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 @@ 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
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 @@ 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 @@ 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 @@ 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 @@ @@ -222,9 +222,9 @@ Since you are one of our users, we would like to know how you use the package anIt analyses the data with convenient functions that use well-known methods.
susceptibility()
and resistance()
functions, or be even more specific with the proportion_R()
, proportion_IR()
, proportion_I()
, proportion_SI()
and proportion_S()
functions. Similarly, the number of isolates can be determined with the count_resistant()
, count_susceptible()
and count_all()
functions. All these functions can be used with the dplyr
package (e.g. in conjunction with summarise()
)susceptibility()
and resistance()
functions, or be even more specific with the proportion_R()
, proportion_IR()
, proportion_I()
, proportion_SI()
and proportion_S()
functions. Similarly, the number of isolates can be determined with the count_resistant()
, count_susceptible()
and count_all()
functions. All these functions can be used with the dplyr
package (e.g. in conjunction with summarise()
)geom_rsi()
, a function made for the ggplot2
packageresistance_predict()
functionNEWS.md
- Functions get_episode()
and is_new_episode()
to determine (patient) episodes which are not necessarily based on microorganisms. The get_episode()
function returns the index number of the episode per group, while the is_new_episode()
function returns values TRUE
/FALSE
to indicate whether an item in a vector is the start of a new episode. They also support dplyr
s grouping (i.e. using group_by()
):
Functions get_episode()
and is_new_episode()
to determine (patient) episodes which are not necessarily based on microorganisms. The get_episode()
function returns the index number of the episode per group, while the is_new_episode()
function returns values TRUE
/FALSE
to indicate whether an item in a vector is the start of a new episode. They also support dplyr
s grouping (i.e. using group_by()
):
library(dplyr)
example_isolates %>%
- group_by(patient_id, hospital_id) %>%
- filter(is_new_episode(date, episode_days = 60))
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.
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.
Support for veterinary ATC codes
Improvements for as.rsi()
:
Support for using dplyr
’s across()
to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.
Support for using dplyr
’s across()
to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.
# until dplyr 1.0.0
-your_data %>% mutate_if(is.mic, as.rsi)
-your_data %>% mutate_if(is.disk, as.rsi)
+your_data %>% mutate_if(is.mic, as.rsi)
+your_data %>% mutate_if(is.disk, as.rsi)
# since dplyr 1.0.0
-your_data %>% mutate(across(where(is.mic), as.rsi))
-your_data %>% mutate(across(where(is.disk), as.rsi))
Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g. as.rsi(df, col1:col9)
Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.
Function ab_from_text()
to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses as.ab()
internally
Tidyverse selection helpers for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like dplyr::select()
and tidyr::pivot_longer()
:
Tidyverse selection helpers for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like dplyr::select()
and tidyr::pivot_longer()
:
library(dplyr)
# Columns 'IPM' and 'MEM' are in the example_isolates data set
example_isolates %>%
- select(carbapenems())
+ select(carbapenems())
#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)
Added mo_domain()
as an alias to mo_kingdom()
Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
Interpretation from MIC values (and disk zones) to R/SI can now be used with mutate_at()
of the dplyr
package:
Interpretation from MIC values (and disk zones) to R/SI can now be used with mutate_at()
of the dplyr
package:
yourdata %>%
- mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = "E. coli")
+ mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = "E. coli")
yourdata %>%
- mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = .$mybacteria)
Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
Added uti
(as abbreviation of urinary tract infections) as argument to as.rsi()
, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
library(dplyr)
example_isolates %>%
- group_by(bug = mo_name(mo)) %>%
- summarise(amoxicillin = resistance(AMX),
+ group_by(bug = mo_name(mo)) %>%
+ summarise(amoxicillin = resistance(AMX),
amox_clav = resistance(AMC)) %>%
- filter(!is.na(amoxicillin) | !is.na(amox_clav))
+ filter(!is.na(amoxicillin) | !is.na(amox_clav))
Support for a new MDRO guideline: Magiorakos AP, Srinivasan A et al. “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).
@@ -922,7 +922,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # (run this on your own console, as this page does not support colour printing) library(dplyr) example_isolates %>% - select(mo:AMC) %>% + select(mo:AMC) %>% as_tibble()
septic_patients %>%
- select(AMX, CIP) %>%
+ select(AMX, CIP) %>%
rsi_df()
# antibiotic interpretation value isolates
# 1 Amoxicillin SI 0.4442636 546
@@ -1139,7 +1139,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
boxplot()
# grouped boxplots:
septic_patients %>%
- group_by(hospital_id) %>%
+ group_by(hospital_id) %>%
freq(age) %>%
boxplot()
septic_patients %>%
- mutate(only_firsts = first_isolate(septic_patients, ...)) %>%
- filter(only_firsts == TRUE) %>%
- select(-only_firsts)
New function availability()
to check the number of available (non-empty) results in a data.frame
New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the G-test and more. These are also available (and even easier readable) on our website: https://msberends.gitlab.io/AMR.
Header info is now available as a list, with the header
function
Fix for header text where all observations are NA
New argument droplevels
to exclude empty factor levels when input is a factor
Factor levels will be in header when present in input data (maximum of 5)
Fix for using select()
on frequency tables
Fix for using select()
on frequency tables
scale_y_percent()
now contains the limits
argument
septic_patients %>%
freq(hospital_id) %>%
- select(-count, -cum_count) # only get item, percent, cum_percent
+ select(-count, -cum_count) # only get item, percent, cum_percent
Check for hms::is.hms
Now prints in markdown at default in non-interactive sessions
Support for quasiquotation in the functions series count_*
and portions_*
, and n_rsi
. This allows to check for more than 2 vectors or columns.
-septic_patients %>% select(amox, cipr) %>% count_IR()
+septic_patients %>% select(amox, cipr) %>% count_IR()
# which is the same as:
septic_patients %>% count_IR(amox, cipr)
@@ -1858,7 +1858,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- Full support for Windows, Linux and macOS
- Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
-- Function
n_rsi
to count cases where antibiotic test results were available, to be used in conjunction with dplyr::summarise
, see ?rsi
+- Function
n_rsi
to count cases where antibiotic test results were available, to be used in conjunction with dplyr::summarise
, see ?rsi
- Function
guess_bactid
to determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
- Function
guess_atc
to determine the ATC of an antibiotic based on name, trade name, or known abbreviations
- Function
freq
to create frequency tables, with additional info in a header
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 75b73abf..8245974d 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2020-12-26T23:05Z
+last_built: 2020-12-26T23:29Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6a7a941f..a0f7e853 100644
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@@ -81,7 +81,7 @@