random.R
  47. 2
      R/resistance_predict.R
  48. 2
      R/rsi.R
  49. 2
      R/rsi_calc.R
  50. 2
      R/rsi_df.R
  51. 2
      R/skewness.R
  52. 2
      R/translate.R
  53. 2
      R/vctrs.R
  54. 2
      R/whocc.R
  55. 2
      R/zzz.R
  56. 2
      _pkgdown.yml
  57. 2
      codecov.yml
  58. BIN
      data-raw/AMR_latest.tar.gz
  59. 2
      data-raw/_install_deps.R
  60. 2
      data-raw/_internals.R
  61. 2
      data-raw/loinc.R
  62. 2
      data-raw/poorman_prepend.R
  63. 2
      data-raw/read_EUCAST.R
  64. 2
      data-raw/reproduction_of_antibiotics.R
  65. 2
      data-raw/reproduction_of_antivirals.R
  66. 2
      data-raw/reproduction_of_dosage.R
  67. 2
      data-raw/reproduction_of_example_isolates_unclean.R
  68. 2
      data-raw/reproduction_of_intrinsic_resistant.R
  69. 2
      data-raw/reproduction_of_microorganisms.R
  70. 2
      data-raw/reproduction_of_microorganisms_update.R
  71. 2
      data-raw/reproduction_of_rsi_translation.R
  72. 2
      data-raw/snomed.R
  73. 2
      docs/404.html
  74. 2
      docs/LICENSE-text.html
  75. 458
      docs/articles/AMR.html
  76. BIN
      docs/articles/AMR_files/figure-html/disk_plots-1.png
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      docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
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      docs/articles/AMR_files/figure-html/mic_plots-1.png
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      docs/articles/AMR_files/figure-html/mic_plots-2.png
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      docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
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      docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
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      docs/articles/AMR_files/figure-html/plot 5-1.png
  86. 2
      docs/articles/EUCAST.html
  87. 58
      docs/articles/MDR.html
  88. 2
      docs/articles/PCA.html
  89. 6
      docs/articles/SPSS.html
  90. 2
      docs/articles/WHONET.html
  91. 90
      docs/articles/benchmarks.html
  92. BIN
      docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
  93. 2
      docs/articles/datasets.html
  94. 2
      docs/articles/index.html
  95. 2
      docs/articles/resistance_predict.html
  96. 2
      docs/articles/welcome_to_AMR.html
  97. 2
      docs/authors.html
  98. 2
      docs/extra.css
  99. 2
      docs/extra.js
  100. 2
      docs/index.html
  101. Some files were not shown because too many files have changed in this diff Show More

2
.github/workflows/check.yaml

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
.github/workflows/codecovr.yaml

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
.github/workflows/lintr.yaml

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9077
Date: 2021-12-23
Version: 1.8.0
Date: 2022-01-03
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

4
NEWS.md

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
# `AMR` 1.7.1.9077
## <small>Last updated: 23 December 2021</small>
# `AMR` 1.8.0
All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.

2
R/aa_globals.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/aa_helper_functions.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/aa_helper_pm_functions.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/ab.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/ab_from_text.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/ab_property.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/ab_selectors.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/age.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/amr.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/atc_online.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/availability.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/bug_drug_combinations.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/catalogue_of_life.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/count.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/custom_eucast_rules.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/data.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/deprecated.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/disk.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/episode.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/eucast_rules.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/first_isolate.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/g.test.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/ggplot_pca.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/ggplot_rsi.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/guess_ab_col.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/italicise_taxonomy.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/join_microorganisms.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/key_antimicrobials.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/kurtosis.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/lifecycle.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/like.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/mdro.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/mic.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/mo.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/mo_matching_score.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/mo_property.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/mo_source.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/pca.R

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# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/plot.R

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# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/proportion.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/random.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/resistance_predict.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/rsi.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/rsi_calc.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/rsi_df.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/skewness.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/translate.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/vctrs.R

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# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/whocc.R

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# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
R/zzz.R

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# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
_pkgdown.yml

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
codecov.yml

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

BIN
data-raw/AMR_latest.tar.gz

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data-raw/_install_deps.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/_internals.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/loinc.R

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# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/poorman_prepend.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/read_EUCAST.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/reproduction_of_antibiotics.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/reproduction_of_antivirals.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/reproduction_of_dosage.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/reproduction_of_example_isolates_unclean.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/reproduction_of_intrinsic_resistant.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/reproduction_of_microorganisms.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/reproduction_of_microorganisms_update.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/reproduction_of_rsi_translation.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
data-raw/snomed.R

@ -6,7 +6,7 @@ @@ -6,7 +6,7 @@
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #

2
docs/404.html

@ -43,7 +43,7 @@ @@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9071</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
</span>
</div>

2
docs/LICENSE-text.html

@ -17,7 +17,7 @@ @@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9071</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
</span>
</div>

458
docs/articles/AMR.html

@ -44,7 +44,7 @@ @@ -44,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
</span>
</div>
@ -191,7 +191,7 @@ @@ -191,7 +191,7 @@
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">12 December 2021</h4>
<h4 data-toc-skip class="date">23 December 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -200,7 +200,7 @@ @@ -200,7 +200,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 12 December 2021.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 23 December 2021.</p>
<div class="section level1">
<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h1>
@ -231,21 +231,21 @@ @@ -231,21 +231,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-12-12</td>
<td align="center">2021-12-23</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2021-12-12</td>
<td align="center">2021-12-23</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2021-12-12</td>
<td align="center">2021-12-23</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -342,32 +342,32 @@ @@ -342,32 +342,32 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-11-21</td>
<td align="center">L5</td>
<td align="center">Hospital C</td>
<td align="center">2010-03-07</td>
<td align="center">U8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-03-18</td>
<td align="center">G9</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2015-08-15</td>
<td align="center">A4</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-10-31</td>
<td align="center">Z3</td>
<td align="center">2012-02-22</td>
<td align="center">T7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -375,37 +375,37 @@ @@ -375,37 +375,37 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-05-24</td>
<td align="center">A3</td>
<td align="center">2017-04-28</td>
<td align="center">J10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-01-31</td>
<td align="center">Y10</td>
<td align="center">Hospital C</td>
<td align="center">2013-05-14</td>
<td align="center">X5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-04-13</td>
<td align="center">L6</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">2011-09-09</td>
<td align="center">Z1</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
@ -439,16 +439,16 @@ Longest: 1</p> @@ -439,16 +439,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,451</td>
<td align="right">52.26%</td>
<td align="right">10,451</td>
<td align="right">52.26%</td>
<td align="right">10,513</td>
<td align="right">52.56%</td>
<td align="right">10,513</td>
<td align="right">52.56%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,549</td>
<td align="right">47.75%</td>
<td align="right">9,487</td>
<td align="right">47.44%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -502,7 +502,7 @@ Longest: 1</p> @@ -502,7 +502,7 @@ Longest: 1</p>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,684 'phenotype-based' first isolates (53.4% of total where a</span>
<span class="co"># =&gt; Found 10,677 'phenotype-based' first isolates (53.4% of total where a</span>
<span class="co"># microbial ID was available)</span></code></pre></div>
<p>So only 53.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -512,10 +512,10 @@ Longest: 1</p> @@ -512,10 +512,10 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,684 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,677 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -528,7 +528,7 @@ Longest: 1</p> @@ -528,7 +528,7 @@ Longest: 1</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="10%">
<col width="9%">
<col width="5%">
</colgroup>
@ -550,79 +550,79 @@ Longest: 1</p> @@ -550,79 +550,79 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2015-03-18</td>
<td align="center">G9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="left">1</td>
<td align="center">2010-03-07</td>
<td align="center">U8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">2017-05-24</td>
<td align="center">A3</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="left">2</td>
<td align="center">2015-08-15</td>
<td align="center">A4</td>