2018-12-29 22:24:19 +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" >
2019-11-28 22:32:17 +01:00
< title > Join a table with < a href = 'microorganisms.html' > microorganisms< / a > — join • AMR (for R)< / title >
2018-12-29 22:24:19 +01:00
<!-- 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
2018-12-29 22:24:19 +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 -->
< link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" / >
2019-10-13 09:31:58 +02:00
2018-12-29 22:24:19 +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 -->
2019-10-13 09:31:58 +02:00
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity = "sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin = "anonymous" / >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity = "sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin = "anonymous" / >
2018-12-29 22:24:19 +01:00
<!-- 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 >
2019-10-13 09:31:58 +02:00
<!-- headroom.js -->
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity = "sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin = "anonymous" > < / script >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script >
2018-12-29 22:24:19 +01:00
<!-- pkgdown -->
< link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script >
< link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script >
2019-11-28 22:32:17 +01:00
< meta property = "og:title" content = "Join a table with <a href='microorganisms.html'>microorganisms</a> — join" / >
< meta property = "og:description" content = "Join the data set microorganisms easily to an existing table or character vector." / >
2019-01-02 23:24:07 +01:00
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.png" / >
2018-12-29 22:24:19 +01:00
< meta name = "twitter:card" content = "summary" / >
2019-10-13 09:31:58 +02:00
2018-12-29 22:24:19 +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
2018-12-29 22:24:19 +01:00
< / 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" >
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2020-02-23 20:56:11 +01:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.0.1< / span >
2018-12-29 22:24:19 +01:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
< li >
< a href = "../index.html" >
< span class = "fa fa-home" > < / span >
Home
< / 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 >
2019-05-16 21:20:00 +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 >
< li >
2019-01-11 20:37:23 +01:00
< 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 >
< / li >
< li >
< a href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
< / li >
< li >
< a href = "../news/" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / 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 >
< / 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 >
< / ul >
< / div > <!-- /.nav - collapse -->
< / div > <!-- /.container -->
< / div > <!-- /.navbar -->
2019-10-13 09:31:58 +02:00
2018-12-29 22:24:19 +01:00
< / header >
< div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header" >
2019-11-28 22:32:17 +01:00
< h1 > Join a table with < a href = 'microorganisms.html' > microorganisms< / a > < / h1 >
2018-12-29 22:24:19 +01:00
< div class = "hidden name" > < code > join.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
2019-11-28 22:32:17 +01:00
< p > Join the data set < a href = 'microorganisms.html' > microorganisms< / a > easily to an existing table or character vector.< / p >
2018-12-29 22:24:19 +01:00
< / div >
2019-10-13 09:31:58 +02:00
< pre class = "usage" > < span class = 'fu' > inner_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > suffix< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "2"< / span > , < span class = 'st' > ""< / span > ), < span class = 'no' > ...< / span > )
2018-12-29 22:24:19 +01:00
2019-10-13 09:31:58 +02:00
< span class = 'fu' > left_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > suffix< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "2"< / span > , < span class = 'st' > ""< / span > ), < span class = 'no' > ...< / span > )
2018-12-29 22:24:19 +01:00
2019-10-13 09:31:58 +02:00
< span class = 'fu' > right_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > suffix< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "2"< / span > , < span class = 'st' > ""< / span > ), < span class = 'no' > ...< / span > )
2018-12-29 22:24:19 +01:00
2019-10-13 09:31:58 +02:00
< span class = 'fu' > full_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > suffix< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "2"< / span > , < span class = 'st' > ""< / span > ), < span class = 'no' > ...< / span > )
2018-12-29 22:24:19 +01:00
< span class = 'fu' > semi_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > anti_join_microorganisms< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'no' > ...< / span > )< / pre >
2019-10-13 09:31:58 +02:00
2018-12-29 22:24:19 +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 >
< td > < p > existing table to join, or character vector< / p > < / td >
< / tr >
< tr >
< th > by< / th >
2019-11-28 22:32:17 +01:00
< td > < p > a variable to join by - if left empty will search for a column with class < code > < a href = 'as.mo.html' > mo< / a > < / code > (created with < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > ) or will be < code > "mo"< / code > if that column name exists in < code > x< / code > , could otherwise be a column name of < code > x< / code > with values that exist in < code > microorganisms$mo< / code > (like < code > by = "bacteria_id"< / code > ), or another column in < a href = 'microorganisms.html' > microorganisms< / a > (but then it should be named, like < code > by = c("my_genus_species" = "fullname")< / code > )< / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< tr >
< th > suffix< / th >
< td > < p > if there are non-joined duplicate variables in < code > x< / code > and < code > y< / code > , these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.< / p > < / td >
< / tr >
< tr >
< th > ...< / th >
2019-11-28 22:32:17 +01:00
< td > < p > other parameters to pass on to < code > < a href = 'https://dplyr.tidyverse.org/reference/join.html' > dplyr::join()< / a > < / code > < / p > < / td >
2018-12-29 22:24:19 +01:00
< / tr >
< / table >
2019-10-13 09:31:58 +02:00
2018-12-29 22:24:19 +01:00
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
2019-11-28 23:00:37 +01:00
< p > < strong > Note:< / strong > As opposed to the < code > < a href = 'https://dplyr.tidyverse.org/reference/join.html' > dplyr::join()< / a > < / code > functions of < code > dplyr< / code > , < code > < a href = 'https://rdrr.io/r/base/character.html' > character< / a > < / code > vectors are supported and at default existing columns will get a suffix < code > "2"< / code > and the newly joined columns will not get a suffix. See < code > < a href = 'https://dplyr.tidyverse.org/reference/join.html' > dplyr::join()< / a > < / code > for more information.< / p >
2020-01-05 17:22:09 +01:00
< 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, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.< / p >
< p > If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will 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 >
2019-01-02 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 >
2018-12-29 22:24:19 +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 = 'fu' > left_join_microorganisms< / span > (< span class = 'fu' > < a href = 'as.mo.html' > as.mo< / a > < / span > (< span class = 'st' > "K. pneumoniae"< / span > ))
2019-01-02 23:24:07 +01:00
< span class = 'fu' > left_join_microorganisms< / span > (< span class = 'st' > "B_KLBSL_PNE"< / span > )
2019-10-13 09:31:58 +02:00
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
2019-08-27 16:45:42 +02:00
< span class = 'no' > example_isolates< / span > < span class = 'kw' > %> %< / span > < span class = 'fu' > left_join_microorganisms< / span > ()
2019-01-02 23:24:07 +01:00
2019-10-13 09:31:58 +02:00
< span class = 'no' > df< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (< span class = 'kw' > date< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/seq.html' > seq< / a > < / span > (< span class = 'kw' > from< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/as.Date.html' > as.Date< / a > < / span > (< span class = 'st' > "2018-01-01"< / span > ),
< span class = 'kw' > to< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/as.Date.html' > as.Date< / a > < / span > (< span class = 'st' > "2018-01-07"< / span > ),
2018-12-29 22:24:19 +01:00
< span class = 'kw' > by< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 1< / span > ),
2019-10-13 09:31:58 +02:00
< span class = 'kw' > bacteria< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'as.mo.html' > as.mo< / a > < / span > (< span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "S. aureus"< / span > , < span class = 'st' > "MRSA"< / span > , < span class = 'st' > "MSSA"< / span > , < span class = 'st' > "STAAUR"< / span > ,
2018-12-29 22:24:19 +01:00
< span class = 'st' > "E. coli"< / span > , < span class = 'st' > "E. coli"< / span > , < span class = 'st' > "E. coli"< / span > )),
< span class = 'kw' > stringsAsFactors< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
2019-10-13 09:31:58 +02:00
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/colnames.html' > colnames< / a > < / span > (< span class = 'no' > df< / span > )
2019-01-02 23:24:07 +01:00
< span class = 'no' > df_joined< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > left_join_microorganisms< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "bacteria"< / span > )
2019-10-13 09:31:58 +02:00
< span class = 'fu' > < a href = 'https://rdrr.io/r/base/colnames.html' > colnames< / a > < / span > (< span class = 'no' > df_joined< / span > )< / pre >
2018-12-29 22:24:19 +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 = "#details" > Details< / a > < / li >
2020-01-05 17:22:09 +01:00
< li > < a href = "#stable-lifecycle" > Stable lifecycle< / 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 >
2018-12-29 22:24:19 +01:00
< li > < a href = "#examples" > Examples< / a > < / li >
< / ul >
< / div >
< / div >
2019-10-13 09:31:58 +02:00
2018-12-29 22:24:19 +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 >
2018-12-29 22:24:19 +01:00
< / div >
< div class = "pkgdown" >
2019-10-13 09:31:58 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
2018-12-29 22:24:19 +01:00
< / div >
2019-10-13 09:31:58 +02:00
2018-12-29 22:24:19 +01:00
< / footer >
< / div >
2019-10-13 09:31:58 +02:00
2018-12-29 22:24:19 +01:00
< / body >
< / html >
2019-10-13 09:31:58 +02:00
