diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 9dffe9e0..3ee8a931 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -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. # diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 51a0c607..318ce55f 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -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. # diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index e1987bc6..365e473e 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -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. # diff --git a/DESCRIPTION b/DESCRIPTION index d55a835b..4daa4074 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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 diff --git a/NEWS.md b/NEWS.md index f8c0de6d..7e0cfa53 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.7.1.9077 -## Last updated: 23 December 2021 +# `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. diff --git a/R/aa_globals.R b/R/aa_globals.R index ba333651..4b38b3ac 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -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. # diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 2231edb8..db56b126 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2021 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. # diff --git a/R/aa_helper_pm_functions.R b/R/aa_helper_pm_functions.R index 43767a04..5a11d120 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) 2018-2021 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. # diff --git a/R/ab.R b/R/ab.R index 27e696ba..f385ca7c 100755 --- a/R/ab.R +++ b/R/ab.R @@ -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. # diff --git a/R/ab_from_text.R b/R/ab_from_text.R index e4231c3c..6feba863 100644 --- a/R/ab_from_text.R +++ b/R/ab_from_text.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2021 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. # diff --git a/R/ab_property.R b/R/ab_property.R index e57ae48f..f69b018d 100644 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -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. # diff --git a/R/ab_selectors.R b/R/ab_selectors.R index 1a7f1d01..64c73de8 100644 --- a/R/ab_selectors.R +++ b/R/ab_selectors.R @@ -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. # diff --git a/R/age.R b/R/age.R index fb295fbf..43ebf25a 100755 --- a/R/age.R +++ b/R/age.R @@ -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. # diff --git a/R/amr.R b/R/amr.R index 20345278..a21c3266 100644 --- a/R/amr.R +++ b/R/amr.R @@ -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. # diff --git a/R/atc_online.R b/R/atc_online.R index 87a9fde0..cec296a2 100644 --- a/R/atc_online.R +++ b/R/atc_online.R @@ -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. # diff --git a/R/availability.R b/R/availability.R index d25116a1..8f26ae7b 100644 --- a/R/availability.R +++ b/R/availability.R @@ -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. # diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index 11228639..6288a235 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2021 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. # diff --git a/R/catalogue_of_life.R b/R/catalogue_of_life.R index 94dca6a9..9599d61c 100755 --- a/R/catalogue_of_life.R +++ b/R/catalogue_of_life.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2021 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. # diff --git a/R/count.R b/R/count.R index 7a7d8d45..02f76b41 100755 --- a/R/count.R +++ b/R/count.R @@ -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. # diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R index f4efcf87..55fea580 100644 --- a/R/custom_eucast_rules.R +++ b/R/custom_eucast_rules.R @@ -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. # diff --git a/R/data.R b/R/data.R index 0eb8ea0a..b6230def 100755 --- a/R/data.R +++ b/R/data.R @@ -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. # diff --git a/R/deprecated.R b/R/deprecated.R index 279e58c9..b8d065d9 100755 --- a/R/deprecated.R +++ b/R/deprecated.R @@ -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. # diff --git a/R/disk.R b/R/disk.R index a11ff0f9..494846dd 100644 --- a/R/disk.R +++ b/R/disk.R @@ -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. # diff --git a/R/episode.R b/R/episode.R index bc1462eb..5089c32c 100644 --- a/R/episode.R +++ b/R/episode.R @@ -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. # diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 1a758927..28b1438c 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -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. # diff --git a/R/first_isolate.R b/R/first_isolate.R index 91c4116b..1c44b68a 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -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. # diff --git a/R/g.test.R b/R/g.test.R index ae2ff053..61ad5201 100755 --- a/R/g.test.R +++ b/R/g.test.R @@ -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. # diff --git a/R/ggplot_pca.R b/R/ggplot_pca.R index 0e8685f0..1854e97b 100755 --- a/R/ggplot_pca.R +++ b/R/ggplot_pca.R @@ -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. # diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R index 04d7417d..04fdf43c 100755 --- a/R/ggplot_rsi.R +++ b/R/ggplot_rsi.R @@ -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. # diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R index 6100889d..fa976030 100755 --- a/R/guess_ab_col.R +++ b/R/guess_ab_col.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2021 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. # diff --git a/R/italicise_taxonomy.R b/R/italicise_taxonomy.R index 2e568775..1978303d 100644 --- a/R/italicise_taxonomy.R +++ b/R/italicise_taxonomy.R @@ -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. # diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R index 88f73f30..0b7b4936 100755 --- a/R/join_microorganisms.R +++ b/R/join_microorganisms.R @@ -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. # diff --git a/R/key_antimicrobials.R b/R/key_antimicrobials.R index b9113551..4d349bd8 100755 --- a/R/key_antimicrobials.R +++ b/R/key_antimicrobials.R @@ -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. # diff --git a/R/kurtosis.R b/R/kurtosis.R index ba0e57d1..e6d72e2b 100755 --- a/R/kurtosis.R +++ b/R/kurtosis.R @@ -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. # diff --git a/R/lifecycle.R b/R/lifecycle.R index 3b77c01b..eeb8dfba 100644 --- a/R/lifecycle.R +++ b/R/lifecycle.R @@ -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. # diff --git a/R/like.R b/R/like.R index f49ae0b0..e243a84a 100755 --- a/R/like.R +++ b/R/like.R @@ -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. # diff --git a/R/mdro.R b/R/mdro.R index b683258f..1f396ee1 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -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. # diff --git a/R/mic.R b/R/mic.R index 22b5edff..80c817cc 100755 --- a/R/mic.R +++ b/R/mic.R @@ -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. # diff --git a/R/mo.R b/R/mo.R index 1a18fb8c..4ce1c9d5 100755 --- a/R/mo.R +++ b/R/mo.R @@ -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. # diff --git a/R/mo_matching_score.R b/R/mo_matching_score.R index 8044a3f9..ad50a08a 100755 --- a/R/mo_matching_score.R +++ b/R/mo_matching_score.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2021 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. # diff --git a/R/mo_property.R b/R/mo_property.R index ce8ae222..29929a92 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -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. # diff --git a/R/mo_source.R b/R/mo_source.R index 5f5f83ef..7d37fff1 100644 --- a/R/mo_source.R +++ b/R/mo_source.R @@ -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. # diff --git a/R/pca.R b/R/pca.R index a067ba41..8a3b9371 100755 --- a/R/pca.R +++ b/R/pca.R @@ -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. # diff --git a/R/plot.R b/R/plot.R index 71dda766..d8380daa 100644 --- a/R/plot.R +++ b/R/plot.R @@ -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. # diff --git a/R/proportion.R b/R/proportion.R index a1b4ad9e..a85ee5ca 100755 --- a/R/proportion.R +++ b/R/proportion.R @@ -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. # diff --git a/R/random.R b/R/random.R index 730e8ad5..695efc95 100644 --- a/R/random.R +++ b/R/random.R @@ -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. # diff --git a/R/resistance_predict.R b/R/resistance_predict.R index 5ba2855a..6e1a9158 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -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. # diff --git a/R/rsi.R b/R/rsi.R index bc5c012a..ea7aaedd 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -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. # diff --git a/R/rsi_calc.R b/R/rsi_calc.R index e586092c..4b7a44d5 100755 --- a/R/rsi_calc.R +++ b/R/rsi_calc.R @@ -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. # diff --git a/R/rsi_df.R b/R/rsi_df.R index d2daffb1..2f7b912d 100644 --- a/R/rsi_df.R +++ b/R/rsi_df.R @@ -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. # diff --git a/R/skewness.R b/R/skewness.R index c2d66e01..f078899d 100755 --- a/R/skewness.R +++ b/R/skewness.R @@ -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. # diff --git a/R/translate.R b/R/translate.R index c65ab56f..010ec3d3 100755 --- a/R/translate.R +++ b/R/translate.R @@ -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. # diff --git a/R/vctrs.R b/R/vctrs.R index 66ab097c..b123f91d 100644 --- a/R/vctrs.R +++ b/R/vctrs.R @@ -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. # diff --git a/R/whocc.R b/R/whocc.R index 3da7abe5..f157b6bb 100755 --- a/R/whocc.R +++ b/R/whocc.R @@ -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. # diff --git a/R/zzz.R b/R/zzz.R index 461fc7bc..8bf5abde 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -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. # diff --git a/_pkgdown.yml b/_pkgdown.yml index 2651fe1a..1f896ae3 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -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. # diff --git a/codecov.yml b/codecov.yml index 7b57efbe..44070ee8 100644 --- a/codecov.yml +++ b/codecov.yml @@ -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. # diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index fdb875e7..bf6c5950 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/_install_deps.R b/data-raw/_install_deps.R index a49e2511..ab860436 100644 --- a/data-raw/_install_deps.R +++ b/data-raw/_install_deps.R @@ -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. # diff --git a/data-raw/_internals.R b/data-raw/_internals.R index 745d6415..5bd82ed5 100644 --- a/data-raw/_internals.R +++ b/data-raw/_internals.R @@ -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. # diff --git a/data-raw/loinc.R b/data-raw/loinc.R index e621807c..37fd5ab3 100644 --- a/data-raw/loinc.R +++ b/data-raw/loinc.R @@ -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. # diff --git a/data-raw/poorman_prepend.R b/data-raw/poorman_prepend.R index 44a2039a..a4fc772c 100644 --- a/data-raw/poorman_prepend.R +++ b/data-raw/poorman_prepend.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2021 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. # diff --git a/data-raw/read_EUCAST.R b/data-raw/read_EUCAST.R index dff5f0ab..7769243a 100644 --- a/data-raw/read_EUCAST.R +++ b/data-raw/read_EUCAST.R @@ -6,7 +6,7 @@ # https://github.com/msberends/AMR # # # # LICENCE # -# (c) 2018-2021 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. # diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index 807c7ae6..50fd8505 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) 2018-2021 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. # diff --git a/data-raw/reproduction_of_antivirals.R b/data-raw/reproduction_of_antivirals.R index c21b189e..fb4af03d 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) 2018-2021 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. # diff --git a/data-raw/reproduction_of_dosage.R b/data-raw/reproduction_of_dosage.R index 2a0454f0..54d63575 100644 --- a/data-raw/reproduction_of_dosage.R +++ b/data-raw/reproduction_of_dosage.R @@ -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. # diff --git a/data-raw/reproduction_of_example_isolates_unclean.R b/data-raw/reproduction_of_example_isolates_unclean.R index 60e25729..df746f90 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) 2018-2021 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. # diff --git a/data-raw/reproduction_of_intrinsic_resistant.R b/data-raw/reproduction_of_intrinsic_resistant.R index 2682c88f..a6767afc 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) 2018-2021 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. # diff --git a/data-raw/reproduction_of_microorganisms.R b/data-raw/reproduction_of_microorganisms.R index 75975cf9..3ba4bd15 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) 2018-2021 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. # diff --git a/data-raw/reproduction_of_microorganisms_update.R b/data-raw/reproduction_of_microorganisms_update.R index f08c4111..944ba12d 100644 --- a/data-raw/reproduction_of_microorganisms_update.R +++ b/data-raw/reproduction_of_microorganisms_update.R @@ -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. # diff --git a/data-raw/reproduction_of_rsi_translation.R b/data-raw/reproduction_of_rsi_translation.R index 34665730..39fd3b2c 100644 --- a/data-raw/reproduction_of_rsi_translation.R +++ b/data-raw/reproduction_of_rsi_translation.R @@ -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. # diff --git a/data-raw/snomed.R b/data-raw/snomed.R index a6d95525..be4488fe 100644 --- a/data-raw/snomed.R +++ b/data-raw/snomed.R @@ -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. # diff --git a/docs/404.html b/docs/404.html index 17d5686e..13c09a7f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -43,7 +43,7 @@
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 3176a290..bc650579 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html index 4358ece9..52bc2f71 100644 --- a/docs/articles/AMR.html +++ b/docs/articles/AMR.html @@ -44,7 +44,7 @@ @@ -191,7 +191,7 @@vignettes/AMR.Rmd
AMR.Rmd
Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 12 December 2021.
+Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 23 December 2021.
Now, let’s start the cleaning and the analysis!
@@ -439,16 +439,16 @@ Longest: 1So only 53.4% is suitable for resistance analysis! We can now filter on it with the filter()
function, also from the dplyr
package:
@@ -512,10 +512,10 @@ Longest: 1-data_1st <- data %>% filter_first_isolate()
So we end up with 10,684 isolates for analysis. Now our data looks like:
+So we end up with 10,677 isolates for analysis. Now our data looks like:
-head(data_1st)
2 | -2015-03-18 | -G9 | -Hospital D | -B_STPHY_AURS | -R | -S | -S | -S | -M | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -||||||
4 | -2017-05-24 | -A3 | -Hospital A | -B_STPHY_AURS | -S | -S | -R | -R | -M | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -||||||
5 | -2013-01-31 | -Y10 | -Hospital C | +1 | +2010-03-07 | +U8 | +Hospital B | B_ESCHR_COLI | -S | -S | R | +R | +S | S | F | Gram-negative | @@ -598,29 +566,13 @@ Longest: 1TRUE | ||
10 | -2014-07-29 | -G3 | -Hospital D | -B_STRPT_PNMN | -R | -R | -R | -R | -M | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -||||||
11 | -2010-12-28 | -G5 | -Hospital B | +2 | +2015-08-15 | +A4 | +Hospital C | B_ESCHR_COLI | -R | -R | +S | +S | S | S | M | @@ -629,20 +581,68 @@ Longest: 1coli | TRUE | ||
14 | -2015-01-05 | -A8 | +|||||||||||||||||
4 | +2017-04-28 | +J10 | Hospital A | -B_STPHY_AURS | +B_KLBSL_PNMN | R | S | S | S | M | -Gram-positive | -Staphylococcus | -aureus | +Gram-negative | +Klebsiella | +pneumoniae | +TRUE | +||
6 | +2011-09-09 | +Z1 | +Hospital A | +B_ESCHR_COLI | +R | +R | +R | +S | +F | +Gram-negative | +Escherichia | +coli | +TRUE | +||||||
7 | +2017-04-11 | +I3 | +Hospital B | +B_ESCHR_COLI | +S | +S | +R | +R | +M | +Gram-negative | +Escherichia | +coli | +TRUE | +||||||
10 | +2011-06-22 | +D10 | +Hospital B | +B_KLBSL_PNMN | +R | +S | +S | +S | +M | +Gram-negative | +Klebsiella | +pneumoniae | TRUE | ||||||
1 | Escherichia coli | -4,660 | -43.62% | -4,660 | -43.62% | +4,609 | +43.17% | +4,609 | +43.17% | ||||||||||
2 | Staphylococcus aureus | -2,727 | -25.52% | -7,387 | +2,773 | +25.97% | +7,382 | 69.14% | |||||||||||
3 | Streptococcus pneumoniae | -2,106 | -19.71% | -9,493 | -88.85% | +2,087 | +19.55% | +9,469 | +88.69% | ||||||||||
4 | Klebsiella pneumoniae | -1,191 | -11.15% | -10,684 | +1,208 | +11.31% | +10,677 | 100.00% | |||||||||||
2017-05-24 | -A3 | -Hospital A | -B_STPHY_AURS | +2017-04-11 | +I3 | +Hospital B | +B_ESCHR_COLI | S | S | R | R | M | -Gram-positive | -Staphylococcus | -aureus | +Gram-negative | +Escherichia | +coli | TRUE |
2014-07-29 | -G3 | -Hospital D | -B_STRPT_PNMN | -R | -R | -R | -R | -M | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -|||||||
2014-10-24 | -S9 | -Hospital A | -B_STRPT_PNMN | -R | -R | -S | -R | -F | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -|||||||
2012-08-31 | -A1 | +2013-07-04 | +C4 | Hospital B | B_STRPT_PNMN | R | @@ -817,27 +787,12 @@ Longest: 24TRUE | ||||||||||||
2016-04-25 | -Z10 | -Hospital C | -B_KLBSL_PNMN | -R | -S | -S | -R | -F | -Gram-negative | -Klebsiella | -pneumoniae | -TRUE | -|||||||
2011-04-30 | -J10 | -Hospital D | +2010-11-18 | +F8 | +Hospital B | B_STPHY_AURS | -S | -S | +R | +R | S | R | M | @@ -846,6 +801,51 @@ Longest: 24aureus | TRUE | ||||
2017-06-06 | +H4 | +Hospital D | +B_ESCHR_COLI | +R | +R | +S | +R | +M | +Gram-negative | +Escherichia | +coli | +TRUE | +|||||||
2014-02-16 | +V2 | +Hospital C | +B_STRPT_PNMN | +R | +R | +S | +R | +F | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +|||||||
2013-02-16 | +M1 | +Hospital D | +B_STRPT_PNMN | +R | +R | +S | +R | +M | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +
If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the bug_drug_combinations()
function:
As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (proportion_R()
, equal to resistance()
) and susceptibility as the proportion of S and I (proportion_SI()
, equal to susceptibility()
). These functions can be used on their own:
data_1st %>% resistance(AMX)
-# [1] 0.5497005
Or can be used in conjunction with group_by()
and summarise()
, both from the dplyr
package:
data_1st %>%
@@ -988,19 +988,19 @@ Longest: 24
Hospital A
-0.5528455
+0.5349716
Hospital B
-0.5463890
+0.5482514
Hospital C
-0.5533333
+0.5800508
Hospital D
-0.5482679
+0.5244591
@@ -1019,23 +1019,23 @@ Longest: 24
Hospital A
-0.5528455
-3075
+0.5349716
+3174
Hospital B
-0.5463890
-3794
+0.5482514
+3803
Hospital C
-0.5533333
-1650
+0.5800508
+1574
Hospital D
-0.5482679
-2165
+0.5244591
+2126
@@ -1056,27 +1056,27 @@ Longest: 24
Escherichia
-0.7682403
-0.8729614
-0.9766094
+0.7656759
+0.8683011
+0.9709264
Klebsiella
-0.8337531
-0.8916877
-0.9806885
+0.8162252
+0.8799669
+0.9726821
Staphylococcus
-0.7887789
-0.8804547
-0.9790979
+0.7991345
+0.8820772
+0.9772809
Streptococcus
-0.5318139
+0.5462386
0.0000000
-0.5318139
+0.5462386
@@ -1101,23 +1101,23 @@ Longest: 24
Hospital A
-55.3%
-26.3%
+53.5%
+26.0%
Hospital B
-54.6%
-27.2%
+54.8%
+26.1%
Hospital C
-55.3%
-25.7%
+58.0%
+28.5%
Hospital D
-54.8%
-26.5%
+52.4%
+25.4%
@@ -1201,16 +1201,16 @@ Longest: 24
mic_values <- random_mic(size = 100)
mic_values
# Class <mic>
-# [1] 0.0625 0.002 0.002 0.001 4 1 0.0625 32 0.5 0.5
-# [11] 0.25 0.025 0.001 64 0.5 0.5 2 0.005 16 0.5
-# [21] 0.25 64 4 0.002 128 0.01 64 0.25 0.01 0.005
-# [31] 32 32 16 0.25 0.002 1 128 128 0.25 0.001
-# [41] 0.0625 0.125 0.001 128 0.0625 0.001 1 0.25 2 0.001
-# [51] 0.005 4 8 2 0.125 0.0625 16 0.25 64 8
-# [61] 0.005 32 0.0625 0.01 0.002 32 8 64 16 2
-# [71] 1 2 32 2 8 0.001 0.25 8 8 64
-# [81] 128 0.01 0.0625 0.125 0.002 8 0.025 0.0625 0.0625 8
-# [91] 0.005 16 4 8 0.25 0.025 8 0.002 0.25 0.25
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
# ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia
-# coli). Run `mo_uncertainties()` to review this uncertainty.
+# coli). Run `mo_uncertainties()` to review this.
disk_values
# Class <disk>
-# [1] 22 25 27 18 21 30 29 21 21 24 26 18 23 28 22 24 18 20 19 18 27 23 25 23 21
-# [26] 24 22 22 23 27 23 19 22 20 17 19 30 19 23 19 23 21 24 30 30 26 25 27 17 29
-# [51] 25 30 31 26 17 18 30 24 18 25 21 19 31 24 20 24 18 25 26 24 19 30 27 21 26
-# [76] 20 17 31 28 31 26 27 30 17 27 19 26 26 31 17 30 23 20 17 30 19 19 20 21 19
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
head(my_TB_data)
# rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1 R R I S I I
-# 2 I I I I R S
-# 3 I R S I R S
-# 4 R S I I I R
-# 5 S S R I I S
-# 6 R R R I S R
+# 1 I R I S R S
+# 2 I S R R S R
+# 3 R I S I R S
+# 4 S S I R I S
+# 5 S R S S S I
+# 6 S R R S R I
# kanamycin
-# 1 I
-# 2 R
-# 3 S
+# 1 S
+# 2 I
+# 3 R
# 4 R
-# 5 R
+# 5 I
# 6 R
We can now add the interpretation of MDR-TB to our data set. You can use:
@@ -413,40 +413,40 @@ Unique: 51 Mono-resistant -3246 -64.92% -3246 -64.92% +3250 +65.00% +3250 +65.00% 2 Negative -999 -19.98% -4245 -84.90% +975 +19.50% +4225 +84.50% 3 Multi-drug-resistant -437 -8.74% -4682 -93.64% +474 +9.48% +4699 +93.98% 4 Poly-resistant -218 -4.36% -4900 -98.00% +203 +4.06% +4902 +98.04% diff --git a/docs/articles/PCA.html b/docs/articles/PCA.html index 76f8c61e..143ecafb 100644 --- a/docs/articles/PCA.html +++ b/docs/articles/PCA.html @@ -44,7 +44,7 @@ 5 Extensively drug-resistant -100 -2.00% +98 +1.96% 5000 100.00%
vignettes/SPSS.Rmd
SPSS.Rmd
R has a huge community.
-Many R users just ask questions on websites like StackOverflow.com, the largest online community for programmers. At the time of writing, 429,535 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.
+Many R users just ask questions on websites like StackOverflow.com, the largest online community for programmers. At the time of writing, 430,288 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.
R understands any data type, including SPSS/SAS/Stata.
diff --git a/docs/articles/WHONET.html b/docs/articles/WHONET.html index b068f93e..866a7a1a 100644 --- a/docs/articles/WHONET.html +++ b/docs/articles/WHONET.html @@ -44,7 +44,7 @@ diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html index 601f335c..0e2362a8 100644 --- a/docs/articles/benchmarks.html +++ b/docs/articles/benchmarks.html @@ -44,7 +44,7 @@ @@ -222,23 +222,23 @@ as.mo("MRSA"), # Methicillin Resistant S. aureus as.mo("VISA"), # Vancomycin Intermediate S. aureus times = 25) -print(S.aureus, unit = "ms", signif = 2) +print(S.aureus, unit = "ms", signif = 2) # Unit: milliseconds # expr min lq mean median uq max neval -# as.mo("sau") 12.0 12.0 17.0 14.0 15.0 56 25 -# as.mo("stau") 51.0 60.0 81.0 87.0 98.0 120 25 -# as.mo("STAU") 51.0 64.0 83.0 90.0 98.0 130 25 -# as.mo("staaur") 9.7 12.0 15.0 15.0 15.0 46 25 -# as.mo("STAAUR") 11.0 14.0 17.0 15.0 16.0 45 25 -# as.mo("S. aureus") 24.0 31.0 43.0 33.0 63.0 77 25 -# as.mo("S aureus") 26.0 28.0 45.0 34.0 62.0 76 25 -# as.mo("Staphylococcus aureus") 3.0 3.7 5.4 3.8 4.6 37 25 -# as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 270.0 260.0 270.0 310 25 -# as.mo("Sthafilokkockus aaureuz") 180.0 190.0 210.0 200.0 220.0 260 25 -# as.mo("MRSA") 10.0 13.0 20.0 15.0 17.0 73 25 -# as.mo("VISA") 20.0 23.0 38.0 26.0 49.0 150 25 +# as.mo("sau") 10.0 12.0 20.0 12.0 15.0 53 25 +# as.mo("stau") 49.0 54.0 72.0 58.0 91.0 97 25 +# as.mo("STAU") 50.0 54.0 71.0 57.0 90.0 110 25 +# as.mo("staaur") 10.0 12.0 17.0 12.0 14.0 51 25 +# as.mo("STAAUR") 10.0 12.0 17.0 12.0 14.0 54 25 +# as.mo("S. aureus") 26.0 27.0 40.0 31.0 56.0 74 25 +# as.mo("S aureus") 26.0 27.0 39.0 29.0 58.0 68 25 +# as.mo("Staphylococcus aureus") 3.5 3.9 6.6 4.1 4.8 38 25 +# as.mo("Staphylococcus aureus (MRSA)") 230.0 240.0 250.0 240.0 250.0 280 25 +# as.mo("Sthafilokkockus aaureuz") 180.0 190.0 200.0 190.0 200.0 290 25 +# as.mo("MRSA") 11.0 12.0 19.0 13.0 14.0 50 25 +# as.mo("VISA") 21.0 22.0 32.0 25.0 50.0 60 25 -In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 69 times slower to determine.
+In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 47 times slower to determine.
To improve performance, we implemented two important algorithms to save unnecessary calculations: repetitive results and already precalculated results.
So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.31 seconds. That is 155 nanoseconds on average. You only lose time on your unique input values.
+# mo_name(x) 196 209 274 223 364 388 10 +So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.223 seconds. That is 112 nanoseconds on average. You only lose time on your unique input values.
So going from mo_name("Staphylococcus aureus")
to "Staphylococcus aureus"
takes 0.0025 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:
run_it <- microbenchmark(A = mo_species("aureus"),
@@ -304,17 +304,17 @@
G = mo_phylum("Firmicutes"),
H = mo_kingdom("Bacteria"),
times = 10)
-print(run_it, unit = "ms", signif = 3)
+print(run_it, unit = "ms", signif = 3)
# Unit: milliseconds
# expr min lq mean median uq max neval
-# A 1.62 1.67 1.81 1.71 1.75 2.45 10
-# B 1.59 1.62 1.94 1.75 2.15 3.08 10
-# C 1.61 1.64 1.74 1.70 1.73 2.09 10
-# D 1.58 1.66 1.87 1.69 2.07 2.63 10
-# E 1.59 1.61 1.70 1.64 1.72 2.15 10
-# F 1.57 1.60 1.69 1.66 1.71 2.07 10
-# G 1.56 1.60 1.75 1.67 1.73 2.21 10
-# H 1.60 1.62 1.67 1.64 1.70 1.81 10
Of course, when running mo_phylum("Firmicutes")
the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes"
anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.
Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.
diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png index 6a1c71ce..790aadca 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 7ed04594..a6519ece 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ diff --git a/docs/articles/index.html b/docs/articles/index.html index 66781702..e1f9169a 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ diff --git a/docs/articles/resistance_predict.html b/docs/articles/resistance_predict.html index a32b2d14..34249b87 100644 --- a/docs/articles/resistance_predict.html +++ b/docs/articles/resistance_predict.html @@ -44,7 +44,7 @@ diff --git a/docs/articles/welcome_to_AMR.html b/docs/articles/welcome_to_AMR.html index 36fd9518..5539d3ba 100644 --- a/docs/articles/welcome_to_AMR.html +++ b/docs/articles/welcome_to_AMR.html @@ -44,7 +44,7 @@ diff --git a/docs/authors.html b/docs/authors.html index c26fc9cb..f3155709 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ diff --git a/docs/extra.css b/docs/extra.css index 1d5ec8ab..ddc0c382 100644 --- a/docs/extra.css +++ b/docs/extra.css @@ -7,7 +7,7 @@ # 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. # diff --git a/docs/extra.js b/docs/extra.js index b037832e..b0fa1c77 100644 --- a/docs/extra.js +++ b/docs/extra.js @@ -7,7 +7,7 @@ # 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. # diff --git a/docs/index.html b/docs/index.html index c42af85e..8f0ab1d5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ diff --git a/docs/news/index.html b/docs/news/index.html index 6038153f..4ca70892 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ @@ -157,13 +157,11 @@AMR
1.7.1.9077AMR
1.8.0All 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.
p_symbol()
and all filter_*()
functions (except for filter_first_isolate()
), which were all deprecated in a previous package versionkey_antibiotics()
and key_antibiotics_equal()
functions, which were deprecated and superseded by key_antimicrobials()
and antimicrobials_equal()
get_locale()
to get_AMR_locale()
to prevent conflicts with other packagesSupport for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the rsi_translation
data set. This data set now more strictly follows the WHONET software as well.
Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for eucast_rules()
, mo_is_intrinsic_resistant()
and mdro()
. The intrinsic_resistant
data set was also updated accordingly.
Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish
Function ab_ddd_units()
to get units of DDDs (daily defined doses), deprecating the use of ab_ddd(..., units = TRUE)
to be more consistent in data types of function output
antibiotics
data set now contains all ATC codes that are available through the WHOCC website, regardless of drugs being present in more than one ATC group. This means that:
as.ab()
and all ab_*()
functionsfortify()
extensions for plotting methodsfortify()
extensions for plotting methodsNA
values of the classes <mic>
, <disk>
and <rsi>
are now exported objects of this package, e.g. NA_mic_
is an NA
of class mic
(just like the base R NA_character_
is an NA
of class character
)proportion_df()
, count_df()
and rsi_df()
functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packagesget_episode()
and is_new_episode()
can now cope with NA
s
first_isolate()
and key_antimicrobials()
functions has been completely rewritten.betalactams()
as additional antbiotic column selector and function filter_betalactams()
as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.ggplot()
method for resistance_predict()
+ggplot()
method for resistance_predict()
Support for custom MDRO guidelines, using the new custom_mdro_guideline()
function, please see mdro()
for additional info
ggplot()
generics for classes <mic>
and <disk>
ggplot()
generics for classes <mic>
and <disk>
Function mo_is_yeast()
, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
@@ -438,7 +435,7 @@
translate
)plot()
and with ggplot2 using ggplot()
on any vector of MIC and disk diffusion valuesplot()
and with ggplot2 using ggplot()
on any vector of MIC and disk diffusion valuesmicroorganisms
data setis.rsi.eligible()
now detects if the column name resembles an antibiotic name or code and now returns TRUE
immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.get_episode()
and is_new_episode()
now support less than a day as value for argument episode_days
(e.g., to include one patient/test per hour)ampc_cephalosporin_resistance
in eucast_rules()
now also applies to value “I” (not only “S”)print()
and summary()
on a Principal Components Analysis object (pca()
) now print additional group info if the original data was grouped using dplyr::group_by()
+print()
and summary()
on a Principal Components Analysis object (pca()
) now print additional group info if the original data was grouped using dplyr::group_by()
guess_ab_col()
. As this also internally improves the reliability of first_isolate()
and mdro()
, this might have a slight impact on the results of those functions.mo_name()
when used in other languages than EnglishRemoved code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
Making this package independent of especially the tidyverse (e.g. packages dplyr
and tidyr
) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.
Negative effects of this change are:
-freq()
that was borrowed from the cleaner
package was removed. Use cleaner::freq()
, or run library("cleaner")
before you use freq()
.freq()
that was borrowed from the cleaner
package was removed. Use cleaner::freq()
, or run library("cleaner")
before you use freq()
.mo
or rsi
in a tibble will no longer be in colour and printing rsi
in a tibble will show the class <ord>
, not <rsi>
anymore. This is purely a visual effect.mo_*
family (like mo_name()
and mo_gramstain()
) are noticeably slower when running on hundreds of thousands of rows.mo
and ab
now both also inherit class character
, to support any data transformation. This change invalidates code that checks for class length == 1.This is important, because a value like "testvalue"
could never be understood by e.g. mo_name()
, although the class would suggest a valid microbial code.
Function freq()
has moved to a new package, clean
(CRAN link), since creating frequency tables actually does not fit the scope of this package. The freq()
function still works, since it is re-exported from the clean
package (which will be installed automatically upon updating this AMR
package).
Function freq()
has moved to a new package, clean
(CRAN link), since creating frequency tables actually does not fit the scope of this package. The freq()
function still works, since it is re-exported from the clean
package (which will be installed automatically upon updating this AMR
package).
Renamed data set septic_patients
to example_isolates
age()
function gained a new argument exact
to determine ages with decimalsguess_mo()
, guess_atc()
, EUCAST_rules()
, interpretive_reading()
, rsi()
freq()
):
+freq()
):
speed improvement for microbial IDs
fixed factor level names for R Markdown
when all values are unique it now shows a message instead of a warning
age_groups()
, to let groups of fives and tens end with 100+ instead of 120+freq()
for when all values are NA
+freq()
for when all values are NA
first_isolate()
for when dates are missingguess_ab_col()
@@ -1451,7 +1448,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
"HIGH S"
will return S
freq()
function):
+freq()
function):
Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
@@ -1460,15 +1457,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # OLD WAY septic_patients %>% mutate(genus = mo_genus(mo)) %>% - freq(genus) + freq(genus) # NEW WAY septic_patients %>% - freq(mo_genus(mo)) + freq(mo_genus(mo)) # Even supports grouping variables: septic_patients %>% group_by(gender) %>% - freq(mo_genus(mo))
Header info is now available as a list, with the header
function
The argument header
is now set to TRUE
at default, even for markdown
Using portion_*
functions now throws a warning when total available isolate is below argument minimum
Functions as.mo
, as.rsi
, as.mic
, as.atc
and freq
will not set package name as attribute anymore
Frequency tables - freq()
:
Frequency tables - freq()
:
Support for grouping variables, test with:
+ freq(gender)Support for (un)selecting columns:
Check for hms::is.hms
Removed diacritics from all authors (columns microorganisms$ref
and microorganisms.old$ref
) to comply with CRAN policy to only allow ASCII characters
Fix for mo_property
not working properly
Fix for eucast_rules
where some Streptococci would become ceftazidime R in EUCAST rule 4.5
Support for named vectors of class mo
, useful for top_freq()
Support for named vectors of class mo
, useful for top_freq()
ggplot_rsi
and scale_y_percent
have breaks
argument
AI improvements for as.mo
:
For lists, subsetting is possible:
my_list = list(age = septic_patients$age, gender = septic_patients$gender)
-my_list %>% freq(age)
-my_list %>% freq(gender)