diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 9dffe9e02..3ee8a9314 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 51a0c607d..318ce55f8 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 e1987bc69..365e473e2 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 d55a835b4..4daa40749 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 f8c0de6de..7e0cfa531 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 ba3336512..4b38b3ac1 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 2231edb85..db56b1264 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 43767a044..5a11d120f 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 27e696ba4..f385ca7c2 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 e4231c3c2..6feba8638 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 e57ae48fa..f69b018dc 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 1a7f1d014..64c73de8e 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 fb295fbfb..43ebf25a0 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 203452785..a21c3266f 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 87a9fde07..cec296a2f 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 d25116a13..8f26ae7b2 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 112286396..6288a2353 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 94dca6a99..9599d61cf 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 7a7d8d450..02f76b411 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 f4efcf87d..55fea5800 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 0eb8ea0a0..b6230defe 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 279e58c93..b8d065d96 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 a11ff0f9a..494846ddc 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 bc1462eb0..5089c32c8 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 1a7589271..28b1438c1 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 91c4116bc..1c44b68a1 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 ae2ff053a..61ad5201a 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 0e8685f0a..1854e97b1 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 04d7417d7..04fdf43c8 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 6100889d2..fa9760301 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 2e5687754..1978303da 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 88f73f30c..0b7b49360 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 b91135515..4d349bd88 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 ba0e57d1f..e6d72e2b8 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 3b77c01bf..eeb8dfbae 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 f49ae0b0d..e243a84a5 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 b683258f9..1f396ee11 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 22b5edff1..80c817cc4 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 1a18fb8c6..4ce1c9d5b 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 8044a3f96..ad50a08af 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 ce8ae222a..29929a922 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 5f5f83efc..7d37fff1d 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 a067ba419..8a3b9371e 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 71dda7664..d8380daa8 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 a1b4ad9e9..a85ee5caa 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 730e8ad59..695efc956 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 5ba2855aa..6e1a9158c 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 bc5c012aa..ea7aaedd6 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 e586092c1..4b7a44d5f 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 d2daffb10..2f7b912d4 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 c2d66e012..f078899dd 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 c65ab56fc..010ec3d3f 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 66ab097c9..b123f91d5 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 3da7abe5f..f157b6bb4 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 461fc7bc6..8bf5abdeb 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 2651fe1a0..1f896ae3c 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 7b57efbec..44070ee8a 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 fdb875e73..bf6c59509 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 a49e2511c..ab860436d 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 745d6415e..5bd82ed59 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 e621807ce..37fd5ab38 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 44a2039a1..a4fc772cd 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 dff5f0ab8..7769243a8 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 807c7ae63..50fd85050 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 c21b189ea..fb4af03de 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 2a0454f01..54d63575f 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 60e25729d..df746f908 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 2682c88f4..a6767afcf 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 75975cf98..3ba4bd15e 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 f08c41113..944ba12d7 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 346657301..39fd3b2c7 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 a6d95525f..be4488fe0 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 17d5686e0..13c09a7f0 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 3176a2906..bc650579b 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 4358ece9e..52bc2f716 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 76f8c61e9..143ecafb4 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 b068f93e7..866a7a1aa 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 601f335ce..0e2362a8f 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 25In 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 6a1c71cee..790aadcab 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 7ed045940..a6519ece3 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 667817022..e1f9169a0 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 a32b2d14c..34249b876 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 36fd95182..5539d3ba4 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 c26fc9cbf..f3155709f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ diff --git a/docs/extra.css b/docs/extra.css index 1d5ec8ab2..ddc0c382a 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 b037832e8..b0fa1c774 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 c42af85e6..8f0ab1d59 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 6038153f6..4ca708920 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)