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" / >
2018-12-23 21:26:21 +01:00
<!-- jquery -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity = "sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin = "anonymous" > < / script >
<!-- Bootstrap -->
2018-12-29 22:24:19 +01:00
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2018-12-23 21:26:21 +01:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity = "sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin = "anonymous" > < / script >
<!-- Font Awesome icons -->
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity = "sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin = "anonymous" / >
<!-- clipboard.js -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity = "sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin = "anonymous" > < / script >
<!-- sticky kit -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity = "sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin = "anonymous" > < / script >
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
2018-12-29 22:24:19 +01:00
<!-- docsearch -->
< script src = "../docsearch.js" > < / script >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity = "sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin = "anonymous" / >
< link href = "../docsearch.css" rel = "stylesheet" >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity = "sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin = "anonymous" > < / script >
2018-12-23 21:26:21 +01:00
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
< meta property = "og:title" content = "Property of a microorganism — mo_property" / >
2019-08-09 14:28:46 +02:00
< 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 for input of these functions to use microbial abbreviations, codes and names. See Examples." / >
2018-12-29 22:24:19 +01:00
2019-01-02 23:24:07 +01:00
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.png" / >
2018-12-23 21:26:21 +01:00
< meta name = "twitter:card" content = "summary" / >
<!-- 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]-->
< / head >
< body >
< 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 >
2019-08-13 16:15:08 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 0.7.1.9055< / 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 >
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 >
2018-12-29 22:24:19 +01:00
< form class = "navbar-form navbar-right" role = "search" >
< div class = "form-group" >
< input type = "search" class = "form-control" name = "search-input" id = "search-input" placeholder = "Search..." aria-label = "Search for..." autocomplete = "off" >
< / div >
< / form >
2018-12-23 21:26:21 +01:00
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
< h1 > Property of a microorganism< / h1 >
< div class = "hidden name" > < code > mo_property.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
2019-08-09 14:28:46 +02:00
< 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 for input of these functions to use microbial abbreviations, codes and names. See Examples.< / 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
< 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 >
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 >
2018-12-31 01:48:53 +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 >
2019-05-10 16:44:59 +02:00
< 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://www.rdocumentation.org/packages/base/topics/options' > getOption< / a > ("AMR_locale")< / 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 >
2018-12-31 01:48:53 +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 >
2019-03-18 14:29:41 +01:00
< td > < p > browse the URL using < code > < a href = 'https://www.rdocumentation.org/packages/utils/topics/browseURL' > 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 >
2019-05-20 12:00:18 +02:00
< td > < p > one of the column names of the < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > data set or < code > "shortname"< / code > < / p > < / td >
2018-12-23 21:26:21 +01:00
< / tr >
< / table >
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< ul >
2019-02-18 02:33:37 +01:00
< li > < p > An < code > integer< / code > in case of < code > mo_year< / code > < / p > < / li >
2018-12-23 21:26:21 +01:00
< li > < p > A < code > list< / code > in case of < code > mo_taxonomy< / code > < / p > < / li >
2019-02-22 22:12:10 +01:00
< li > < p > A named < code > character< / code > in case of < code > mo_url< / code > < / p > < / li >
2018-12-23 21:26:21 +01:00
< li > < p > A < code > character< / code > in all other cases< / p > < / li >
< / ul >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2019-02-20 00:04:48 +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 >
2019-03-18 14:29:41 +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 >
2018-12-23 21:26:21 +01:00
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
2019-02-28 13:56:28 +01:00
< 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 >
< 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 >
< p > [1] Becker K < em > et al.< / em > < strong > Coagulase-Negative Staphylococci< / strong > . 2014. Clin Microbiol Rev. 27(4): 870– 926. < a href = 'https://dx.doi.org/10.1128/CMR.00109-13' > https://dx.doi.org/10.1128/CMR.00109-13< / a > < / p >
2019-05-10 16:44:59 +02:00
< p > [2] 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 >
2019-03-26 14:24:03 +01:00
< p > [3] Lancefield RC < strong > A serological differentiation of human and other groups of hemolytic streptococci< / strong > . 1933. J Exp Med. 57(4): 571– 95. < a href = 'https://dx.doi.org/10.1084/jem.57.4.571' > https://dx.doi.org/10.1084/jem.57.4.571< / a > < / p >
2019-06-03 17:45:22 +02:00
< p > [4] 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 >
2018-12-23 21:26:21 +01:00
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 >
2019-05-31 14:25:11 +02:00
< 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 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 >
2019-01-02 23:24:07 +01:00
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
2018-12-31 01:48:53 +01:00
< div class = 'dont-index' > < p > < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > < / p > < / div >
2018-12-23 21:26:21 +01:00
< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
2019-01-02 23:24:07 +01:00
< pre class = "examples" > < span class = 'co' > # NOT RUN {< / span >
2019-08-09 14:28:46 +02:00
< 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 >
< span class = 'fu' > mo_order< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Enterobacteriales"< / span >
< 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 >
< 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 >
< 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 >
2019-08-09 14:28:46 +02:00
< span class = 'co' > # }< / span > < span class = 'co' > # NOT RUN {< / span >
< 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 > )
2019-06-11 14:18:25 +02:00
< span class = 'co' > # get a list with the taxonomy, the authors and the URL to the online database< / span >
< 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 >
< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
< h2 > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
< li > < a href = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#value" > Value< / a > < / li >
< li > < a href = "#details" > Details< / a > < / li >
2019-02-20 00:04:48 +01:00
< li > < a href = "#catalogue-of-life" > Catalogue of Life< / a > < / li >
2018-12-23 21:26:21 +01:00
< li > < a href = "#source" > Source< / a > < / li >
2019-01-02 23:24:07 +01:00
< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
2018-12-23 21:26:21 +01:00
< li > < a href = "#see-also" > See also< / a > < / li >
< li > < a href = "#examples" > Examples< / a > < / li >
< / ul >
< / div >
< / div >
< footer >
< div class = "copyright" >
2019-08-14 14:57:06 +02:00
< 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/' > Alex 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" >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.3.0.< / p >
< / div >
< / footer >
< / div >
2018-12-29 22:24:19 +01:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity = "sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin = "anonymous" > < / script >
< script >
docsearch({
apiKey: 'f737050abfd4d726c63938e18f8c496e',
indexName: 'amr',
inputSelector: 'input#search-input.form-control',
transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
return hit;
});
}
});
< / script >
2018-12-23 21:26:21 +01:00
< / body >
< / html >