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 >
2020-05-16 13:05:47 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.1.0.9004< / 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 >
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
