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 @@ AMR (for R) - 1.7.1.9071 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9071 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9068 + 1.8.0 @@ -191,7 +191,7 @@

How to conduct AMR data analysis

Dr. Matthijs Berends

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12 December 2021

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23 December 2021

Source: vignettes/AMR.Rmd @@ -200,7 +200,7 @@ -

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.

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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.

Introduction

@@ -231,21 +231,21 @@ -2021-12-12 +2021-12-23 abcd Escherichia coli S S -2021-12-12 +2021-12-23 abcd Escherichia coli S R -2021-12-12 +2021-12-23 efgh Escherichia coli R @@ -342,32 +342,32 @@ -2014-11-21 -L5 -Hospital C +2010-03-07 +U8 +Hospital B Escherichia coli S R S S -M +F -2015-03-18 -G9 -Hospital D -Staphylococcus aureus -R +2015-08-15 +A4 +Hospital C +Escherichia coli +S S S S M -2011-10-31 -Z3 +2012-02-22 +T7 Hospital A -Escherichia coli +Staphylococcus aureus S S S @@ -375,37 +375,37 @@ F -2017-05-24 -A3 +2017-04-28 +J10 Hospital A -Staphylococcus aureus +Klebsiella pneumoniae +S +S +S S -I -R -R M -2013-01-31 -Y10 -Hospital C +2013-05-14 +X5 +Hospital A Escherichia coli S +I S -R S F -2013-04-13 -L6 -Hospital B -Klebsiella pneumoniae -S -I -S +2011-09-09 +Z1 +Hospital A +Escherichia coli +R +R +R S -M +F @@ -439,16 +439,16 @@ Longest: 1

1 M -10,451 -52.26% -10,451 -52.26% +10,513 +52.56% +10,513 +52.56% 2 F -9,549 -47.75% +9,487 +47.44% 20,000 100.00% @@ -502,7 +502,7 @@ Longest: 1

# ℹ Using column 'patient_id' as input for `col_patient_id`. # Basing inclusion on all antimicrobial results, using a points threshold of # 2 -# => Found 10,684 'phenotype-based' first isolates (53.4% of total where a +# => Found 10,677 'phenotype-based' first isolates (53.4% of total where a # microbial ID was available)

So only 53.4% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:

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 data_1st <- data %>% 
   filter_first_isolate()

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So we end up with 10,684 isolates for analysis. Now our data looks like:

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So we end up with 10,677 isolates for analysis. Now our data looks like:

 
 head(data_1st)

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data_1st %>% freq(genus, species)
Frequency table
Class: character

-Length: 10,684

-Available: 10,684 (100.0%, NA: 0 = 0.0%)

+Length: 10,677

+Available: 10,677 (100.0%, NA: 0 = 0.0%)

 Unique: 4
Shortest: 16

 Longest: 24

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22015-03-18G9Hospital DB_STPHY_AURS12010-03-07U8Hospital BB_ESCHR_COLIR
 R
 S
 SSMGram-positiveStaphylococcusaureusFGram-negativeEscherichiacoli
 TRUE
 

 
42017-05-24A3Hospital AB_STPHY_AURS22015-08-15A4Hospital CB_ESCHR_COLISS
 S
 SRR
 MGram-positiveStaphylococcusaureusGram-negativeEscherichiacoli
 TRUE
 

 
52013-01-31Y10Hospital CB_ESCHR_COLI42017-04-28J10Hospital AB_KLBSL_PNMNR
 S
 SR
 SFM
 Gram-negativeEscherichiacoliKlebsiellapneumoniae
 TRUE
 

 
102014-07-29G3Hospital DB_STRPT_PNMNR62011-09-09Z1Hospital AB_ESCHR_COLI
 R
 R
 RMGram-positiveStreptococcuspneumoniaeSFGram-negativeEscherichiacoli
 TRUE
 

 
112010-12-28G572017-04-11I3
 Hospital B
 B_ESCHR_COLIRR
 S
 SRR
 M
 Gram-negative
 Escherichia
 TRUE
 

 
142015-01-05A8Hospital AB_STPHY_AURS102011-06-22D10Hospital BB_KLBSL_PNMN
 R
 S
 S
 S
 MGram-positiveStaphylococcusaureusGram-negativeKlebsiellapneumoniae
 TRUE
 

 
 
 
 
 
 

 1
 Escherichia coli4,66043.62%4,66043.62%4,60943.17%4,60943.17%
 

 

 2
 Staphylococcus aureus2,72725.52%7,3872,77325.97%7,382
 69.14%
 

 

 3
 Streptococcus pneumoniae2,10619.71%9,49388.85%2,08719.55%9,46988.69%
 

 

 4
 Klebsiella pneumoniae1,19111.15%10,6841,20811.31%10,677
 100.00%
 

 
 
 
 
2017-05-24A3Hospital AB_STPHY_AURS2017-04-11I3Hospital BB_ESCHR_COLI
 S
 S
 R
 R
 MGram-positiveStaphylococcusaureusGram-negativeEscherichiacoli
 TRUE
 

 
2014-07-29G3Hospital D2013-07-04C4Hospital B
 B_STRPT_PNMN
 R
 RRS
 R
 M
 Gram-positive
 TRUE
 

 
2014-10-24S9Hospital AB_STRPT_PNMN2010-11-18F8Hospital BB_STPHY_AURS
 R
 R
 S
 RFM
 Gram-positiveStreptococcuspneumoniaeStaphylococcusaureus
 TRUE
 

 
2012-08-31A1Hospital BB_STRPT_PNMN2017-06-06H4Hospital DB_ESCHR_COLI
 R
 R
 S
 R
 MGram-positiveStreptococcuspneumoniaeGram-negativeEscherichiacoli
 TRUE
 

 
2016-04-25Z102014-02-16V2
 Hospital CB_KLBSL_PNMNB_STRPT_PNMNR
 RS
 S
 R
 FGram-negativeKlebsiellaGram-positiveStreptococcus
 pneumoniae
 TRUE
 

 
2011-04-30J102013-02-16M1
 Hospital DB_STPHY_AURSSSB_STRPT_PNMNRR
 S
 R
 M
 Gram-positiveStaphylococcusaureusStreptococcuspneumoniae
 TRUE
 

 
 

 E. coli
 AMX214814423684660219011223074609
 

 

 E. coli
 AMC34181623359170
 108046604609
 

 

 E. coli
 CIP33763366
 01284466012434609
 

 

 E. coli
 GEN40684002
 059246606074609
 

 

 K. pneumoniae
 AMX
 0
 01191119112081208
 

 

 K. pneumoniae
 AMC947461981191951352221208
 

 
 

@@ -933,34 +933,34 @@ Longest: 24

 
 E. coli
 GEN
-4068
+4002
 0
-592
-4660
+607
+4609
 
 
 K. pneumoniae
 GEN
-1062
+1063
 0
-129
-1191
+145
+1208
 
 
 S. aureus
 GEN
-2401
+2446
 0
-326
-2727
+327
+2773
 
 
 S. pneumoniae
 GEN
 0
 0
-2106
-2106
+2087
+2087
 
 
 
@@ -974,7 +974,7 @@ Longest: 24

 
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

+# [1] 0.544254

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
+# [1] 0.5 1 0.002 0.125 0.025 2 8 0.125 0.125 4 +# [11] 0.0625 0.001 0.025 0.001 8 64 0.025 32 0.001 64 +# [21] 8 0.001 16 0.5 0.0625 0.002 128 8 0.125 4 +# [31] 0.125 64 32 0.001 0.0625 0.005 2 4 0.125 32 +# [41] 0.125 0.5 0.0625 128 0.125 0.125 0.01 0.25 0.5 0.002 +# [51] 8 8 0.002 0.002 0.25 256 1 8 2 2 +# [61] 0.0625 0.005 0.005 16 0.5 0.025 16 8 8 0.0625 +# [71] 0.002 0.125 0.025 0.025 1 32 0.25 16 128 8 +# [81] 0.0625 0.025 64 0.001 0.5 4 8 4 16 32 +# [91] 0.005 8 0.125 256 64 0.001 1 32 0.005 0.025 
 # base R:
 plot(mic_values)
@@ -1236,13 +1236,13 @@ Longest: 24

 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
+# [1] 29 17 17 18 17 29 28 25 21 24 30 29 20 26 21 28 22 21 28 25 25 22 29 29 27 +# [26] 19 30 19 25 28 27 26 19 16 29 20 19 25 16 27 25 19 30 23 20 20 25 23 25 17 +# [51] 19 21 20 25 19 25 22 16 29 25 25 21 29 29 28 24 30 23 22 22 31 26 20 19 30 +# [76] 30 28 26 25 26 27 16 25 27 21 29 17 31 16 27 22 19 26 20 21 19 27 21 24 27 
 # base R:
 plot(disk_values, mo = "E. coli", ab = "cipro")
diff --git a/docs/articles/AMR_files/figure-html/disk_plots-1.png b/docs/articles/AMR_files/figure-html/disk_plots-1.png index 19d40106..bad9c989 100644 Binary files a/docs/articles/AMR_files/figure-html/disk_plots-1.png and b/docs/articles/AMR_files/figure-html/disk_plots-1.png differ diff --git a/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png b/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png index a1fdcbc9..331ff07a 100644 Binary files a/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png and b/docs/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png differ diff --git a/docs/articles/AMR_files/figure-html/mic_plots-1.png b/docs/articles/AMR_files/figure-html/mic_plots-1.png index cbd763a9..9088b85f 100644 Binary files a/docs/articles/AMR_files/figure-html/mic_plots-1.png and b/docs/articles/AMR_files/figure-html/mic_plots-1.png differ diff --git a/docs/articles/AMR_files/figure-html/mic_plots-2.png b/docs/articles/AMR_files/figure-html/mic_plots-2.png index ca428b32..ac936a0b 100644 Binary files a/docs/articles/AMR_files/figure-html/mic_plots-2.png and b/docs/articles/AMR_files/figure-html/mic_plots-2.png differ diff --git a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png index 61717f47..05c50b61 100644 Binary files a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png and b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png differ diff --git a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png index f1a7f32d..3d282199 100644 Binary files a/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png and b/docs/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png differ diff --git a/docs/articles/AMR_files/figure-html/plot 1-1.png b/docs/articles/AMR_files/figure-html/plot 1-1.png index 2024b212..a25ce222 100644 Binary files a/docs/articles/AMR_files/figure-html/plot 1-1.png and b/docs/articles/AMR_files/figure-html/plot 1-1.png differ diff --git a/docs/articles/AMR_files/figure-html/plot 3-1.png b/docs/articles/AMR_files/figure-html/plot 3-1.png index b262dddb..ba8cb20d 100644 Binary files a/docs/articles/AMR_files/figure-html/plot 3-1.png and b/docs/articles/AMR_files/figure-html/plot 3-1.png differ diff --git a/docs/articles/AMR_files/figure-html/plot 4-1.png b/docs/articles/AMR_files/figure-html/plot 4-1.png index 9a787e2b..5a2f053e 100644 Binary files a/docs/articles/AMR_files/figure-html/plot 4-1.png and b/docs/articles/AMR_files/figure-html/plot 4-1.png differ diff --git a/docs/articles/AMR_files/figure-html/plot 5-1.png b/docs/articles/AMR_files/figure-html/plot 5-1.png index 6222a82e..43a9fada 100644 Binary files a/docs/articles/AMR_files/figure-html/plot 5-1.png and b/docs/articles/AMR_files/figure-html/plot 5-1.png differ diff --git a/docs/articles/EUCAST.html b/docs/articles/EUCAST.html index 09985633..5a66ace5 100644 --- a/docs/articles/EUCAST.html +++ b/docs/articles/EUCAST.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9068 + 1.8.0 diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html index f2f2d128..e306389f 100644 --- a/docs/articles/MDR.html +++ b/docs/articles/MDR.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9068 + 1.8.0 @@ -358,18 +358,18 @@ Unique: 2

 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: 5

 
 1
 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%
 
 
 5
 Extensively drug-resistant
-100
-2.00%
+98
+1.96%
 5000
 100.00%
 
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 @@
       
       
         AMR (for R)
-        1.7.1.9068
+        1.8.0
diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html index 0a72e9b5..ebb99c2d 100644 --- a/docs/articles/SPSS.html +++ b/docs/articles/SPSS.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9074 + 1.8.0 @@ -191,7 +191,7 @@

How to import data from SPSS / SAS / Stata

Dr. Matthijs Berends

-

14 December 2021

+

23 December 2021

Source: vignettes/SPSS.Rmd @@ -226,7 +226,7 @@

  • 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 @@ AMR (for R) - 1.7.1.9068 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9073 + 1.8.0 @@ -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.

    Repetitive results @@ -258,8 +258,8 @@ # what do these values look like? They are of class <mo>: head(x) # Class <mo> -# [1] B_STRPT_PNMN B_ESCHR_COLI B_STPHY_AURS B_STPHY_CONS B_ENTRC -# [6] B_STPHY_HMNS +# [1] B_STPHY_AURS B_STRPT_EQNS B_KLBSL_PNMN B_STPHY_EPDR B_STPHY_AURS +# [6] B_CRYNB_STRT # as the example_isolates data set has 2,000 rows, we should have 2 million items length(x) @@ -272,11 +272,11 @@ # now let's see: run_it <- microbenchmark(mo_name(x), 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 -# mo_name(x) 205 234 315 310 393 447 10

    -

    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.

    Precalculated results @@ -287,12 +287,12 @@ B = mo_name("S. aureus"), C = mo_name("Staphylococcus aureus"), 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 7.89 8.95 14.80 9.21 10.50 64.60 10 -# B 22.60 26.10 33.80 26.90 29.80 89.20 10 -# C 1.76 2.04 2.44 2.49 2.73 3.37 10

    +# A 8.00 9.16 9.19 9.28 9.46 9.73 10 +# B 23.40 27.20 32.60 27.90 28.10 80.20 10 +# C 1.85 2.25 2.40 2.47 2.62 2.90 10

    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
    +# A 1.76 1.80 2.07 1.95 2.26 2.90 10 +# B 1.69 1.73 1.90 1.81 2.03 2.48 10 +# C 1.71 1.77 1.92 1.91 2.05 2.17 10 +# D 1.68 1.71 1.76 1.76 1.82 1.88 10 +# E 1.68 1.70 1.89 1.89 2.04 2.26 10 +# F 1.67 1.75 1.93 1.89 2.11 2.35 10 +# G 1.70 1.76 1.97 1.88 2.12 2.43 10 +# H 1.67 1.71 1.83 1.75 1.98 2.14 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.

    @@ -347,19 +347,19 @@ ru = mo_name(CoNS, language = "ru"), sv = mo_name(CoNS, language = "sv"), times = 100) -print(run_it, unit = "ms", signif = 4) +print(run_it, unit = "ms", signif = 4) # Unit: milliseconds -# expr min lq mean median uq max neval -# da 1.9160 2.012 2.308 2.213 2.445 4.040 100 -# de 1.9130 2.057 3.165 2.358 2.495 44.140 100 -# en 0.8684 0.910 1.076 1.004 1.137 2.173 100 -# es 1.9060 2.066 3.304 2.335 2.595 60.500 100 -# fr 1.7950 1.888 2.169 2.104 2.338 3.366 100 -# it 1.8830 2.025 2.809 2.342 2.536 45.730 100 -# nl 1.9370 2.034 3.482 2.316 2.626 60.780 100 -# pt 1.8450 1.983 3.125 2.293 2.447 43.830 100 -# ru 1.8260 1.932 3.454 2.018 2.413 87.210 100 -# sv 1.8260 1.930 3.428 2.207 2.441 72.080 100
    +# expr min lq mean median uq max neval +# da 1.9470 2.0220 2.190 2.0720 2.358 3.234 100 +# de 1.9560 2.0330 3.649 2.1610 2.401 50.670 100 +# en 0.8937 0.9124 1.022 0.9776 1.120 1.748 100 +# es 1.9710 2.0290 2.216 2.1000 2.391 3.109 100 +# fr 1.8280 1.8960 3.214 1.9420 2.237 71.550 100 +# it 1.9370 1.9970 2.163 2.0610 2.339 3.210 100 +# nl 1.9710 2.0280 2.698 2.1110 2.421 49.340 100 +# pt 1.8920 1.9600 2.119 2.0200 2.261 3.265 100 +# ru 1.8630 1.9420 2.779 2.0270 2.335 66.660 100 +# sv 1.8680 1.9190 4.062 1.9890 2.263 78.870 100

    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 @@ AMR (for R) - 1.7.1.9077 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9075 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9068 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9070 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9071 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9071 + 1.8.0 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 @@ AMR (for R) - 1.7.1.9077 + 1.8.0 @@ -157,13 +157,11 @@
    -

    -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.

    -

    Breaking changes

    +

    Breaking changes

    • Removed p_symbol() and all filter_*() functions (except for filter_first_isolate()), which were all deprecated in a previous package version
    • Removed the key_antibiotics() and key_antibiotics_equal() functions, which were deprecated and superseded by key_antimicrobials() and antimicrobials_equal()
      • @@ -171,7 +169,7 @@
    • Renamed function get_locale() to get_AMR_locale() to prevent conflicts with other packages
    -

    New

    +

    New

    • Support 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

      • @@ -186,7 +184,7 @@

    • 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

    -

    Changed

    +

    Changed

    • Updated the bacterial taxonomy to 5 October 2021 (according to LPSN), including all 11 new staphylococcal species named since 1 January last year
    • The 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:
      • Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
        • @@ -246,7 +244,7 @@
      • Improved plot legends for MICs and disk diffusion values
      • Improved speed of as.ab() and all ab_*() functions
        • -
      • Added fortify() extensions for plotting methods
        • +
      • Added fortify() extensions for plotting methods
      • NA 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)
      • The proportion_df(), count_df() and rsi_df() functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packages
        • @@ -258,10 +256,9 @@ get_episode() and is_new_episode() can now cope with NAs
    -

    Other

    +

    Other

    • This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations.
    -

    AMR 1.7.12021-06-03

    @@ -304,7 +301,7 @@
  • The documentation of the first_isolate() and key_antimicrobials() functions has been completely rewritten.
  • Function 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.
    • -
  • A ggplot() method for resistance_predict() +
  • A ggplot() method for resistance_predict()
    • @@ -387,7 +384,7 @@ #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"

  • 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 @@
 
    • Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
      • 
 
    • All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
      • 
 
    • Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see translate)
      • 
-
    • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
      • 
+
    • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
      •
  • Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the microorganisms data set
  • @@ -454,7 +451,7 @@ is.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.
  • Functions 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)
  • Argument ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)
    • -
  • Functions 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() +
  • Functions 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()
  • Improved speed and reliability of 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.
  • Fix for mo_name() when used in other languages than English
    • @@ -733,7 +730,7 @@

    Removed 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:

    - -
  • Frequency tables (freq() function): +
  • Frequency tables (freq() function):