2018-12-23 21:26:21 +01:00
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
< html lang = "en" >
< head >
< meta charset = "utf-8" >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
2018-12-29 22:24:19 +01:00
< title > Property of a microorganism — mo_property • AMR (for R)< / title >
<!-- favicons -->
< link rel = "icon" type = "image/png" sizes = "16x16" href = "../favicon-16x16.png" >
< link rel = "icon" type = "image/png" sizes = "32x32" href = "../favicon-32x32.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "180x180" href = "../apple-touch-icon.png" / >
< link rel = "apple-touch-icon" type = "image/png" sizes = "120x120" href = "../apple-touch-icon-120x120.png" / >
< link rel = "apple-touch-icon" type = "image/png" sizes = "76x76" href = "../apple-touch-icon-76x76.png" / >
< link rel = "apple-touch-icon" type = "image/png" sizes = "60x60" href = "../apple-touch-icon-60x60.png" / >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
<!-- jquery -->
2020-04-13 21:09:56 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity = "sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin = "anonymous" > < / script >
2018-12-23 21:26:21 +01:00
<!-- Bootstrap -->
2020-04-13 21:09:56 +02:00
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
2020-04-13 21:09:56 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity = "sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin = "anonymous" > < / script >
2018-12-23 21:26:21 +01:00
2020-04-17 19:16:30 +02:00
<!-- bootstrap - toc -->
< link rel = "stylesheet" href = "../bootstrap-toc.css" >
< script src = "../bootstrap-toc.js" > < / script >
2018-12-23 21:26:21 +01:00
<!-- Font Awesome icons -->
2020-04-17 19:16:30 +02:00
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity = "sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin = "anonymous" / >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity = "sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin = "anonymous" / >
2018-12-23 21:26:21 +01:00
<!-- clipboard.js -->
2020-04-17 19:16:30 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script >
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
<!-- headroom.js -->
2020-04-17 19:16:30 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity = "sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin = "anonymous" > < / script >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script >
2018-12-23 21:26:21 +01:00
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
2018-12-29 22:24:19 +01:00
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
< meta property = "og:title" content = "Property of a microorganism — mo_property" / >
2019-11-30 12:01:50 +01:00
< meta property = "og:description" content = "Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with as.mo(), which makes it possible to use microbial abbreviations, codes and names as input. Please see Examples." / >
2020-04-17 19:16:30 +02:00
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.svg" / >
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
<!-- mathjax -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity = "sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin = "anonymous" > < / script >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity = "sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin = "anonymous" > < / script >
<!-- [if lt IE 9]>
< script src = "https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js" > < / script >
< script src = "https://oss.maxcdn.com/respond/1.4.2/respond.min.js" > < / script >
<![endif]-->
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< / head >
2020-04-17 19:16:30 +02:00
< body data-spy = "scroll" data-target = "#toc" >
2018-12-23 21:26:21 +01:00
< div class = "container template-reference-topic" >
< header >
< div class = "navbar navbar-default navbar-fixed-top" role = "navigation" >
< div class = "container" >
< div class = "navbar-header" >
< button type = "button" class = "navbar-toggle collapsed" data-toggle = "collapse" data-target = "#navbar" aria-expanded = "false" >
< span class = "sr-only" > Toggle navigation< / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< / button >
< span class = "navbar-brand" >
2018-12-29 22:24:19 +01:00
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2020-05-28 10:51:56 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.1.0.9021< / span >
2018-12-23 21:26:21 +01:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
< li >
< a href = "../index.html" >
2018-12-29 22:24:19 +01:00
< span class = "fa fa-home" > < / span >
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Home
2018-12-23 21:26:21 +01:00
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< li class = "dropdown" >
< a href = "#" class = "dropdown-toggle" data-toggle = "dropdown" role = "button" aria-expanded = "false" >
< span class = "fa fa-question-circle" > < / span >
How to
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
< span class = "caret" > < / span >
2018-12-29 22:24:19 +01:00
< / a >
2019-01-02 23:24:07 +01:00
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
Conduct AMR analysis
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../articles/resistance_predict.html" >
2019-01-02 23:24:07 +01:00
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
2020-04-13 21:09:56 +02:00
< li >
< a href = "../articles/PCA.html" >
< span class = "fa fa-compress" > < / span >
Conduct principal component analysis for AMR
< / a >
< / li >
2019-05-28 16:50:40 +02:00
< li >
< a href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
Determine multi-drug resistance (MDR)
< / a >
< / li >
2019-01-29 00:06:50 +01:00
< li >
< a href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
Work with WHONET data
< / a >
< / li >
2019-02-14 15:18:17 +01:00
< li >
< a href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
Import data from SPSS/SAS/Stata
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< li >
< a href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../reference/mo_property.html" >
2019-01-02 23:24:07 +01:00
< span class = "fa fa-bug" > < / span >
Get properties of a microorganism
< / a >
< / li >
< li >
2019-05-10 16:44:59 +02:00
< a href = "../reference/ab_property.html" >
2019-01-02 23:24:07 +01:00
< span class = "fa fa-capsules" > < / span >
Get properties of an antibiotic
< / a >
< / li >
2019-01-11 20:37:23 +01:00
< li >
< a href = "../articles/benchmarks.html" >
< span class = "fa fa-shipping-fast" > < / span >
Other: benchmarks
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
2018-12-29 22:24:19 +01:00
< / li >
< li >
< a href = "../reference/" >
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
2018-12-23 21:26:21 +01:00
< / li >
< li >
2018-12-29 22:24:19 +01:00
< a href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2018-12-29 22:24:19 +01:00
< li >
< a href = "../news/" >
< span class = "far fa far fa-newspaper" > < / span >
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Changelog
2018-12-23 21:26:21 +01:00
< / a >
< / li >
2019-01-02 23:24:07 +01:00
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
2018-12-29 22:24:19 +01:00
< a href = "https://gitlab.com/msberends/AMR" >
< span class = "fab fa fab fa-gitlab" > < / span >
Source Code
< / a >
2018-12-23 21:26:21 +01:00
< / li >
2019-01-02 23:24:07 +01:00
< li >
2018-12-29 22:24:19 +01:00
< a href = "../LICENSE-text.html" >
< span class = "fa fa-book" > < / span >
Licence
< / a >
< / li >
2018-12-23 21:26:21 +01:00
< / ul >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > Property of a microorganism< / h1 >
2020-04-17 19:16:30 +02:00
< small class = "dont-index" > Source: < a href = 'https://gitlab.com/msberends/AMR/blob/master/R/mo_property.R' > < code > R/mo_property.R< / code > < / a > < / small >
2018-12-23 21:26:21 +01:00
< div class = "hidden name" > < code > mo_property.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
2019-11-30 12:01:50 +01:00
< p > Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > , which makes it possible to use microbial abbreviations, codes and names as input. Please see < em > Examples< / em > .< / p >
2018-12-23 21:26:21 +01:00
< / div >
2019-05-13 12:21:57 +02:00
< pre class = "usage" > < span class = 'fu' > mo_name< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_fullname< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_shortname< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_subspecies< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_species< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_genus< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_family< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_order< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_class< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_phylum< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_kingdom< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_type< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_gramstain< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2020-01-27 19:14:23 +01:00
< span class = 'fu' > mo_snomed< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
< span class = 'fu' > mo_ref< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_authors< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_year< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
2019-02-22 22:12:10 +01:00
< span class = 'fu' > mo_rank< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_taxonomy< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2018-12-23 21:26:21 +01:00
2019-06-16 21:42:40 +02:00
< span class = 'fu' > mo_synonyms< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
2019-06-11 14:18:25 +02:00
< span class = 'fu' > mo_info< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
2019-02-22 22:12:10 +01:00
< span class = 'fu' > mo_url< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > open< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'no' > ...< / span > )
2019-02-20 00:04:48 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_property< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > property< / span > < span class = 'kw' > =< / span > < span class = 'st' > "fullname"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )< / pre >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > x< / th >
2019-11-28 22:32:17 +01:00
< td > < p > any (vector of) text that can be coerced to a valid microorganism code with < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > language< / th >
2019-11-28 22:32:17 +01:00
< td > < p > language of the returned text, defaults to system language (see < code > < a href = 'translate.html' > get_locale()< / a > < / code > ) and can also be set with < code > < a href = 'https://rdrr.io/r/base/options.html' > getOption("AMR_locale")< / a > < / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< tr >
< th > ...< / th >
2019-11-28 22:32:17 +01:00
< td > < p > other parameters passed on to < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
2019-02-22 22:12:10 +01:00
< tr >
< th > open< / th >
2019-11-28 22:32:17 +01:00
< td > < p > browse the URL using < code > < a href = 'https://rdrr.io/r/utils/browseURL.html' > utils::browseURL()< / a > < / code > < / p > < / td >
2019-02-22 22:12:10 +01:00
< / tr >
2018-12-23 21:26:21 +01:00
< tr >
< th > property< / th >
2019-11-28 22:32:17 +01:00
< td > < p > one of the column names of the < a href = 'microorganisms.html' > microorganisms< / a > data set or < code > "shortname"< / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< / table >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< ul >
2019-11-28 22:32:17 +01:00
< li > < p > An < code > < a href = 'https://rdrr.io/r/base/integer.html' > integer< / a > < / code > in case of < code > mo_year()< / code > < / p > < / li >
2019-11-30 12:01:50 +01:00
< li > < p > A < code > < a href = 'https://rdrr.io/r/base/list.html' > list< / a > < / code > in case of < code > mo_taxonomy()< / code > and < code > mo_info()< / code > < / p > < / li >
2019-11-28 22:32:17 +01:00
< li > < p > A named < code > < a href = 'https://rdrr.io/r/base/character.html' > character< / a > < / code > in case of < code > mo_url()< / code > < / p > < / li >
2020-01-27 19:14:23 +01:00
< li > < p > A < code > < a href = 'https://rdrr.io/r/base/double.html' > double< / a > < / code > in case of < code > mo_snomed()< / code > < / p > < / li >
2019-11-28 22:32:17 +01:00
< li > < p > A < code > < a href = 'https://rdrr.io/r/base/character.html' > character< / a > < / code > in all other cases< / p > < / li >
2018-12-23 21:26:21 +01:00
< / ul >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2019-11-28 22:32:17 +01:00
< p > All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for < code > mo_ref()< / code > , < code > mo_authors()< / code > and < code > mo_year()< / code > . This leads to the following results:< / p > < ul >
2019-05-20 12:00:18 +02:00
< li > < p > < code > mo_name("Chlamydia psittaci")< / code > will return < code > "Chlamydophila psittaci"< / code > (with a warning about the renaming)< / p > < / li >
2018-12-23 21:26:21 +01:00
< li > < p > < code > mo_ref("Chlamydia psittaci")< / code > will return < code > "Page, 1968"< / code > (with a warning about the renaming)< / p > < / li >
< li > < p > < code > mo_ref("Chlamydophila psittaci")< / code > will return < code > "Everett et al., 1999"< / code > (without a warning)< / p > < / li >
< / ul >
2019-10-13 09:31:58 +02:00
2020-04-30 09:05:03 +02:00
< p > The short name - < code > mo_shortname()< / code > - almost always returns the first character of the genus and the full species, like < em > "E. coli"< / em > . Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like < em > "CoNS"< / em > (Coagulase-Negative Staphylococci) and < em > "GBS"< / em > (Group B Streptococci).< / p >
2019-11-30 12:01:50 +01:00
< p > The Gram stain - < code > mo_gramstain()< / code > - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value < code > NA< / code > .< / p >
2019-05-10 16:44:59 +02:00
< p > All output will be < a href = 'translate.html' > translate< / a > d where possible.< / p >
2019-03-18 14:29:41 +01:00
< p > The function < code > mo_url()< / code > will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.< / p >
2020-05-25 01:01:14 +02:00
< h2 class = "hasAnchor" id = "stable-lifecycle" > < a class = "anchor" href = "#stable-lifecycle" > < / a > Stable lifecycle< / h2 >
< p > < img src = 'figures/lifecycle_stable.svg' style = margin-bottom:5px / > < br / >
The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > stable< / strong > . In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.< / p >
< p > If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.< / p >
2019-02-20 00:04:48 +01:00
< h2 class = "hasAnchor" id = "catalogue-of-life" > < a class = "anchor" href = "#catalogue-of-life" > < / a > Catalogue of Life< / h2 >
2018-12-23 21:26:21 +01:00
2019-10-13 09:31:58 +02:00
< p > < img src = 'figures/logo_col.png' height = 40px style = margin-bottom:5px / > < br / >
2019-08-13 16:15:08 +02:00
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (< a href = 'http://www.catalogueoflife.org' > http://www.catalogueoflife.org< / a > ). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.< / p >
2019-11-28 22:32:17 +01:00
< p > < a href = 'catalogue_of_life.html' > Click here< / a > for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with < code > < a href = 'catalogue_of_life_version.html' > catalogue_of_life_version()< / a > < / code > .< / p >
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
2019-10-13 09:31:58 +02:00
2019-11-28 22:32:17 +01:00
< ol >
< li > < p > Becker K < em > et al.< / em > < strong > Coagulase-Negative Staphylococci< / strong > . 2014. Clin Microbiol Rev. 27(4): 870– < a href = 'https://dx.doi.org/10.1128/CMR.00109-13' > https://dx.doi.org/10.1128/CMR.00109-13< / a > < / p > < / li >
< li > < p > Becker K < em > et al.< / em > < strong > Implications of identifying the recently defined members of the < em > S. aureus< / em > complex, < em > S. argenteus< / em > and < em > S. schweitzeri< / em > : A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).< / strong > 2019. Clin Microbiol Infect. < a href = 'https://doi.org/10.1016/j.cmi.2019.02.028' > https://doi.org/10.1016/j.cmi.2019.02.028< / a > < / p > < / li >
< li > < p > Lancefield RC < strong > A serological differentiation of human and other groups of hemolytic streptococci< / strong > . 1933. J Exp Med. 57(4): 571– < a href = 'https://dx.doi.org/10.1084/jem.57.4.571' > https://dx.doi.org/10.1084/jem.57.4.571< / a > < / p > < / li >
< li > < p > Catalogue of Life: Annual Checklist (public online taxonomic database), < a href = 'http://www.catalogueoflife.org' > http://www.catalogueoflife.org< / a > (check included annual version with < code > < a href = 'catalogue_of_life_version.html' > catalogue_of_life_version()< / a > < / code > ).< / p > < / li >
< / ol >
2019-01-02 23:24:07 +01:00
< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
2019-10-13 09:31:58 +02:00
2020-02-17 14:38:01 +01:00
< p > On our website < a href = 'https://msberends.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
2019-11-28 22:32:17 +01:00
< div class = 'dont-index' > < p > < a href = 'microorganisms.html' > microorganisms< / a > < / p > < / div >
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
2019-10-13 09:31:58 +02:00
< pre class = "examples" > < span class = 'co' > # taxonomic tree -----------------------------------------------------------< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_kingdom< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria"< / span >
< span class = 'fu' > mo_phylum< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Proteobacteria"< / span >
< span class = 'fu' > mo_class< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Gammaproteobacteria"< / span >
2019-11-24 22:48:56 +01:00
< span class = 'fu' > mo_order< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Enterobacterales"< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_family< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Enterobacteriaceae"< / span >
< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Escherichia"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "coli"< / span >
2019-02-20 00:04:48 +01:00
< span class = 'fu' > mo_subspecies< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # ""< / span >
2019-01-02 23:24:07 +01:00
2019-08-09 14:28:46 +02:00
< span class = 'co' > # colloquial properties ----------------------------------------------------< / span >
2019-05-13 12:21:57 +02:00
< span class = 'fu' > mo_name< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Escherichia coli"< / span >
2020-01-27 19:14:23 +01:00
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Escherichia coli" - same as mo_name()< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "E. coli"< / span >
2019-08-09 14:28:46 +02:00
< span class = 'co' > # other properties ---------------------------------------------------------< / span >
2019-06-11 14:18:25 +02:00
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Gram-negative"< / span >
2020-01-27 19:14:23 +01:00
< span class = 'fu' > mo_snomed< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # 112283007, 116395006, ... (SNOMED codes)< / span >
2019-06-11 14:18:25 +02:00
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" (equal to kingdom, but may be translated)< / span >
2019-02-22 22:12:10 +01:00
< span class = 'fu' > mo_rank< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "species"< / span >
2019-05-10 16:44:59 +02:00
< span class = 'fu' > mo_url< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # get the direct url to the online database entry< / span >
2019-06-16 21:42:40 +02:00
< span class = 'fu' > mo_synonyms< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # get previously accepted taxonomic names< / span >
2019-01-02 23:24:07 +01:00
2019-08-09 14:28:46 +02:00
< span class = 'co' > # scientific reference -----------------------------------------------------< / span >
2019-02-22 22:12:10 +01:00
< span class = 'fu' > mo_ref< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Castellani et al., 1919"< / span >
< span class = 'fu' > mo_authors< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Castellani et al."< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_year< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # 1919< / span >
2019-08-09 14:28:46 +02:00
< span class = 'co' > # abbreviations known in the field -----------------------------------------< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "MRSA"< / span > ) < span class = 'co' > # "Staphylococcus"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "MRSA"< / span > ) < span class = 'co' > # "aureus"< / span >
2019-08-09 14:28:46 +02:00
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "VISA"< / span > ) < span class = 'co' > # "S. aureus"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "VISA"< / span > ) < span class = 'co' > # "Gram-positive"< / span >
2019-01-02 23:24:07 +01:00
2019-08-09 14:28:46 +02:00
< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "EHEC"< / span > ) < span class = 'co' > # "Escherichia"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "EHEC"< / span > ) < span class = 'co' > # "coli"< / span >
2018-12-23 21:26:21 +01:00
2019-08-09 14:28:46 +02:00
< span class = 'co' > # known subspecies ---------------------------------------------------------< / span >
2019-05-20 12:00:18 +02:00
< span class = 'fu' > mo_name< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "Campylobacter jejuni doylei"< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "Campylobacter"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "jejuni"< / span >
2019-05-20 12:00:18 +02:00
< span class = 'fu' > mo_subspecies< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "doylei"< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "K. pneu rh"< / span > ) < span class = 'co' > # "Klebsiella pneumoniae rhinoscleromatis"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "K. pneu rh"< / span > ) < span class = 'co' > # "K. pneumoniae"< / span >
2019-10-13 09:31:58 +02:00
< span class = 'co' > # \donttest{< / span >
2019-08-09 14:28:46 +02:00
< span class = 'co' > # Becker classification, see ?as.mo ----------------------------------------< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. epi"< / span > ) < span class = 'co' > # "Staphylococcus epidermidis"< / span >
2019-03-18 14:29:41 +01:00
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. epi"< / span > , < span class = 'kw' > Becker< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "Coagulase-negative Staphylococcus (CoNS)"< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. epi"< / span > ) < span class = 'co' > # "S. epidermidis"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. epi"< / span > , < span class = 'kw' > Becker< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "CoNS"< / span >
2019-08-09 14:28:46 +02:00
< span class = 'co' > # Lancefield classification, see ?as.mo ------------------------------------< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyo"< / span > ) < span class = 'co' > # "Streptococcus pyogenes"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyo"< / span > , < span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "Streptococcus group A"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. pyo"< / span > ) < span class = 'co' > # "S. pyogenes"< / span >
2019-06-27 11:57:45 +02:00
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. pyo"< / span > , < span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "GAS" (='Group A Streptococci')< / span >
2019-01-02 23:24:07 +01:00
2018-12-23 21:26:21 +01:00
2019-02-22 22:12:10 +01:00
< span class = 'co' > # language support for German, Dutch, Spanish, Portuguese, Italian and French< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "de"< / span > ) < span class = 'co' > # "Gramnegativ"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "nl"< / span > ) < span class = 'co' > # "Gram-negatief"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "es"< / span > ) < span class = 'co' > # "Gram negativo"< / span >
2018-12-23 21:26:21 +01:00
< span class = 'co' > # mo_type is equal to mo_kingdom, but mo_kingdom will remain official< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_kingdom< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" on a German system< / span >
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bakterien" on a German system< / span >
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" on an English system< / span >
2018-12-23 21:26:21 +01:00
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyogenes"< / span > ,
< span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
2019-01-02 23:24:07 +01:00
< span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "de"< / span > ) < span class = 'co' > # "Streptococcus Gruppe A"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyogenes"< / span > ,
2018-12-23 21:26:21 +01:00
< span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
2019-01-02 23:24:07 +01:00
< span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "nl"< / span > ) < span class = 'co' > # "Streptococcus groep A"< / span >
2018-12-23 21:26:21 +01:00
2019-05-10 16:44:59 +02:00
< span class = 'co' > # get a list with the complete taxonomy (from kingdom to subspecies)< / span >
2019-01-02 23:24:07 +01:00
< span class = 'fu' > mo_taxonomy< / span > (< span class = 'st' > "E. coli"< / span > )
2019-11-28 22:32:17 +01:00
< span class = 'co' > # get a list with the taxonomy, the authors, Gram-stain and URL to the online database< / span >
2019-06-11 14:18:25 +02:00
< span class = 'fu' > mo_info< / span > (< span class = 'st' > "E. coli"< / span > )
2019-01-02 23:24:07 +01:00
< span class = 'co' > # }< / span > < / pre >
2018-12-23 21:26:21 +01:00
< / div >
2020-04-13 21:09:56 +02:00
< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
2020-04-17 19:16:30 +02:00
< nav id = "toc" data-toggle = "toc" class = "sticky-top" >
< h2 data-toc-skip > Contents< / h2 >
< / nav >
2018-12-23 21:26:21 +01:00
< / div >
< / div >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< footer >
< div class = "copyright" >
2020-01-26 20:38:54 +01:00
< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alexander W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
2018-12-23 21:26:21 +01:00
< / div >
< div class = "pkgdown" >
2020-04-29 14:33:44 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.1.< / p >
2018-12-23 21:26:21 +01:00
< / div >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< / footer >
< / div >
2019-10-13 09:31:58 +02:00
2018-12-23 21:26:21 +01:00
< / body >
< / html >
2019-10-13 09:31:58 +02:00
