2019-01-02 23:24:07 +01:00
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --> < html lang = "en" >
< head >
< meta http-equiv = "Content-Type" content = "text/html; charset=UTF-8" >
< meta charset = "utf-8" >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
< title > How to create frequency tables • 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" >
<!-- 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" >
< 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 > <!-- 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 > < link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script > < meta property = "og:title" content = "How to create frequency tables" >
< meta property = "og:description" content = "" >
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.png" >
< 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-article" >
< 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 >
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Released version" > 0.5.0.9009< / span >
< / 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 >
< 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
< span class = "caret" > < / span >
< / a >
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
Conduct AMR analysis
< / a >
< / li >
< li >
< a href = "../articles/Predict.html" >
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
< li >
< a href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< / li >
< li >
< a href = "../articles/mo_property.html" >
< span class = "fa fa-bug" > < / span >
Get properties of a microorganism
< / a >
< / li >
< li >
< a href = "../articles/ab_property.html" >
< span class = "fa fa-capsules" > < / span >
Get properties of an antibiotic
< / a >
< / li >
< li >
< a href = "../articles/freq.html" >
< span class = "fa fa-sort-amount-down" > < / span >
Create frequency tables
< / a >
< / li >
< li >
< a href = "../articles/G_test.html" >
< span class = "fa fa-clipboard-check" > < / span >
Use the G-test
< / a >
< / li >
< / ul >
< / 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 >
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
< a href = "https://gitlab.com/msberends/AMR" >
< span class = "fab fa fab fa-gitlab" > < / span >
Source Code
< / a >
< / li >
< li >
< a href = "../LICENSE-text.html" >
< span class = "fa fa-book" > < / span >
Licence
< / a >
< / li >
< / ul >
< 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 >
< / div >
<!-- /.nav - collapse -->
< / div >
<!-- /.container -->
< / div >
<!-- /.navbar -->
< / header > < div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header toc-ignore" >
< h1 > How to create frequency tables< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
< div class = "hidden name" > < code > freq.Rmd< / code > < / div >
< / div >
< div id = "introduction" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#introduction" class = "anchor" > < / a > Introduction< / h2 >
< p > Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the < code > freq< / code > function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. We take the < code > septic_patients< / code > dataset (included in this AMR package) as example.< / p >
< / div >
< div id = "frequencies-of-one-variable" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#frequencies-of-one-variable" class = "anchor" > < / a > Frequencies of one variable< / h2 >
< p > To only show and quickly review the content of one variable, you can just select this variable in various ways. Let’ < code > gender< / code > variable of the < code > septic_patients< / code > dataset:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > septic_patients %> %< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (gender)< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > gender< / code > < / strong > < / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > M< / td >
< td align = "right" > 1,031< / td >
< td align = "right" > 51.6%< / td >
< td align = "right" > 1,031< / td >
< td align = "right" > 51.6%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > F< / td >
< td align = "right" > 969< / td >
< td align = "right" > 48.5%< / td >
< td align = "right" > 2,000< / td >
< td align = "right" > 100.0%< / td >
< / tr >
< / tbody >
< / table >
< p > This immediately shows the class of the variable, its length and availability (i.e. < code > NA< / code > ), the amount of unique values and (most importantly) that among septic patients men are more prevalent than women.< / p >
< / div >
< div id = "frequencies-of-more-than-one-variable" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#frequencies-of-more-than-one-variable" class = "anchor" > < / a > Frequencies of more than one variable< / h2 >
< p > Multiple variables will be pasted into one variable to review individual cases, keeping a univariate frequency table.< / p >
< p > For illustration, we could add some more variables to the < code > septic_patients< / code > dataset to learn about bacterial properties:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > my_patients < -< span class = "st" > < / span > septic_patients %> %< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/join.html" > left_join_microorganisms< / a > < / span > ()
< span class = "co" > # Joining, by = "mo"< / span > < / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > Now all variables of the < code > microorganisms< / code > dataset have been joined to the < code > septic_patients< / code > dataset. The < code > microorganisms< / code > dataset consists of the following variables:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/colnames" > colnames< / a > < / span > (microorganisms)
< span class = "co" > # [1] "mo" "tsn" "genus" "species" "subspecies"< / span >
< span class = "co" > # [6] "fullname" "family" "order" "class" "phylum" < / span >
< span class = "co" > # [11] "subkingdom" "kingdom" "gramstain" "prevalence" "ref"< / span > < / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/dim" > dim< / a > < / span > (septic_patients)
< span class = "co" > # [1] 2000 49< / span >
< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/dim" > dim< / a > < / span > (my_patients)
< span class = "co" > # [1] 2000 63< / span > < / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > So now the < code > genus< / code > and < code > species< / code > variables are available. A frequency table of these combined variables can be created like this:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > my_patients %> %
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (genus, species, < span class = "dt" > nmax =< / span > < span class = "dv" > 15< / span > )< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > genus< / code > and < code > species< / code > < / strong > < / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > Escherichia coli< / td >
< td align = "right" > 467< / td >
< td align = "right" > 23.4%< / td >
< td align = "right" > 467< / td >
< td align = "right" > 23.4%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > Staphylococcus coagulase negative< / td >
< td align = "right" > 313< / td >
< td align = "right" > 15.7%< / td >
< td align = "right" > 780< / td >
< td align = "right" > 39.0%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > Staphylococcus aureus< / td >
< td align = "right" > 235< / td >
< td align = "right" > 11.8%< / td >
< td align = "right" > 1,015< / td >
< td align = "right" > 50.7%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > Staphylococcus epidermidis< / td >
< td align = "right" > 174< / td >
< td align = "right" > 8.7%< / td >
< td align = "right" > 1,189< / td >
< td align = "right" > 59.5%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 5< / td >
< td align = "left" > Streptococcus pneumoniae< / td >
< td align = "right" > 117< / td >
< td align = "right" > 5.9%< / td >
< td align = "right" > 1,306< / td >
< td align = "right" > 65.3%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 6< / td >
< td align = "left" > Staphylococcus hominis< / td >
< td align = "right" > 81< / td >
< td align = "right" > 4.1%< / td >
< td align = "right" > 1,387< / td >
< td align = "right" > 69.4%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 7< / td >
< td align = "left" > Klebsiella pneumoniae< / td >
< td align = "right" > 58< / td >
< td align = "right" > 2.9%< / td >
< td align = "right" > 1,445< / td >
< td align = "right" > 72.3%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 8< / td >
< td align = "left" > Enterococcus faecalis< / td >
< td align = "right" > 39< / td >
< td align = "right" > 2.0%< / td >
< td align = "right" > 1,484< / td >
< td align = "right" > 74.2%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 9< / td >
< td align = "left" > Proteus mirabilis< / td >
< td align = "right" > 36< / td >
< td align = "right" > 1.8%< / td >
< td align = "right" > 1,520< / td >
< td align = "right" > 76.0%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 10< / td >
< td align = "left" > Pseudomonas aeruginosa< / td >
< td align = "right" > 30< / td >
< td align = "right" > 1.5%< / td >
< td align = "right" > 1,550< / td >
< td align = "right" > 77.5%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 11< / td >
< td align = "left" > Serratia marcescens< / td >
< td align = "right" > 25< / td >
< td align = "right" > 1.3%< / td >
< td align = "right" > 1,575< / td >
< td align = "right" > 78.8%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 12< / td >
< td align = "left" > Enterobacter cloacae< / td >
< td align = "right" > 23< / td >
< td align = "right" > 1.2%< / td >
< td align = "right" > 1,598< / td >
< td align = "right" > 79.9%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 13< / td >
< td align = "left" > Enterococcus faecium< / td >
< td align = "right" > 21< / td >
< td align = "right" > 1.1%< / td >
< td align = "right" > 1,619< / td >
< td align = "right" > 81.0%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 14< / td >
< td align = "left" > Staphylococcus capitis< / td >
< td align = "right" > 21< / td >
< td align = "right" > 1.1%< / td >
< td align = "right" > 1,640< / td >
< td align = "right" > 82.0%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 15< / td >
< td align = "left" > Bacteroides fragilis< / td >
< td align = "right" > 20< / td >
< td align = "right" > 1.0%< / td >
< td align = "right" > 1,660< / td >
< td align = "right" > 83.0%< / td >
< / tr >
< / tbody >
< / table >
< p > (omitted 81 entries, n = 340 [17.0%])< / p >
< / div >
< div id = "frequencies-of-numeric-values" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#frequencies-of-numeric-values" class = "anchor" > < / a > Frequencies of numeric values< / h2 >
< p > Frequency tables can be created of any input.< / p >
< p > In case of numeric values (like integers, doubles, etc.) additional descriptive statistics will be calculated and shown into the header:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span class = "co" > # # get age distribution of unique patients< / span >
septic_patients %> %< span class = "st" > < / span >
< span class = "st" > < / span > < span class = "kw" > distinct< / span > (patient_id, < span class = "dt" > .keep_all =< / span > < span class = "ot" > TRUE< / span > ) %> %< span class = "st" > < / span >
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (age, < span class = "dt" > nmax =< / span > < span class = "dv" > 5< / span > , < span class = "dt" > header =< / span > < span class = "ot" > TRUE< / span > )< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > age< / code > < / strong > < br >
Class: numeric< br >
Length: 981 (of which NA: 0 = 0.00%)< br >
Unique: 73< / p >
< p > Mean: 71.08< br >
SD: 14.05 (CV: 0.20, MAD: 13.34)< br >
Five-Num: 14 | 63 | 74 | 82 | 97 (IQR: 19, CQV: 0.13)< br >
Outliers: 15 (unique count: 12)< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "right" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "right" > 83< / td >
< td align = "right" > 44< / td >
< td align = "right" > 4.5%< / td >
< td align = "right" > 44< / td >
< td align = "right" > 4.5%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "right" > 76< / td >
< td align = "right" > 43< / td >
< td align = "right" > 4.4%< / td >
< td align = "right" > 87< / td >
< td align = "right" > 8.9%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "right" > 75< / td >
< td align = "right" > 37< / td >
< td align = "right" > 3.8%< / td >
< td align = "right" > 124< / td >
< td align = "right" > 12.6%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "right" > 82< / td >
< td align = "right" > 33< / td >
< td align = "right" > 3.4%< / td >
< td align = "right" > 157< / td >
< td align = "right" > 16.0%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 5< / td >
< td align = "right" > 78< / td >
< td align = "right" > 32< / td >
< td align = "right" > 3.3%< / td >
< td align = "right" > 189< / td >
< td align = "right" > 19.3%< / td >
< / tr >
< / tbody >
< / table >
< p > (omitted 68 entries, n = 792 [80.7%])< / p >
< p > So the following properties are determined, where < code > NA< / code > values are always ignored:< / p >
< ul >
< li > < p > < strong > Mean< / strong > < / p > < / li >
< li > < p > < strong > Standard deviation< / strong > < / p > < / li >
< li > < p > < strong > Coefficient of variation< / strong > (CV), the standard deviation divided by the mean< / p > < / li >
< li > < p > < strong > Five numbers of Tukey< / strong > (min, Q1, median, Q3, max)< / p > < / li >
< li > < p > < strong > Coefficient of quartile variation< / strong > (CQV, sometimes called coefficient of dispersion), calculated as (Q3 - Q1) / (Q3 + Q1) using quantile with < code > type = 6< / code > as quantile algorithm to comply with SPSS standards< / p > < / li >
< li > < p > < strong > Outliers< / strong > (total count and unique count)< / p > < / li >
< / ul >
< p > So for example, the above frequency table quickly shows the median age of patients being 74.< / p >
< / div >
< div id = "frequencies-of-factors" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#frequencies-of-factors" class = "anchor" > < / a > Frequencies of factors< / h2 >
< p > To sort frequencies of factors on factor level instead of item count, use the < code > sort.count< / code > parameter.< / p >
< p > < code > sort.count< / code > is < code > TRUE< / code > by default. Compare this default behaviour…< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > septic_patients %> %
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (hospital_id)< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > hospital_id< / code > < / strong > < / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > D< / td >
< td align = "right" > 762< / td >
< td align = "right" > 38.1%< / td >
< td align = "right" > 762< / td >
< td align = "right" > 38.1%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > B< / td >
< td align = "right" > 663< / td >
< td align = "right" > 33.2%< / td >
< td align = "right" > 1,425< / td >
< td align = "right" > 71.3%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > A< / td >
< td align = "right" > 321< / td >
< td align = "right" > 16.1%< / td >
< td align = "right" > 1,746< / td >
< td align = "right" > 87.3%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > C< / td >
< td align = "right" > 254< / td >
< td align = "right" > 12.7%< / td >
< td align = "right" > 2,000< / td >
< td align = "right" > 100.0%< / td >
< / tr >
< / tbody >
< / table >
< p > … with this, where items are now sorted on count:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > septic_patients %> %
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (hospital_id, < span class = "dt" > sort.count =< / span > < span class = "ot" > FALSE< / span > )< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > hospital_id< / code > < / strong > < / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > A< / td >
< td align = "right" > 321< / td >
< td align = "right" > 16.1%< / td >
< td align = "right" > 321< / td >
< td align = "right" > 16.1%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > B< / td >
< td align = "right" > 663< / td >
< td align = "right" > 33.2%< / td >
< td align = "right" > 984< / td >
< td align = "right" > 49.2%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > C< / td >
< td align = "right" > 254< / td >
< td align = "right" > 12.7%< / td >
< td align = "right" > 1,238< / td >
< td align = "right" > 61.9%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > D< / td >
< td align = "right" > 762< / td >
< td align = "right" > 38.1%< / td >
< td align = "right" > 2,000< / td >
< td align = "right" > 100.0%< / td >
< / tr >
< / tbody >
< / table >
< p > All classes will be printed into the header (default is < code > FALSE< / code > when using markdown like this document). Variables with the new < code > rsi< / code > class of this AMR package are actually ordered factors and have three classes (look at < code > Class< / code > in the header):< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > septic_patients %> %
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (amox, < span class = "dt" > header =< / span > < span class = "ot" > TRUE< / span > )< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > amox< / code > < / strong > < br >
Class: factor > ordered > rsi (numeric)< br >
Levels: S < I < R< br >
Length: 2,000 (of which NA: 828 = 41.40%)< br >
Unique: 3< / p >
< p > %IR: 58.53% (ratio S : IR = 1.0 : 1.4)< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > R< / td >
< td align = "right" > 683< / td >
< td align = "right" > 58.3%< / td >
< td align = "right" > 683< / td >
< td align = "right" > 58.3%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > S< / td >
< td align = "right" > 486< / td >
< td align = "right" > 41.5%< / td >
< td align = "right" > 1,169< / td >
< td align = "right" > 99.7%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > I< / td >
< td align = "right" > 3< / td >
< td align = "right" > 0.3%< / td >
< td align = "right" > 1,172< / td >
< td align = "right" > 100.0%< / td >
< / tr >
< / tbody >
< / table >
< / div >
< div id = "frequencies-of-dates" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#frequencies-of-dates" class = "anchor" > < / a > Frequencies of dates< / h2 >
< p > Frequencies of dates will show the oldest and newest date in the data, and the amount of days between them:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > septic_patients %> %
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (date, < span class = "dt" > nmax =< / span > < span class = "dv" > 5< / span > , < span class = "dt" > header =< / span > < span class = "ot" > TRUE< / span > )< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > date< / code > < / strong > < br >
Class: Date (numeric)< br >
Length: 2,000 (of which NA: 0 = 0.00%)< br >
Unique: 1,140< / p >
< p > Oldest: 2 January 2002< br >
Newest: 28 December 2017 (+5,839)< br >
Median: 31 July 2009 (47.39%)< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > 2016-05-21< / td >
< td align = "right" > 10< / td >
< td align = "right" > 0.5%< / td >
< td align = "right" > 10< / td >
< td align = "right" > 0.5%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > 2004-11-15< / td >
< td align = "right" > 8< / td >
< td align = "right" > 0.4%< / td >
< td align = "right" > 18< / td >
< td align = "right" > 0.9%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > 2013-07-29< / td >
< td align = "right" > 8< / td >
< td align = "right" > 0.4%< / td >
< td align = "right" > 26< / td >
< td align = "right" > 1.3%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > 2017-06-12< / td >
< td align = "right" > 8< / td >
< td align = "right" > 0.4%< / td >
< td align = "right" > 34< / td >
< td align = "right" > 1.7%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 5< / td >
< td align = "left" > 2015-11-19< / td >
< td align = "right" > 7< / td >
< td align = "right" > 0.4%< / td >
< td align = "right" > 41< / td >
< td align = "right" > 2.1%< / td >
< / tr >
< / tbody >
< / table >
< p > (omitted 1,135 entries, n = 1,959 [98.0%])< / p >
< / div >
< div id = "assigning-a-frequency-table-to-an-object" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#assigning-a-frequency-table-to-an-object" class = "anchor" > < / a > Assigning a frequency table to an object< / h2 >
< p > A frequency table is actaually a regular < code > data.frame< / code > , with the exception that it contains an additional class.< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > my_df < -< span class = "st" > < / span > septic_patients %> %< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (age)
< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/class" > class< / a > < / span > (my_df)< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > [1] “frequency_tbl” “data.frame”< / p >
< p > Because of this additional class, a frequency table prints like the examples above. But the object itself contains the complete table without a row limitation:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/dim" > dim< / a > < / span > (my_df)< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > [1] 74 5< / p >
< / div >
< div id = "additional-parameters" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#additional-parameters" class = "anchor" > < / a > Additional parameters< / h2 >
< div id = "parameter-na-rm" class = "section level3" >
< h3 class = "hasAnchor" >
< a href = "#parameter-na-rm" class = "anchor" > < / a > Parameter < code > na.rm< / code >
< / h3 >
< p > With the < code > na.rm< / code > parameter (defaults to < code > TRUE< / code > , but they will always be shown into the header), you can include < code > NA< / code > values in the frequency table:< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > septic_patients %> %
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (amox, < span class = "dt" > na.rm =< / span > < span class = "ot" > FALSE< / span > )< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > amox< / code > < / strong > < / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > (NA)< / td >
< td align = "right" > 828< / td >
< td align = "right" > 41.4%< / td >
< td align = "right" > 828< / td >
< td align = "right" > 41.4%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > R< / td >
< td align = "right" > 683< / td >
< td align = "right" > 34.2%< / td >
< td align = "right" > 1,511< / td >
< td align = "right" > 75.6%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > S< / td >
< td align = "right" > 486< / td >
< td align = "right" > 24.3%< / td >
< td align = "right" > 1,997< / td >
< td align = "right" > 99.9%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > I< / td >
< td align = "right" > 3< / td >
< td align = "right" > 0.2%< / td >
< td align = "right" > 2,000< / td >
< td align = "right" > 100.0%< / td >
< / tr >
< / tbody >
< / table >
< / div >
< div id = "parameter-row-names" class = "section level3" >
< h3 class = "hasAnchor" >
< a href = "#parameter-row-names" class = "anchor" > < / a > Parameter < code > row.names< / code >
< / h3 >
< p > The default frequency tables shows row indices. To remove them, use < code > row.names = FALSE< / code > :< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > septic_patients %> %
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (hospital_id, < span class = "dt" > row.names =< / span > < span class = "ot" > FALSE< / span > )< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > hospital_id< / code > < / strong > < / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > D< / td >
< td align = "right" > 762< / td >
< td align = "right" > 38.1%< / td >
< td align = "right" > 762< / td >
< td align = "right" > 38.1%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > B< / td >
< td align = "right" > 663< / td >
< td align = "right" > 33.2%< / td >
< td align = "right" > 1,425< / td >
< td align = "right" > 71.3%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > A< / td >
< td align = "right" > 321< / td >
< td align = "right" > 16.1%< / td >
< td align = "right" > 1,746< / td >
< td align = "right" > 87.3%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > C< / td >
< td align = "right" > 254< / td >
< td align = "right" > 12.7%< / td >
< td align = "right" > 2,000< / td >
< td align = "right" > 100.0%< / td >
< / tr >
< / tbody >
< / table >
< / div >
< div id = "parameter-markdown" class = "section level3" >
< h3 class = "hasAnchor" >
< a href = "#parameter-markdown" class = "anchor" > < / a > Parameter < code > markdown< / code >
< / h3 >
< p > The < code > markdown< / code > parameter is < code > TRUE< / code > at default in non-interactive sessions, like in reports created with R Markdown. This will always print all rows, unless < code > nmax< / code > is set.< / p >
2019-01-04 09:49:42 +01:00
< div class = "sourceCode" > < pre class = "sourceCode r" > < code class = "sourceCode r" > septic_patients %> %
< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/freq.html" > freq< / a > < / span > (hospital_id, < span class = "dt" > markdown =< / span > < span class = "ot" > TRUE< / span > )< / code > < / pre > < / div >
2019-01-02 23:24:07 +01:00
< p > < strong > Frequency table of < code > hospital_id< / code > < / strong > < / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > < / th >
< th align = "left" > Item< / th >
< th align = "right" > Count< / th >
< th align = "right" > Percent< / th >
< th align = "right" > Cum. Count< / th >
< th align = "right" > Cum. Percent< / th >
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > D< / td >
< td align = "right" > 762< / td >
< td align = "right" > 38.1%< / td >
< td align = "right" > 762< / td >
< td align = "right" > 38.1%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > B< / td >
< td align = "right" > 663< / td >
< td align = "right" > 33.2%< / td >
< td align = "right" > 1,425< / td >
< td align = "right" > 71.3%< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > A< / td >
< td align = "right" > 321< / td >
< td align = "right" > 16.1%< / td >
< td align = "right" > 1,746< / td >
< td align = "right" > 87.3%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > C< / td >
< td align = "right" > 254< / td >
< td align = "right" > 12.7%< / td >
< td align = "right" > 2,000< / td >
< td align = "right" > 100.0%< / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
< div id = "tocnav" >
< h2 class = "hasAnchor" >
< a href = "#tocnav" class = "anchor" > < / a > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
< li > < a href = "#introduction" > Introduction< / a > < / li >
< li > < a href = "#frequencies-of-one-variable" > Frequencies of one variable< / a > < / li >
< li > < a href = "#frequencies-of-more-than-one-variable" > Frequencies of more than one variable< / a > < / li >
< li > < a href = "#frequencies-of-numeric-values" > Frequencies of numeric values< / a > < / li >
< li > < a href = "#frequencies-of-factors" > Frequencies of factors< / a > < / li >
< li > < a href = "#frequencies-of-dates" > Frequencies of dates< / a > < / li >
< li > < a href = "#assigning-a-frequency-table-to-an-object" > Assigning a frequency table to an object< / a > < / li >
< li > < a href = "#additional-parameters" > Additional parameters< / a > < / li >
< / ul >
< / div >
< / div >
< / div >
< footer > < div class = "copyright" >
< 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/c.glasner/" > Corinna Glasner< / 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 > .< / p >
< / div >
< div class = "pkgdown" >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.3.0.< / p >
< / div >
< / footer >
< / div >
< 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 >
< / body >
< / html >
