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

How to conduct AMR data analysis

Dr. Matthijs Berends

-

12 December 2021

+

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.

+

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 @@ -342,71 +342,71 @@ -2014-11-21 -L5 -Hospital C -Escherichia coli -S -R -S -S -M - - -2015-03-18 -G9 -Hospital D -Staphylococcus aureus -R -S -S -S -M - - -2011-10-31 -Z3 -Hospital A -Escherichia coli -S -S -S -S -F - - -2017-05-24 -A3 -Hospital A -Staphylococcus aureus -S -I -R -R -M - - -2013-01-31 -Y10 -Hospital C -Escherichia coli -S -S -R -S -F - - -2013-04-13 -L6 +2010-03-07 +U8 Hospital B +Escherichia coli +S +R +S +S +F + + +2015-08-15 +A4 +Hospital C +Escherichia coli +S +S +S +S +M + + +2012-02-22 +T7 +Hospital A +Staphylococcus aureus +S +S +S +S +F + + +2017-04-28 +J10 +Hospital A Klebsiella pneumoniae S -I +S S S M + +2013-05-14 +X5 +Hospital A +Escherichia coli +S +I +S +S +F + + +2011-09-09 +Z1 +Hospital A +Escherichia coli +R +R +R +S +F +

Now, let’s start the cleaning and the analysis!

@@ -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:

@@ -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)

-
+
@@ -528,7 +528,7 @@ Longest: 1
-+
@@ -550,46 +550,14 @@ Longest: 1

-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
-
-
+
+
@@ -598,29 +566,13 @@ Longest: 1

-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
-
-
+
+
@@ -629,20 +581,68 @@ Longest: 1

-
-
-
-
+
+
+
+
-
+
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -666,8 +666,8 @@ Longest: 1
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

@@ -684,33 +684,33 @@ Longest: 24

-
-
-
-
+
+
+
+
-
-
-
+
+
+
-
-
-
-
+
+
+
+
-
-
-
+
+
+
@@ -757,53 +757,23 @@ Longest: 24

-
-
-
-
+
+
+
+
-
-
-
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
@@ -817,27 +787,12 @@ Longest: 24

-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
-
-
+
+
@@ -846,6 +801,51 @@ Longest: 24

+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

 
 
 

 
 
 


 
 
 
 
 
 
22015-03-18G9Hospital DB_STPHY_AURSRSSSMGram-positiveStaphylococcusaureusTRUE
42017-05-24A3Hospital AB_STPHY_AURSSSRRMGram-positiveStaphylococcusaureusTRUE
52013-01-31Y10Hospital C12010-03-07U8Hospital B
 B_ESCHR_COLISS
 RRS
 S
 F
 Gram-negative
 TRUE
 

 
102014-07-29G3Hospital DB_STRPT_PNMNRRRRMGram-positiveStreptococcuspneumoniaeTRUE
112010-12-28G5Hospital B22015-08-15A4Hospital C
 B_ESCHR_COLIRRSS
 S
 S
 M
 coli
 TRUE
 
142015-01-05A8
42017-04-28J10
 Hospital AB_STPHY_AURSB_KLBSL_PNMN
 R
 S
 S
 S
 MGram-positiveStaphylococcusaureusGram-negativeKlebsiellapneumoniaeTRUE
62011-09-09Z1Hospital AB_ESCHR_COLIRRRSFGram-negativeEscherichiacoliTRUE
72017-04-11I3Hospital BB_ESCHR_COLISSRRMGram-negativeEscherichiacoliTRUE
102011-06-22D10Hospital BB_KLBSL_PNMNRSSSMGram-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 DB_STRPT_PNMNRRRRMGram-positiveStreptococcuspneumoniaeTRUE
2014-10-24S9Hospital AB_STRPT_PNMNRRSRFGram-positiveStreptococcuspneumoniaeTRUE
2012-08-31A12013-07-04C4
 Hospital B
 B_STRPT_PNMN
 R
 TRUE
 

 
2016-04-25Z10Hospital CB_KLBSL_PNMNRSSRFGram-negativeKlebsiellapneumoniaeTRUE
2011-04-30J10Hospital D2010-11-18F8Hospital B
 B_STPHY_AURSSSRR
 S
 R
 M
 aureus
 TRUE
 
2017-06-06H4Hospital DB_ESCHR_COLIRRSRMGram-negativeEscherichiacoliTRUE
2014-02-16V2Hospital CB_STRPT_PNMNRRSRFGram-positiveStreptococcuspneumoniaeTRUE
2013-02-16M1Hospital DB_STRPT_PNMNRRSRMGram-positiveStreptococcuspneumoniaeTRUE

 
 

 
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:

@@ -867,50 +867,50 @@ Longest: 24

 
 E. coli
 AMX
-2148
-144
-2368
-4660
+2190
+112
+2307
+4609
 
 
 E. coli
 AMC
-3418
-162
+3359
+170
 1080
-4660
+4609
 
 
 E. coli
 CIP
-3376
+3366
 0
-1284
-4660
+1243
+4609
 
 
 E. coli
 GEN
-4068
+4002
 0
-592
-4660
+607
+4609
 
 
 K. pneumoniae
 AMX
 0
 0
-1191
-1191
+1208
+1208
 
 
 K. pneumoniae
 AMC
-947
-46
-198
-1191
+951
+35
+222
+1208
 
 
 
@@ -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 19d40106d..bad9c9897 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 a1fdcbc9b..331ff07a5 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 cbd763a99..9088b85f7 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 ca428b327..ac936a0b6 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 61717f47a..05c50b619 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 f1a7f32d3..3d2821991 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 2024b212a..a25ce2229 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 b262dddbc..ba8cb20d3 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 9a787e2b0..5a2f053ef 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 6222a82e1..43a9fada8 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 099856331..5a66ace5e 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 f2f2d1285..e306389f2 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 76f8c61e9..143ecafb4 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 0a72e9b5a..ebb99c2df 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 b068f93e7..866a7a1aa 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 601f335ce..0e2362a8f 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 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 @@ AMR (for R) - 1.7.1.9077 + 1.8.0 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 @@ 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 a32b2d14c..34249b876 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 36fd95182..5539d3ba4 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 c26fc9cbf..f3155709f 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 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 @@ AMR (for R) - 1.7.1.9071 + 1.8.0 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 @@ 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):