Takes an object of class smdi and styles it to a publication-ready gt table

This function takes either an object of class smdi or data.frame or tibble as input and styles it to a publication-ready table based on the gt package. The output is of class gt and can take further gt-based arguments for customization.

Usage

smdi_style_gt(
  smdi_object = NULL,
  include_little = TRUE,
  font_size = 13,
  tbl_width = 800
)

Arguments

smdi_object: object of class "smdi" or data.frame/tibble
include_little: can be logical (TRUE/FALSE) for displaying Little's p-value that is part of an "smdi" object or a separate object of class "little"
font_size: integer to determine table font size
tbl_width: integer to determine table width

Value

returns a formatted gt table object

Details

Examples

library(smdi)
library(dplyr)

smdi_diagnose(
  data = smdi_data,
  covar = "egfr_cat",
  model = "cox",
  form_lhs = "Surv(eventtime, status)"
  ) %>%
smdi_style_gt()
#> <div id="ochcnkhjza" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
#>   <style>#ochcnkhjza table {
#>   font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
#>   -webkit-font-smoothing: antialiased;
#>   -moz-osx-font-smoothing: grayscale;
#> }
#> 
#> #ochcnkhjza thead, #ochcnkhjza tbody, #ochcnkhjza tfoot, #ochcnkhjza tr, #ochcnkhjza td, #ochcnkhjza th {
#>   border-style: none;
#> }
#> 
#> #ochcnkhjza p {
#>   margin: 0;
#>   padding: 0;
#> }
#> 
#> #ochcnkhjza .gt_table {
#>   display: table;
#>   border-collapse: collapse;
#>   line-height: normal;
#>   margin-left: auto;
#>   margin-right: auto;
#>   color: #333333;
#>   font-size: 13px;
#>   font-weight: normal;
#>   font-style: normal;
#>   background-color: #FFFFFF;
#>   width: 800px;
#>   border-top-style: solid;
#>   border-top-width: 2px;
#>   border-top-color: #A8A8A8;
#>   border-right-style: none;
#>   border-right-width: 2px;
#>   border-right-color: #D3D3D3;
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #A8A8A8;
#>   border-left-style: none;
#>   border-left-width: 2px;
#>   border-left-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_caption {
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#> }
#> 
#> #ochcnkhjza .gt_title {
#>   color: #333333;
#>   font-size: 125%;
#>   font-weight: initial;
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   border-bottom-color: #FFFFFF;
#>   border-bottom-width: 0;
#> }
#> 
#> #ochcnkhjza .gt_subtitle {
#>   color: #333333;
#>   font-size: 85%;
#>   font-weight: initial;
#>   padding-top: 3px;
#>   padding-bottom: 5px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   border-top-color: #FFFFFF;
#>   border-top-width: 0;
#> }
#> 
#> #ochcnkhjza .gt_heading {
#>   background-color: #FFFFFF;
#>   text-align: center;
#>   border-bottom-color: #FFFFFF;
#>   border-left-style: none;
#>   border-left-width: 1px;
#>   border-left-color: #D3D3D3;
#>   border-right-style: none;
#>   border-right-width: 1px;
#>   border-right-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_bottom_border {
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_col_headings {
#>   border-top-style: solid;
#>   border-top-width: 2px;
#>   border-top-color: #D3D3D3;
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#>   border-left-style: none;
#>   border-left-width: 1px;
#>   border-left-color: #D3D3D3;
#>   border-right-style: none;
#>   border-right-width: 1px;
#>   border-right-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_col_heading {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   font-size: 100%;
#>   font-weight: normal;
#>   text-transform: inherit;
#>   border-left-style: none;
#>   border-left-width: 1px;
#>   border-left-color: #D3D3D3;
#>   border-right-style: none;
#>   border-right-width: 1px;
#>   border-right-color: #D3D3D3;
#>   vertical-align: bottom;
#>   padding-top: 5px;
#>   padding-bottom: 6px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   overflow-x: hidden;
#> }
#> 
#> #ochcnkhjza .gt_column_spanner_outer {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   font-size: 100%;
#>   font-weight: normal;
#>   text-transform: inherit;
#>   padding-top: 0;
#>   padding-bottom: 0;
#>   padding-left: 4px;
#>   padding-right: 4px;
#> }
#> 
#> #ochcnkhjza .gt_column_spanner_outer:first-child {
#>   padding-left: 0;
#> }
#> 
#> #ochcnkhjza .gt_column_spanner_outer:last-child {
#>   padding-right: 0;
#> }
#> 
#> #ochcnkhjza .gt_column_spanner {
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#>   vertical-align: bottom;
#>   padding-top: 5px;
#>   padding-bottom: 5px;
#>   overflow-x: hidden;
#>   display: inline-block;
#>   width: 100%;
#> }
#> 
#> #ochcnkhjza .gt_spanner_row {
#>   border-bottom-style: hidden;
#> }
#> 
#> #ochcnkhjza .gt_group_heading {
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   font-size: 100%;
#>   font-weight: initial;
#>   text-transform: inherit;
#>   border-top-style: solid;
#>   border-top-width: 2px;
#>   border-top-color: #D3D3D3;
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#>   border-left-style: none;
#>   border-left-width: 1px;
#>   border-left-color: #D3D3D3;
#>   border-right-style: none;
#>   border-right-width: 1px;
#>   border-right-color: #D3D3D3;
#>   vertical-align: middle;
#>   text-align: left;
#> }
#> 
#> #ochcnkhjza .gt_empty_group_heading {
#>   padding: 0.5px;
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   font-size: 100%;
#>   font-weight: initial;
#>   border-top-style: solid;
#>   border-top-width: 2px;
#>   border-top-color: #D3D3D3;
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#>   vertical-align: middle;
#> }
#> 
#> #ochcnkhjza .gt_from_md > :first-child {
#>   margin-top: 0;
#> }
#> 
#> #ochcnkhjza .gt_from_md > :last-child {
#>   margin-bottom: 0;
#> }
#> 
#> #ochcnkhjza .gt_row {
#>   padding-top: 3px;
#>   padding-bottom: 3px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   margin: 10px;
#>   border-top-style: solid;
#>   border-top-width: 1px;
#>   border-top-color: #D3D3D3;
#>   border-left-style: none;
#>   border-left-width: 1px;
#>   border-left-color: #D3D3D3;
#>   border-right-style: none;
#>   border-right-width: 1px;
#>   border-right-color: #D3D3D3;
#>   vertical-align: middle;
#>   overflow-x: hidden;
#> }
#> 
#> #ochcnkhjza .gt_stub {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   font-size: 100%;
#>   font-weight: initial;
#>   text-transform: inherit;
#>   border-right-style: solid;
#>   border-right-width: 2px;
#>   border-right-color: #D3D3D3;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ochcnkhjza .gt_stub_row_group {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   font-size: 100%;
#>   font-weight: initial;
#>   text-transform: inherit;
#>   border-right-style: solid;
#>   border-right-width: 2px;
#>   border-right-color: #D3D3D3;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   vertical-align: top;
#> }
#> 
#> #ochcnkhjza .gt_row_group_first td {
#>   border-top-width: 2px;
#> }
#> 
#> #ochcnkhjza .gt_row_group_first th {
#>   border-top-width: 2px;
#> }
#> 
#> #ochcnkhjza .gt_summary_row {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   text-transform: inherit;
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ochcnkhjza .gt_first_summary_row {
#>   border-top-style: solid;
#>   border-top-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_first_summary_row.thick {
#>   border-top-width: 2px;
#> }
#> 
#> #ochcnkhjza .gt_last_summary_row {
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_grand_summary_row {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   text-transform: inherit;
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ochcnkhjza .gt_first_grand_summary_row {
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   border-top-style: double;
#>   border-top-width: 6px;
#>   border-top-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_last_grand_summary_row_top {
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#>   border-bottom-style: double;
#>   border-bottom-width: 6px;
#>   border-bottom-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_striped {
#>   background-color: rgba(128, 128, 128, 0.05);
#> }
#> 
#> #ochcnkhjza .gt_table_body {
#>   border-top-style: solid;
#>   border-top-width: 2px;
#>   border-top-color: #D3D3D3;
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_footnotes {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   border-bottom-style: none;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#>   border-left-style: none;
#>   border-left-width: 2px;
#>   border-left-color: #D3D3D3;
#>   border-right-style: none;
#>   border-right-width: 2px;
#>   border-right-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_footnote {
#>   margin: 0px;
#>   font-size: 90%;
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ochcnkhjza .gt_sourcenotes {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   border-bottom-style: none;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#>   border-left-style: none;
#>   border-left-width: 2px;
#>   border-left-color: #D3D3D3;
#>   border-right-style: none;
#>   border-right-width: 2px;
#>   border-right-color: #D3D3D3;
#> }
#> 
#> #ochcnkhjza .gt_sourcenote {
#>   font-size: 90%;
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ochcnkhjza .gt_left {
#>   text-align: left;
#> }
#> 
#> #ochcnkhjza .gt_center {
#>   text-align: center;
#> }
#> 
#> #ochcnkhjza .gt_right {
#>   text-align: right;
#>   font-variant-numeric: tabular-nums;
#> }
#> 
#> #ochcnkhjza .gt_font_normal {
#>   font-weight: normal;
#> }
#> 
#> #ochcnkhjza .gt_font_bold {
#>   font-weight: bold;
#> }
#> 
#> #ochcnkhjza .gt_font_italic {
#>   font-style: italic;
#> }
#> 
#> #ochcnkhjza .gt_super {
#>   font-size: 65%;
#> }
#> 
#> #ochcnkhjza .gt_footnote_marks {
#>   font-size: 75%;
#>   vertical-align: 0.4em;
#>   position: initial;
#> }
#> 
#> #ochcnkhjza .gt_asterisk {
#>   font-size: 100%;
#>   vertical-align: 0;
#> }
#> 
#> #ochcnkhjza .gt_indent_1 {
#>   text-indent: 5px;
#> }
#> 
#> #ochcnkhjza .gt_indent_2 {
#>   text-indent: 10px;
#> }
#> 
#> #ochcnkhjza .gt_indent_3 {
#>   text-indent: 15px;
#> }
#> 
#> #ochcnkhjza .gt_indent_4 {
#>   text-indent: 20px;
#> }
#> 
#> #ochcnkhjza .gt_indent_5 {
#>   text-indent: 25px;
#> }
#> </style>
#>   <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
#>   <thead>
#>     <tr class="gt_col_headings">
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Covariate">Covariate</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="ASMD (min/max)&lt;span class=&quot;gt_footnote_marks&quot; style=&quot;white-space:nowrap;font-style:italic;font-weight:normal;&quot;&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt;">ASMD (min/max)<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span></th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="p Hotelling&lt;span class=&quot;gt_footnote_marks&quot; style=&quot;white-space:nowrap;font-style:italic;font-weight:normal;&quot;&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt;">p Hotelling<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span></th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="AUC&lt;span class=&quot;gt_footnote_marks&quot; style=&quot;white-space:nowrap;font-style:italic;font-weight:normal;&quot;&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/span&gt;">AUC<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>2</sup></span></th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="beta univariate (95% CI)&lt;span class=&quot;gt_footnote_marks&quot; style=&quot;white-space:nowrap;font-style:italic;font-weight:normal;&quot;&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt;">beta univariate (95% CI)<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>3</sup></span></th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="beta (95% CI)&lt;span class=&quot;gt_footnote_marks&quot; style=&quot;white-space:nowrap;font-style:italic;font-weight:normal;&quot;&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt;">beta (95% CI)<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>3</sup></span></th>
#>     </tr>
#>   </thead>
#>   <tbody class="gt_table_body">
#>     <tr><td headers="covariate" class="gt_row gt_left">egfr_cat</td>
#> <td headers="asmd_median_min_max" class="gt_row gt_left">0.243 (0.010, 0.485)</td>
#> <td headers="hotteling_p" class="gt_row gt_left">&lt;.001</td>
#> <td headers="rf_auc" class="gt_row gt_left">0.629</td>
#> <td headers="estimate_univariate" class="gt_row gt_left">0.06 (95% CI -0.03, 0.15)</td>
#> <td headers="estimate_adjusted" class="gt_row gt_left">-0.01 (95% CI -0.10, 0.09)</td></tr>
#>   </tbody>
#>   
#>   <tfoot class="gt_footnotes">
#>     <tr>
#>       <td class="gt_footnote" colspan="6"> p little: &lt;.001,  Abbreviations: ASMD = Median absolute standardized mean difference across all covariates, AUC = Area under the curve, beta = beta coefficient, CI = Confidence interval, max = Maximum, min = Minimum</td>
#>     </tr>
#>     <tr>
#>       <td class="gt_footnote" colspan="6"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span> Group 1 diagnostic: Differences in patient characteristics between patients with and without covariate</td>
#>     </tr>
#>     <tr>
#>       <td class="gt_footnote" colspan="6"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>2</sup></span> Group 2 diagnostic: Ability to predict missingness</td>
#>     </tr>
#>     <tr>
#>       <td class="gt_footnote" colspan="6"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>3</sup></span> Group 3 diagnostic: Assessment if missingness is associated with the outcome (univariate, adjusted)</td>
#>     </tr>
#>   </tfoot>
#> </table>
#> </div>

Takes an object of class smdi and styles it to a publication-ready gt table

Usage

Arguments

Value

Details

See also

Examples