From 958f761af39d1f9cf7985561df4d15ce38b2500f Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat, 8 Jul 2023 19:10:45 +0000 Subject: [PATCH] Built site for AMR: 2.0.0.9028@3829311 --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 14 +- articles/EUCAST.html | 2 +- articles/MDR.html | 58 ++-- articles/PCA.html | 2 +- articles/WHONET.html | 4 +- articles/datasets.html | 366 ++++++++++++++++------ articles/index.html | 2 +- articles/other_pkg.html | 2 +- articles/resistance_predict.html | 2 +- articles/welcome_to_AMR.html | 2 +- authors.html | 2 +- extra.css | 6 +- extra.js | 6 +- index.html | 2 +- news/index.html | 18 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 4 +- reference/Rplot005.png | Bin 13286 -> 13308 bytes reference/Rplot006.png | Bin 13308 -> 13300 bytes reference/Rplot007.png | Bin 13376 -> 12598 bytes reference/Rplot008.png | Bin 19019 -> 20844 bytes reference/Rplot009.png | Bin 8638 -> 8525 bytes reference/WHOCC.html | 2 +- reference/WHONET.html | 2 +- reference/ab_from_text.html | 2 +- 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 | 2 +- reference/antibiotic_class_selectors.html | 6 +- reference/antibiotics.html | 2 +- reference/as.ab.html | 2 +- reference/as.av.html | 2 +- reference/as.disk.html | 34 +- reference/as.mic.html | 10 +- reference/as.mo.html | 8 +- reference/as.sir.html | 302 +++++++++--------- 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 | 2 +- reference/clinical_breakpoints.html | 77 +++-- reference/count.html | 2 +- reference/custom_eucast_rules.html | 2 +- reference/dosage.html | 2 +- reference/eucast_rules.html | 13 +- reference/example_isolates.html | 2 +- reference/example_isolates_unclean.html | 2 +- reference/first_isolate.html | 2 +- reference/g.test.html | 2 +- reference/get_episode.html | 108 ++++--- reference/ggplot_pca.html | 2 +- reference/ggplot_sir.html | 2 +- reference/guess_ab_col.html | 2 +- reference/index.html | 11 +- reference/intrinsic_resistant.html | 2 +- reference/italicise_taxonomy.html | 2 +- reference/join.html | 2 +- reference/key_antimicrobials.html | 2 +- reference/kurtosis.html | 6 +- reference/like.html | 2 +- reference/mdro.html | 2 +- reference/mean_amr_distance.html | 74 ++--- reference/microorganisms.codes.html | 38 +-- reference/microorganisms.groups.html | 236 ++++++++++++++ reference/microorganisms.html | 17 +- reference/mo_matching_score.html | 14 +- reference/mo_property.html | 2 +- reference/mo_source.html | 2 +- reference/pca.html | 2 +- reference/plot-1.png | Bin 26921 -> 25913 bytes reference/plot-2.png | Bin 26511 -> 27080 bytes reference/plot-3.png | Bin 27943 -> 27589 bytes reference/plot-4.png | Bin 39903 -> 39036 bytes reference/plot-5.png | Bin 39244 -> 39730 bytes reference/plot-6.png | Bin 38409 -> 38934 bytes reference/plot-7.png | Bin 37415 -> 36890 bytes reference/plot-8.png | Bin 56722 -> 60701 bytes reference/plot-9.png | Bin 26378 -> 26187 bytes reference/plot.html | 2 +- reference/proportion.html | 2 +- reference/random.html | 34 +- reference/resistance_predict.html | 2 +- reference/skewness.html | 4 +- reference/translate.html | 2 +- search.json | 2 +- sitemap.xml | 3 + 94 files changed, 1026 insertions(+), 573 deletions(-) create mode 100644 reference/microorganisms.groups.html diff --git a/404.html b/404.html index 37bc36c9..0976f49c 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 2.0.0.9026 + 2.0.0.9028 + + + + + +
+
+
+

Data Set with 444 Microorganisms In Species Groups

+ Source: R/data.R +
microorganisms.groups.Rd
+
+ +
+

A data set containing species groups and microbiological complexes, which are used in the clinical breakpoints table.

+
+ +
+

Usage

+ 
microorganisms.groups
+
+ +
+

Format

+

A tibble with 444 observations and 4 variables:

  • mo_group
    ID of the species group / microbiological complex

    • +

  • mo
    ID of the microorganism belonging in the species group / microbiological complex

    • +

  • mo_group_name
    Name of the species group / microbiological complex, as retrieved with mo_name()

    • +

  • mo_name
    Name of the microorganism belonging in the species group / microbiological complex, as retrieved with mo_name()

    • +
+
+

Details

+

Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

+
+
+

See also

+

as.mo() microorganisms

+
+ +
+

Examples

+ 
microorganisms.groups
+#> # A tibble: 444 × 4
+#>    mo_group       mo           mo_group_name                   mo_name          
+#>    <mo>           <mo>         <chr>                           <chr>            
+#>  1 B_ACNTB_BMNN-C B_ACNTB_BMNN Acinetobacter baumannii complex Acinetobacter ba…
+#>  2 B_ACNTB_BMNN-C B_ACNTB_CLCC Acinetobacter baumannii complex Acinetobacter ca…
+#>  3 B_ACNTB_BMNN-C B_ACNTB_DJKS Acinetobacter baumannii complex Acinetobacter di…
+#>  4 B_ACNTB_BMNN-C B_ACNTB_NSCM Acinetobacter baumannii complex Acinetobacter no…
+#>  5 B_ACNTB_BMNN-C B_ACNTB_PITT Acinetobacter baumannii complex Acinetobacter pi…
+#>  6 B_ACNTB_BMNN-C B_ACNTB_SFRT Acinetobacter baumannii complex Acinetobacter se…
+#>  7 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex    Bacteroides frag…
+#>  8 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex    Bacteroides ovat…
+#>  9 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex    Bacteroides thet…
+#> 10 B_BCTRD_FRGL-C B_BCTRD_VLGT Bacteroides fragilis complex    Bacteroides vulg…
+#> # ℹ 434 more rows
+
+# these are all species in the Bacteroides fragilis group, as per WHONET:
+microorganisms.groups[microorganisms.groups$mo_group == "B_BCTRD_FRGL-C", ]
+#> # A tibble: 5 × 4
+#>   mo_group       mo           mo_group_name                mo_name              
+#>   <mo>           <mo>         <chr>                        <chr>                
+#> 1 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex Bacteroides fragilis 
+#> 2 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex Bacteroides ovatus   
+#> 3 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex Bacteroides thetaiot…
+#> 4 B_BCTRD_FRGL-C B_BCTRD_VLGT Bacteroides fragilis complex Bacteroides vulgatus 
+#> 5 B_BCTRD_FRGL-C B_PRBCT_DSTS Bacteroides fragilis complex Parabacteroides dist…
+
+
+
+ + +
+ + + + + + + diff --git a/reference/microorganisms.html b/reference/microorganisms.html index 2ee13478..43e3e25b 100644 --- a/reference/microorganisms.html +++ b/reference/microorganisms.html @@ -1,5 +1,5 @@ -Data Set with 52 158 Microorganisms — microorganisms • AMR (for R)Data Set with 52 169 Microorganisms — microorganisms • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9026 + 2.0.0.9028