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Produce a summary HTML table of key demographic variables

Source: R/kable_one.R
kable_one.Rd

Sometimes it is desirable to produce a summary of key demographic variables for presentation. The table_one and kable_one methods are a quick way to do so – they not only summarize key demographic variables from SummarizedExperiment-class object(s) in the HMP16SData package but remove abbreviations and underscores in column and variable names that might otherwise be ambigious. The table_one method returns a tidy (i.e. one sample observation per line) data.frame object or a named list of tidy data.frame objects. The kable_one method can then be used to produce a publication-ready HTML table that could, for example, be pasted into a word processor.

Usage

kable_one(x, significant_figures = 2)

Arguments

x

A data.frame object or a named list of data.frame objects returned from the table_one method

significant_figures

The number of significant figures to be used for decimals in the HTML table; if no value is specified, the default is 2

Value

A summary HTML table of key demographic variables

See also

table_one

Examples

V13() %>%
    table_one() %>%
    kable_one()
#> see ?HMP16SData and browseVignettes('HMP16SData') for documentation
#> loading from cache
#> <table class="table table-condensed" style="margin-left: auto; margin-right: auto;">
#>  <thead>
#>   <tr>
#>    <th style="text-align:left;border: none; color: #000000;border-bottom: thin solid; text-align: center;">  </th>
#>    <th style="text-align:right;border: none; color: #000000;border-bottom: thin solid; text-align: center;"> N </th>
#>    <th style="text-align:right;border: none; color: #000000;border-bottom: thin solid; text-align: center;"> % </th>
#>   </tr>
#>  </thead>
#> <tbody>
#>   <tr grouplength="3"><td colspan="3" style="border: none; color: #000000;"><strong>Visit Number</strong></td></tr>
#> <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> One </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 1,642 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 56.66 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Two </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 1,244 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 42.93 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Three </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 12 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 0.41 </td>
#>   </tr>
#>   <tr grouplength="2"><td colspan="3" style="border: none; color: #000000;"><strong>Sex</strong></td></tr>
#> <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Female </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 1,521 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 52.48 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Male </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 1,377 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 47.52 </td>
#>   </tr>
#>   <tr grouplength="12"><td colspan="3" style="border: none; color: #000000;"><strong>Run Center</strong></td></tr>
#> <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Genome Sequencing Center at Washington University </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 1,717 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 59.25 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> J. Craig Venter Institute </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 506 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 17.46 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Baylor College of Medicine </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 289 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 9.97 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> J. Craig Venter Institute, Genome Sequencing Center at Washington University </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 97 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 3.35 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Baylor College of Medicine, Genome Sequencing Center at Washington University </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 91 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 3.14 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> J. Craig Venter Institute, Broad Institute </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 86 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 2.97 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Baylor College of Medicine, Broad Institute </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 76 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 2.62 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Baylor College of Medicine, J. Craig Venter Institute </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 15 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 0.52 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Broad Institute, Baylor College of Medicine </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 13 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 0.45 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Genome Sequencing Center at Washington University, Baylor College of Medicine </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 0.21 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Genome Sequencing Center at Washington University, J. Craig Venter Institute </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 1 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 0.03 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Missing </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 1 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 0.03 </td>
#>   </tr>
#>   <tr grouplength="5"><td colspan="3" style="border: none; color: #000000;"><strong>HMP Body Site</strong></td></tr>
#> <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Oral </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 1,622 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 55.97 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Skin </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 664 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 22.91 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Urogenital Tract </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 264 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 9.11 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Gastrointestinal Tract </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 187 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.45 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Airways </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 161 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 5.56 </td>
#>   </tr>
#>   <tr grouplength="18"><td colspan="3" style="border: none; color: #000000;"><strong>HMP Body Subsite</strong></td></tr>
#> <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Tongue Dorsum </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 190 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.56 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Supragingival Plaque </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 189 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.52 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Right Retroauricular Crease </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 187 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.45 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Stool </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 187 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.45 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Left Retroauricular Crease </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 186 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.42 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Palatine Tonsils </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 186 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.42 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Buccal Mucosa </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 183 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.31 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Subgingival Plaque </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 183 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.31 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Attached Keratinized Gingiva </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 181 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.25 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Hard Palate </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 178 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 6.14 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Throat </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 170 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 5.87 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Saliva </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 162 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 5.59 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Anterior Nares </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 161 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 5.56 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Right Antecubital Fossa </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 146 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 5.04 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Left Antecubital Fossa </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 145 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 5.00 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Mid Vagina </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 89 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 3.07 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;" indentlevel="1"> Posterior Fornix </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 88 </td>
#>    <td style="text-align:right;border: none; color: #000000;"> 3.04 </td>
#>   </tr>
#>   <tr>
#>    <td style="text-align:left;padding-left: 2em;border: none; color: #000000;border-bottom: thin solid;" indentlevel="1"> Vaginal Introitus </td>
#>    <td style="text-align:right;border: none; color: #000000;border-bottom: thin solid;"> 87 </td>
#>    <td style="text-align:right;border: none; color: #000000;border-bottom: thin solid;"> 3.00 </td>
#>   </tr>
#> </tbody>
#> </table>