From 3f99e4a668e7a5319184750dc969c10822aec94c Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 5 Oct 2022 10:32:07 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9004@0d8b098 --- 404.html | 6 +- LICENSE-text.html | 6 +- articles/AMR.html | 522 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 38139 -> 39145 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 52733 -> 55141 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 28090 -> 28697 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 38934 -> 37511 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 37571 -> 37774 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 51262 -> 50639 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 43098 -> 43234 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28456 -> 28430 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78070 -> 78076 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49910 -> 49858 bytes articles/EUCAST.html | 6 +- articles/MDR.html | 64 +-- articles/PCA.html | 6 +- articles/SPSS.html | 10 +- articles/WHONET.html | 6 +- articles/datasets.html | 352 ++++++------ articles/index.html | 6 +- articles/resistance_predict.html | 6 +- .../figure-html/unnamed-chunk-6-1.png | Bin 77232 -> 77158 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 68850 -> 68866 bytes articles/welcome_to_AMR.html | 13 +- authors.html | 46 +- extra.css | 10 +- extra.js | 10 +- index.html | 21 +- news/index.html | 70 ++- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 6 +- reference/AMR.html | 136 ++++- reference/Rplot005.png | Bin 13167 -> 12805 bytes reference/Rplot006.png | Bin 12685 -> 12327 bytes reference/Rplot007.png | Bin 13536 -> 13593 bytes reference/Rplot008.png | Bin 18046 -> 18623 bytes reference/Rplot009.png | Bin 8490 -> 8435 bytes reference/Rplot010.png | Bin 20453 -> 20433 bytes reference/WHOCC.html | 6 +- reference/WHONET.html | 6 +- reference/ab_from_text.html | 6 +- reference/ab_property.html | 6 +- reference/age.html | 26 +- reference/age_groups.html | 6 +- reference/antibiotic_class_selectors.html | 6 +- reference/antibiotics.html | 6 +- reference/as.ab.html | 6 +- reference/as.disk.html | 6 +- reference/as.mic.html | 14 +- reference/as.mo.html | 234 +++----- reference/as.rsi.html | 54 +- reference/atc_online.html | 6 +- reference/availability.html | 6 +- reference/bug_drug_combinations.html | 22 +- reference/catalogue_of_life.html | 230 -------- reference/catalogue_of_life_version.html | 181 ------ reference/count.html | 6 +- reference/custom_eucast_rules.html | 74 ++- reference/dosage.html | 6 +- reference/eucast_rules.html | 19 +- reference/example_isolates.html | 6 +- reference/example_isolates_unclean.html | 6 +- reference/figures/logo_col.png | Bin 17868 -> 0 bytes reference/first_isolate.html | 10 +- reference/g.test.html | 6 +- reference/get_episode.html | 140 ++--- reference/ggplot_pca.html | 6 +- reference/ggplot_rsi-10.png | Bin 52732 -> 52730 bytes reference/ggplot_rsi.html | 6 +- reference/guess_ab_col.html | 6 +- reference/index.html | 31 +- reference/intrinsic_resistant.html | 12 +- reference/italicise_taxonomy.html | 6 +- reference/join.html | 81 +-- reference/key_antimicrobials.html | 6 +- reference/kurtosis.html | 10 +- reference/like.html | 6 +- reference/mdro.html | 6 +- reference/mean_amr_distance.html | 82 +-- reference/microorganisms.codes.html | 22 +- reference/microorganisms.html | 109 ++-- reference/microorganisms.old.html | 206 ------- reference/mo_matching_score.html | 36 +- reference/mo_property.html | 321 ++++++++--- reference/mo_source.html | 6 +- reference/pca.html | 6 +- reference/plot-1.png | Bin 27283 -> 27290 bytes reference/plot-2.png | Bin 26483 -> 27527 bytes reference/plot-3.png | Bin 28246 -> 28451 bytes reference/plot-4.png | Bin 39019 -> 39086 bytes reference/plot-5.png | Bin 38172 -> 39067 bytes reference/plot-6.png | Bin 36892 -> 37709 bytes reference/plot-7.png | Bin 38024 -> 38015 bytes reference/plot-8.png | Bin 54631 -> 55435 bytes reference/plot-9.png | Bin 26150 -> 26151 bytes reference/plot.html | 8 +- reference/proportion.html | 6 +- reference/random.html | 38 +- reference/resistance_predict.html | 8 +- reference/rsi_translation.html | 6 +- reference/skewness.html | 8 +- reference/translate.html | 62 ++- search.json | 2 +- sitemap.xml | 9 - 104 files changed, 1569 insertions(+), 1946 deletions(-) delete mode 100644 reference/catalogue_of_life.html delete mode 100644 reference/catalogue_of_life_version.html delete mode 100755 reference/figures/logo_col.png delete mode 100644 reference/microorganisms.old.html diff --git a/404.html b/404.html index a067fe022..a02963288 100644 --- a/404.html +++ b/404.html @@ -22,7 +22,7 @@ - + License • AMR (for R)License • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 1.8.1.9049 + 1.8.2.9004 - - - - - -
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The Catalogue of Life

- Source: R/catalogue_of_life.R -
catalogue_of_life.Rd
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This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).

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Catalogue of Life

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-This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, http://www.catalogueoflife.org). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, lpsn.dsmz.de). This supplementation is needed until the CoL+ project is finished, which we await.

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Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with catalogue_of_life_version().

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Included Taxa

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Included are:

  • All ~58,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa

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  • All ~5,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales, as well as ~4,600 other fungal (sub)species. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (such as all species of Aspergillus, Candida, Cryptococcus, Histplasma, Pneumocystis, Saccharomyces and Trichophyton).

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  • All ~2,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as Strongyloides and Taenia)

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  • All ~14,000 previously accepted names of all included (sub)species (these were taxonomically renamed)

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  • The complete taxonomic tree of all included (sub)species: from kingdom to subspecies

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  • The responsible author(s) and year of scientific publication

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The Catalogue of Life (http://www.catalogueoflife.org) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.

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The syntax used to transform the original data to a cleansed R format, can be found here: https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R.

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See also

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Data set microorganisms for the actual data.
-Function as.mo() to use the data for intelligent determination of microorganisms.

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Examples

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# Get version info of included data set
-catalogue_of_life_version()
-#> Included in this AMR package (v1.8.1.9049) are:
-#> 
-#> Catalogue of Life: 2019 Annual Checklist
-#>   Available at: http://www.catalogueoflife.org
-#>   Number of included microbial species: 49,029
-#> List of Prokaryotic names with Standing in Nomenclature (5 October 2021)
-#>   Available at: https://lpsn.dsmz.de
-#>   Number of included bacterial species: 21,701
-#> 
-#> => Total number of species included:  70,764
-#> => Total number of synonyms included: 14,338
-#> 
-#> See for more info `?microorganisms` and `?catalogue_of_life`.
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-# Get a note when a species was renamed
-mo_shortname("Chlamydophila psittaci")
-#> ℹ Chlamydophila psittaci (Everett et al. , 1999) was renamed back to
-#>   Chlamydia psittaci (Page, 1968) [B_CHLMY_PSTT]
-#> [1] "C. psittaci"
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-# Get any property from the entire taxonomic tree for all included species
-mo_class("Escherichia coli")
-#> [1] "Gammaproteobacteria"
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-mo_family("Escherichia coli")
-#> [1] "Enterobacteriaceae"
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-mo_gramstain("Escherichia coli") # based on kingdom and phylum, see ?mo_gramstain
-#> [1] "Gram-negative"
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-mo_ref("Escherichia coli")
-#> [1] "Castellani et al., 1919"
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-# Do not get mistaken - this package is about microorganisms
-mo_kingdom("C. elegans")
-#> ℹ Function `as.mo()` is uncertain about "C. elegans" (assuming Cladosporium
-#>   elegans). Run `mo_uncertainties()` to review this.
-#> [1] "Fungi"
-mo_name("C. elegans")
-#> ℹ Function `as.mo()` is uncertain about "C. elegans" (assuming Cladosporium
-#>   elegans). Run `mo_uncertainties()` to review this.
-#> [1] "Cladosporium elegans"
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Version info of included Catalogue of Life

- Source: R/catalogue_of_life.R -
catalogue_of_life_version.Rd
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This function returns information about the included data from the Catalogue of Life.

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Usage

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catalogue_of_life_version()
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Value

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a list, which prints in pretty format

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Details

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For LPSN, see microorganisms.

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Catalogue of Life

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-This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, http://www.catalogueoflife.org). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, lpsn.dsmz.de). This supplementation is needed until the CoL+ project is finished, which we await.

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Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with catalogue_of_life_version().

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See also

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microorganisms

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Data Set with Previously Accepted Taxonomic Names

- Source: R/data.R -
microorganisms.old.Rd
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A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by as.mo().

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Usage

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microorganisms.old
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Format

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A tibble with 14,338 observations and 4 variables:

  • fullname
    Old full taxonomic name of the microorganism

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  • fullname_new
    New full taxonomic name of the microorganism

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  • ref
    Author(s) and year of concerning scientific publication

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  • prevalence
    Prevalence of the microorganism, see as.mo()

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Source

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Catalogue of Life: Annual Checklist (public online taxonomic database), http://www.catalogueoflife.org (check included annual version with catalogue_of_life_version()).

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Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi:10.1099/ijsem.0.002786

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Details

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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.

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Catalogue of Life

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-This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, http://www.catalogueoflife.org). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, lpsn.dsmz.de). This supplementation is needed until the CoL+ project is finished, which we await.

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Click here for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with catalogue_of_life_version().

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See also

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as.mo() mo_property() microorganisms

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Examples

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microorganisms.old
-#> # A tibble: 14,338 × 4
-#>    fullname                   fullname_new                 ref           preva…¹
-#>    <chr>                      <chr>                        <chr>           <dbl>
-#>  1 Abaphospora petrucciana    Nectria petrucciana          Kirschst, 19…       2
-#>  2 Abathostoma stercoris      Echinocyclidium stercoris    Berger in Co…       3
-#>  3 Abbottina tannerbankensis  Nonion tannerbankensis       McCulloch, 1…       3
-#>  4 Abditodentrix rhomboidalis Tortoplectella rhomboidalis  Millett, 1899       3
-#>  5 Abiotrophia adiacens       Granulicatella adiacens      Kawamura et …       2
-#>  6 Abiotrophia balaenopterae  Granulicatella balaenopterae Lawson et al…       2
-#>  7 Abiotrophia elegans        Granulicatella elegans       Roggenkamp e…       2
-#>  8 Absidia blakesleeana       Lichtheimia blakesleeana     Lendn, 1924         3
-#>  9 Absidia butleri            Gongronella butleri          Lendn, 1926         3
-#> 10 Absidia corymbifera        Lichtheimia corymbifera      Sacc et al.,…       3
-#> # … with 14,328 more rows, and abbreviated variable name ¹​prevalence
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