From cc245a41a0cf4a97e907de33a8586e00acaac549 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 14 Apr 2023 09:23:10 +0000 Subject: [PATCH] Built site for AMR: 2.0.0.9005@147f911 --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 256 +++++++++--------- .../figure-html/unnamed-chunk-13-1.png | Bin 42823 -> 42897 bytes articles/EUCAST.html | 2 +- articles/MDR.html | 58 ++-- articles/PCA.html | 4 +- articles/SPSS.html | 6 +- articles/WHONET.html | 4 +- articles/datasets.html | 10 +- articles/index.html | 2 +- articles/resistance_predict.html | 4 +- articles/welcome_to_AMR.html | 2 +- authors.html | 2 +- index.html | 2 +- news/index.html | 7 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 8 +- reference/Rplot005.png | Bin 13181 -> 13049 bytes reference/Rplot006.png | Bin 13200 -> 13058 bytes reference/Rplot007.png | Bin 14583 -> 12669 bytes reference/Rplot008.png | Bin 18981 -> 19650 bytes reference/Rplot009.png | Bin 8489 -> 8095 bytes reference/WHOCC.html | 2 +- reference/WHONET.html | 34 +-- reference/ab_from_text.html | 13 +- reference/ab_property.html | 2 +- reference/add_custom_antimicrobials.html | 2 +- reference/add_custom_microorganisms.html | 2 +- reference/age.html | 22 +- reference/age_groups.html | 2 +- reference/antibiogram.html | 16 +- reference/antibiotic_class_selectors.html | 179 ++++++------ reference/antibiotics.html | 60 ++-- reference/as.ab.html | 16 +- reference/as.av.html | 2 +- reference/as.disk.html | 2 +- reference/as.mic.html | 2 +- reference/as.mo.html | 2 +- reference/as.sir.html | 60 ++-- reference/atc_online.html | 2 +- reference/av_from_text.html | 2 +- reference/av_property.html | 2 +- reference/availability.html | 2 +- reference/bug_drug_combinations.html | 51 ++-- reference/clinical_breakpoints.html | 30 +- reference/count.html | 2 +- reference/custom_eucast_rules.html | 23 +- reference/dosage.html | 30 +- reference/eucast_rules.html | 2 +- reference/example_isolates.html | 16 +- reference/example_isolates_unclean.html | 4 +- reference/first_isolate.html | 60 ++-- reference/g.test.html | 2 +- reference/get_episode.html | 130 ++++----- reference/ggplot_pca.html | 2 +- reference/ggplot_sir.html | 2 +- reference/guess_ab_col.html | 2 +- reference/index.html | 6 +- reference/intrinsic_resistant.html | 4 +- reference/italicise_taxonomy.html | 2 +- reference/join.html | 16 +- reference/key_antimicrobials.html | 2 +- reference/kurtosis.html | 6 +- reference/like.html | 30 +- reference/mdro.html | 2 +- reference/mean_amr_distance.html | 74 ++--- reference/microorganisms.codes.html | 12 +- reference/microorganisms.html | 33 +-- reference/mo_matching_score.html | 2 +- reference/mo_property.html | 2 +- reference/mo_source.html | 2 +- reference/pca.html | 2 +- reference/plot-1.png | Bin 25821 -> 26294 bytes reference/plot-2.png | Bin 26516 -> 26426 bytes reference/plot-3.png | Bin 27583 -> 28514 bytes reference/plot-4.png | Bin 38688 -> 39163 bytes reference/plot-5.png | Bin 39052 -> 38846 bytes reference/plot-6.png | Bin 38215 -> 38106 bytes reference/plot-7.png | Bin 38603 -> 36968 bytes reference/plot-8.png | Bin 56463 -> 58512 bytes reference/plot-9.png | Bin 26102 -> 24691 bytes reference/plot.html | 2 +- reference/proportion.html | 16 +- reference/random.html | 34 +-- reference/resistance_predict.html | 2 +- reference/skewness.html | 4 +- reference/translate.html | 2 +- search.json | 2 +- 91 files changed, 707 insertions(+), 709 deletions(-) diff --git a/404.html b/404.html index c7cea4e7..d118c1fe 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005
+generated on 14 April 2023.This is basically it for the cleaning, time to start the data inclusion.
@@ -532,7 +532,7 @@ like: #> 8 J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE #> 9 G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE #> 10 P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE -#> # … with 2,616 more rows +#> # ℹ 2,616 more rowsTime for the analysis.
@@ -635,7 +635,7 @@ in: #> 8 2019-06-19 S #> 9 2015-04-27 S #> 10 2011-06-21 S -#> # … with 2,616 more rows +#> # ℹ 2,616 more rows our_data_1st %>% select(bacteria, betalactams()) @@ -654,7 +654,7 @@ in: #> 8 B_ESCHR_COLI S S #> 9 B_STPHY_AURS S S #> 10 B_ESCHR_COLI S S -#> # … with 2,616 more rows +#> # ℹ 2,616 more rows our_data_1st %>% select(bacteria, where(is.sir)) @@ -671,7 +671,7 @@ in: #> 8 B_ESCHR_COLI S S S S #> 9 B_STPHY_AURS S S S S #> 10 B_ESCHR_COLI S S S S -#> # … with 2,616 more rows +#> # ℹ 2,616 more rows # filtering using AB selectors is also possible: our_data_1st %>% @@ -690,7 +690,7 @@ in: #> 8 P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE #> 9 Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE #> 10 K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE -#> # … with 961 more rows +#> # ℹ 961 more rows our_data_1st %>% filter(all(betalactams() == "R")) @@ -709,7 +709,7 @@ in: #> 8 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE #> 9 C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE #> 10 W9 A 2013-10-02 B_ESCHR_COLI R R S S TRUE -#> # … with 461 more rows +#> # ℹ 461 more rows # even works in base R (since R 3.0): our_data_1st[all(betalactams() == "R"), ] @@ -728,7 +728,7 @@ in: #> 8 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE #> 9 C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE #> 10 W9 A 2013-10-02 B_ESCHR_COLI R R S S TRUE -#> # … with 461 more rows +#> # ℹ 461 more rows$(!$KbqD
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