From 8b52f9b1be94169411b5dd170a81da8126949b49 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Sun, 27 Dec 2020 00:30:28 +0100 Subject: [PATCH] (v1.4.0.9047) unit tests --- .github/workflows/check.yaml | 2 +- .github/workflows/codecovr.yaml | 2 +- .github/workflows/lintr.yaml | 2 +- DESCRIPTION | 2 +- NEWS.md | 2 +- R/aa_helper_functions.R | 2 +- R/aa_helper_pm_functions.R | 2 +- R/ab.R | 2 +- R/ab_class_selectors.R | 2 +- R/ab_from_text.R | 2 +- R/ab_property.R | 2 +- R/age.R | 2 +- R/amr.R | 2 +- R/atc_online.R | 2 +- R/availability.R | 2 +- R/bug_drug_combinations.R | 2 +- R/catalogue_of_life.R | 2 +- R/count.R | 2 +- R/data.R | 2 +- R/deprecated.R | 2 +- R/disk.R | 2 +- R/episode.R | 2 +- R/eucast_rules.R | 2 +- R/filter_ab_class.R | 2 +- R/first_isolate.R | 2 +- R/g.test.R | 2 +- R/ggplot_pca.R | 2 +- R/ggplot_rsi.R | 2 +- R/globals.R | 2 +- R/guess_ab_col.R | 2 +- R/join_microorganisms.R | 2 +- R/key_antibiotics.R | 2 +- R/kurtosis.R | 2 +- R/lifecycle.R | 2 +- R/like.R | 2 +- R/mdro.R | 2 +- R/mic.R | 2 +- R/mo.R | 2 +- R/mo_matching_score.R | 2 +- R/mo_property.R | 2 +- R/mo_source.R | 2 +- R/pca.R | 2 +- R/proportion.R | 2 +- R/random.R | 2 +- R/resistance_predict.R | 2 +- R/rsi.R | 2 +- R/rsi_calc.R | 2 +- R/rsi_df.R | 2 +- R/skewness.R | 2 +- R/translate.R | 2 +- R/whocc.R | 2 +- R/zzz.R | 2 +- _pkgdown.yml | 2 +- codecov.yml | 2 +- data-raw/internals.R | 2 +- data-raw/loinc.R | 2 +- data-raw/poorman_prepend.R | 2 +- data-raw/read_EUCAST.R | 2 +- data-raw/reproduction_of_antibiotics.R | 2 +- data-raw/reproduction_of_antivirals.R | 2 +- ...reproduction_of_example_isolates_unclean.R | 2 +- .../reproduction_of_intrinsic_resistant.R | 2 +- data-raw/reproduction_of_microorganisms.R | 2 +- data-raw/snomed.R | 2 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/extra.css | 2 +- docs/extra.js | 2 +- docs/index.html | 12 +-- docs/news/index.html | 76 +++++++++---------- docs/pkgdown.yml | 2 +- docs/reference/index.html | 2 +- docs/survey.html | 2 +- git_merge.sh | 2 +- git_premaster.sh | 2 +- git_siteonly.sh | 2 +- index.md | 2 +- pkgdown/extra.css | 2 +- pkgdown/extra.js | 2 +- tests/testthat.R | 2 +- tests/testthat/test-_deprecated.R | 2 +- tests/testthat/test-_misc.R | 2 +- tests/testthat/test-ab.R | 2 +- tests/testthat/test-ab_from_text.R | 2 +- tests/testthat/test-ab_property.R | 2 +- tests/testthat/test-age.R | 2 +- .../test-antibiotic_class_selectors.R | 2 +- tests/testthat/test-atc_online.R | 2 +- tests/testthat/test-availability.R | 2 +- tests/testthat/test-bug_drug_combinations.R | 2 +- tests/testthat/test-count.R | 2 +- tests/testthat/test-data.R | 2 +- tests/testthat/test-disk.R | 2 +- tests/testthat/test-episode.R | 11 ++- tests/testthat/test-eucast_rules.R | 2 +- tests/testthat/test-filter_ab_class.R | 2 +- tests/testthat/test-first_isolate.R | 2 +- tests/testthat/test-g.test.R | 2 +- tests/testthat/test-get_locale.R | 2 +- tests/testthat/test-ggplot_rsi.R | 2 +- tests/testthat/test-guess_ab_col.R | 2 +- tests/testthat/test-join_microorganisms.R | 2 +- tests/testthat/test-key_antibiotics.R | 2 +- tests/testthat/test-kurtosis.R | 2 +- tests/testthat/test-like.R | 2 +- tests/testthat/test-mdro.R | 2 +- tests/testthat/test-mic.R | 2 +- tests/testthat/test-mo.R | 2 +- tests/testthat/test-mo_property.R | 2 +- tests/testthat/test-pca.R | 2 +- tests/testthat/test-proportion.R | 2 +- tests/testthat/test-random.R | 2 +- tests/testthat/test-resistance_predict.R | 2 +- tests/testthat/test-rsi.R | 4 +- tests/testthat/test-skewness.R | 2 +- tests/testthat/test-zzz.R | 2 +- 118 files changed, 167 insertions(+), 164 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 56779b0e..d6802c8d 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index ad03f567..e1e19c7d 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index ce68eba9..ded45ef9 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/DESCRIPTION b/DESCRIPTION index 72ec77bd..2484b053 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.4.0.9046 +Version: 1.4.0.9047 Date: 2020-12-27 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 0a8b0da5..4be16f2a 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.4.0.9046 +# AMR 1.4.0.9047 ## Last updated: 27 December 2020 ### New diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 95310d95..c3d5b55a 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/aa_helper_pm_functions.R b/R/aa_helper_pm_functions.R index 52dd75a1..d5f8c199 100644 --- a/R/aa_helper_pm_functions.R +++ b/R/aa_helper_pm_functions.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/ab.R b/R/ab.R index 3d67ccdf..cd083967 100755 --- a/R/ab.R +++ b/R/ab.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/ab_class_selectors.R b/R/ab_class_selectors.R index 376e3a6d..caa9aead 100644 --- a/R/ab_class_selectors.R +++ b/R/ab_class_selectors.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/ab_from_text.R b/R/ab_from_text.R index 75e9888f..7c7d0b6a 100644 --- a/R/ab_from_text.R +++ b/R/ab_from_text.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/ab_property.R b/R/ab_property.R index fa5a7e96..68fc4592 100644 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/age.R b/R/age.R index 7a59b7de..e0e6e238 100755 --- a/R/age.R +++ b/R/age.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/amr.R b/R/amr.R index 877dc4e8..bb8a71ae 100644 --- a/R/amr.R +++ b/R/amr.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/atc_online.R b/R/atc_online.R index 444b0e65..85166e94 100644 --- a/R/atc_online.R +++ b/R/atc_online.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/availability.R b/R/availability.R index 8c39cc94..8ace775c 100644 --- a/R/availability.R +++ b/R/availability.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index e9ec0a5a..a9b3a51b 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/catalogue_of_life.R b/R/catalogue_of_life.R index 2ed305cc..f84d781b 100755 --- a/R/catalogue_of_life.R +++ b/R/catalogue_of_life.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/count.R b/R/count.R index 7ebb17da..18c9d855 100755 --- a/R/count.R +++ b/R/count.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/data.R b/R/data.R index c72e0c1c..db8aee53 100755 --- a/R/data.R +++ b/R/data.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/deprecated.R b/R/deprecated.R index 4b810cb7..be26e916 100755 --- a/R/deprecated.R +++ b/R/deprecated.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/disk.R b/R/disk.R index 627f5473..a297692e 100644 --- a/R/disk.R +++ b/R/disk.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/episode.R b/R/episode.R index 775e4820..dd09cc44 100644 --- a/R/episode.R +++ b/R/episode.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 25bdb160..a8fbd45f 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/filter_ab_class.R b/R/filter_ab_class.R index 4f6c2795..e88eeffa 100644 --- a/R/filter_ab_class.R +++ b/R/filter_ab_class.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/first_isolate.R b/R/first_isolate.R index b7c2ef7d..1037d3af 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/g.test.R b/R/g.test.R index 5d301bd2..f34e0931 100755 --- a/R/g.test.R +++ b/R/g.test.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/ggplot_pca.R b/R/ggplot_pca.R index 79281327..d05c6624 100755 --- a/R/ggplot_pca.R +++ b/R/ggplot_pca.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R index fc1f750f..37dc1481 100755 --- a/R/ggplot_rsi.R +++ b/R/ggplot_rsi.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/globals.R b/R/globals.R index 0829d9ee..8bf6f55f 100755 --- a/R/globals.R +++ b/R/globals.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R index 22c39fb6..a0efe158 100755 --- a/R/guess_ab_col.R +++ b/R/guess_ab_col.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R index fa0ce027..d811a9f1 100755 --- a/R/join_microorganisms.R +++ b/R/join_microorganisms.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/key_antibiotics.R b/R/key_antibiotics.R index 4a6dcaba..7cfe13a4 100755 --- a/R/key_antibiotics.R +++ b/R/key_antibiotics.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/kurtosis.R b/R/kurtosis.R index e5d0be77..9e944de2 100755 --- a/R/kurtosis.R +++ b/R/kurtosis.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/lifecycle.R b/R/lifecycle.R index ba6d82c1..3ecdab78 100644 --- a/R/lifecycle.R +++ b/R/lifecycle.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/like.R b/R/like.R index 02e634e3..5923e290 100755 --- a/R/like.R +++ b/R/like.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/mdro.R b/R/mdro.R index f4af4642..6c035d2f 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/mic.R b/R/mic.R index 0750f8bc..7053d706 100755 --- a/R/mic.R +++ b/R/mic.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/mo.R b/R/mo.R index bae0d36c..05c798e5 100755 --- a/R/mo.R +++ b/R/mo.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/mo_matching_score.R b/R/mo_matching_score.R index 808450d3..970812d4 100755 --- a/R/mo_matching_score.R +++ b/R/mo_matching_score.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/mo_property.R b/R/mo_property.R index 276464ca..9b6509e2 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/mo_source.R b/R/mo_source.R index 44da6bfd..6c9cacf6 100644 --- a/R/mo_source.R +++ b/R/mo_source.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/pca.R b/R/pca.R index bb0df021..e5960488 100755 --- a/R/pca.R +++ b/R/pca.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/proportion.R b/R/proportion.R index 6517151a..8a30f4f6 100755 --- a/R/proportion.R +++ b/R/proportion.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/random.R b/R/random.R index 41a863d7..b18791ad 100644 --- a/R/random.R +++ b/R/random.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/resistance_predict.R b/R/resistance_predict.R index 61044341..13cf8bd6 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/rsi.R b/R/rsi.R index 2486f29e..025a3ef1 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/rsi_calc.R b/R/rsi_calc.R index eceebcf6..3c7b05c1 100755 --- a/R/rsi_calc.R +++ b/R/rsi_calc.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/rsi_df.R b/R/rsi_df.R index 50fa711f..47b75277 100644 --- a/R/rsi_df.R +++ b/R/rsi_df.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/skewness.R b/R/skewness.R index c34ad3cb..c40a91d9 100755 --- a/R/skewness.R +++ b/R/skewness.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/translate.R b/R/translate.R index 3a02d232..092fb912 100755 --- a/R/translate.R +++ b/R/translate.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/whocc.R b/R/whocc.R index ea685ffc..2a6a3697 100755 --- a/R/whocc.R +++ b/R/whocc.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/R/zzz.R b/R/zzz.R index ed1bf02f..ef6fd486 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/_pkgdown.yml b/_pkgdown.yml index 00babeaa..383ce99d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/codecov.yml b/codecov.yml index e522ee00..f11d6d58 100644 --- a/codecov.yml +++ b/codecov.yml @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/internals.R b/data-raw/internals.R index f65cc988..111c2192 100644 --- a/data-raw/internals.R +++ b/data-raw/internals.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/loinc.R b/data-raw/loinc.R index b3cf2a5e..1418ad46 100644 --- a/data-raw/loinc.R +++ b/data-raw/loinc.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/poorman_prepend.R b/data-raw/poorman_prepend.R index 6655fb13..63dc72d3 100644 --- a/data-raw/poorman_prepend.R +++ b/data-raw/poorman_prepend.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/read_EUCAST.R b/data-raw/read_EUCAST.R index 45c36efb..d75e9eb4 100644 --- a/data-raw/read_EUCAST.R +++ b/data-raw/read_EUCAST.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index a132238a..98129888 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_antibiotics.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/reproduction_of_antivirals.R b/data-raw/reproduction_of_antivirals.R index 0b44e31b..d4ec92c9 100644 --- a/data-raw/reproduction_of_antivirals.R +++ b/data-raw/reproduction_of_antivirals.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/reproduction_of_example_isolates_unclean.R b/data-raw/reproduction_of_example_isolates_unclean.R index b60f0c0a..ab0077a7 100644 --- a/data-raw/reproduction_of_example_isolates_unclean.R +++ b/data-raw/reproduction_of_example_isolates_unclean.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/reproduction_of_intrinsic_resistant.R b/data-raw/reproduction_of_intrinsic_resistant.R index fc1ac02e..638c4097 100644 --- a/data-raw/reproduction_of_intrinsic_resistant.R +++ b/data-raw/reproduction_of_intrinsic_resistant.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/reproduction_of_microorganisms.R b/data-raw/reproduction_of_microorganisms.R index 4450d0b6..653e14b2 100644 --- a/data-raw/reproduction_of_microorganisms.R +++ b/data-raw/reproduction_of_microorganisms.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/data-raw/snomed.R b/data-raw/snomed.R index 154ddbac..cb348dcc 100644 --- a/data-raw/snomed.R +++ b/data-raw/snomed.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/docs/404.html b/docs/404.html index b3f81387..882bb89d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9046 + 1.4.0.9047 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 039a377e..9685c24b 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9046 + 1.4.0.9047 diff --git a/docs/articles/index.html b/docs/articles/index.html index ac6f49d0..4d611988 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9046 + 1.4.0.9047 diff --git a/docs/authors.html b/docs/authors.html index 5b87ff78..25fc26d4 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9046 + 1.4.0.9047 diff --git a/docs/extra.css b/docs/extra.css index 52296020..8bf2825f 100644 --- a/docs/extra.css +++ b/docs/extra.css @@ -7,7 +7,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/docs/extra.js b/docs/extra.js index b5557041..78f0d9dd 100644 --- a/docs/extra.js +++ b/docs/extra.js @@ -7,7 +7,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2020 Berends MS, Luz CF et al. # +# (c) 2018-2021 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. # diff --git a/docs/index.html b/docs/index.html index 9618e3b2..106a5fd4 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9046 + 1.4.0.9047 @@ -222,9 +222,9 @@ Since you are one of our users, we would like to know how you use the package an library(dplyr) example_isolates %>% - mutate(mo = mo_fullname(mo)) %>% - filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>% - select(mo, aminoglycosides(), carbapenems()) + mutate(mo = mo_fullname(mo)) %>% + filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>% + select(mo, aminoglycosides(), carbapenems()) #> NOTE: Using column 'mo' as input for mo_is_gram_negative() #> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant() #> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), @@ -327,7 +327,7 @@ Since you are one of our users, we would like to know how you use the package an
  • Applying EUCAST expert rules (manual)
  • Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (manual)
  • Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (manual)
    • -
  • Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (link)
    • +
  • Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (link)
  • Principal component analysis for AMR (tutorial)
    • @@ -411,7 +411,7 @@ Since you are one of our users, we would like to know how you use the package an

  • It analyses the data with convenient functions that use well-known methods.

    diff --git a/docs/news/index.html b/docs/news/index.html index 1c36c146..145d0592 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9046 + 1.4.0.9047 @@ -236,9 +236,9 @@ Source: NEWS.md -
    -

    -AMR 1.4.0.9046 Unreleased +
    +

    +AMR 1.4.0.9047 Unreleased

    @@ -249,13 +249,13 @@ New

  • Functions mo_is_gram_negative() and mo_is_gram_positive() as wrappers around mo_gramstain(). They always return TRUE or FALSE (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.

  • Function mo_is_intrinsic_resistant() to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020.

    • @@ -279,15 +279,15 @@
  • -

    Some functions are now context-aware when used inside dplyr verbs, such as filter(), mutate() and summarise(). This means that then the data argument does not need to be set anymore. This is the case for the new functions mo_is_gram_negative(), mo_is_gram_positive(), mo_is_intrinsic_resistant() and for the existing functions first_isolate(), key_antibiotics(), mdro(), brmo(), mrgn(), mdr_tb(), mdr_cmi2012(), eucast_exceptional_phenotypes(). This was already the case for antibiotic selection functions (such as using penicillins() in dplyr::select()).

    +

    Some functions are now context-aware when used inside dplyr verbs, such as filter(), mutate() and summarise(). This means that then the data argument does not need to be set anymore. This is the case for the new functions mo_is_gram_negative(), mo_is_gram_positive(), mo_is_intrinsic_resistant() and for the existing functions first_isolate(), key_antibiotics(), mdro(), brmo(), mrgn(), mdr_tb(), mdr_cmi2012(), eucast_exceptional_phenotypes(). This was already the case for antibiotic selection functions (such as using penicillins() in dplyr::select()).

     
 # to select first isolates that are Gram-negative 
 # and view results of cephalosporins and aminoglycosides:
 library(dplyr)
 example_isolates %>%
-  filter(first_isolate(), mo_is_gram_negative()) %>% 
-  select(mo, cephalosporins(), aminoglycosides()) %>% 
+  filter(first_isolate(), mo_is_gram_negative()) %>% 
+  select(mo, cephalosporins(), aminoglycosides()) %>% 
   as_tibble()

  • For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the typed package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined.

    • @@ -337,8 +337,8 @@ library(AMR) library(dplyr) intrinsic_resistant %>% - filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>% - pull(microorganism) + filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>% + pull(microorganism) #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"

  • Support for veterinary ATC codes

    • @@ -354,16 +354,16 @@

    Improvements for as.rsi():