Format a summariseOverlapCohort result into a visual table. — tableCohortOverlap • PatientProfiles

`r lifecycle::badge("deprecated")`

Usage

tableCohortOverlap(
  result,
  type = "gt",
  formatEstimateName = c(`N (%)` = "<count> (<percentage>%)"),
  header = c("strata"),
  split = c("group", "strata", "additional"),
  groupColumn = NULL,
  minCellCount = 5,
  excludeColumns = c("result_id", "estimate_type"),
  .options = list()
)

Arguments

result: A summariseOverlapCohort result.
type: Type of desired formatted table, possibilities: "gt", "flextable", "tibble".
formatEstimateName: Named list of estimate name's to join, sorted by computation order. Indicate estimate_name's between <...>.
header: A vector containing which elements should go into the header in order. Allowed are: `cdm_name`, `group`, `strata`, `additional`, `variable`, `estimate`, `settings`.
split: A vector containing the name-level groups to split ("group", "strata", "additional"), or an empty character vector to not split.
groupColumn: Column to use as group labels.
minCellCount: Counts below which results will be clouded.
excludeColumns: Columns to drop from the output table.
.options: Named list with additional formatting options. PatientProfiles::optionsTableCohortOverlap() shows allowed arguments and their default values.

Value

A formatted table of the summariseOverlapCohort result.

Examples

# \donttest{
library(PatientProfiles)
cdm <- PatientProfiles::mockPatientProfiles()
overlap <- summariseCohortOverlap(cdm$cohort2)
tableCohortOverlap(overlap)
#> ! Results have not been suppressed.
#> <div id="ynegttjhan" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
#>   <style>#ynegttjhan 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;
#> }
#> 
#> #ynegttjhan thead, #ynegttjhan tbody, #ynegttjhan tfoot, #ynegttjhan tr, #ynegttjhan td, #ynegttjhan th {
#>   border-style: none;
#> }
#> 
#> #ynegttjhan p {
#>   margin: 0;
#>   padding: 0;
#> }
#> 
#> #ynegttjhan .gt_table {
#>   display: table;
#>   border-collapse: collapse;
#>   line-height: normal;
#>   margin-left: auto;
#>   margin-right: auto;
#>   color: #333333;
#>   font-size: 16px;
#>   font-weight: normal;
#>   font-style: normal;
#>   background-color: #FFFFFF;
#>   width: auto;
#>   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;
#> }
#> 
#> #ynegttjhan .gt_caption {
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .gt_bottom_border {
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .gt_column_spanner_outer:first-child {
#>   padding-left: 0;
#> }
#> 
#> #ynegttjhan .gt_column_spanner_outer:last-child {
#>   padding-right: 0;
#> }
#> 
#> #ynegttjhan .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%;
#> }
#> 
#> #ynegttjhan .gt_spanner_row {
#>   border-bottom-style: hidden;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .gt_from_md > :first-child {
#>   margin-top: 0;
#> }
#> 
#> #ynegttjhan .gt_from_md > :last-child {
#>   margin-bottom: 0;
#> }
#> 
#> #ynegttjhan .gt_row {
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .gt_row_group_first td {
#>   border-top-width: 2px;
#> }
#> 
#> #ynegttjhan .gt_row_group_first th {
#>   border-top-width: 2px;
#> }
#> 
#> #ynegttjhan .gt_summary_row {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   text-transform: inherit;
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ynegttjhan .gt_first_summary_row {
#>   border-top-style: solid;
#>   border-top-color: #D3D3D3;
#> }
#> 
#> #ynegttjhan .gt_first_summary_row.thick {
#>   border-top-width: 2px;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .gt_grand_summary_row {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   text-transform: inherit;
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .gt_striped {
#>   background-color: rgba(128, 128, 128, 0.05);
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .gt_footnote {
#>   margin: 0px;
#>   font-size: 90%;
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ynegttjhan .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;
#> }
#> 
#> #ynegttjhan .gt_sourcenote {
#>   font-size: 90%;
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ynegttjhan .gt_left {
#>   text-align: left;
#> }
#> 
#> #ynegttjhan .gt_center {
#>   text-align: center;
#> }
#> 
#> #ynegttjhan .gt_right {
#>   text-align: right;
#>   font-variant-numeric: tabular-nums;
#> }
#> 
#> #ynegttjhan .gt_font_normal {
#>   font-weight: normal;
#> }
#> 
#> #ynegttjhan .gt_font_bold {
#>   font-weight: bold;
#> }
#> 
#> #ynegttjhan .gt_font_italic {
#>   font-style: italic;
#> }
#> 
#> #ynegttjhan .gt_super {
#>   font-size: 65%;
#> }
#> 
#> #ynegttjhan .gt_footnote_marks {
#>   font-size: 75%;
#>   vertical-align: 0.4em;
#>   position: initial;
#> }
#> 
#> #ynegttjhan .gt_asterisk {
#>   font-size: 100%;
#>   vertical-align: 0;
#> }
#> 
#> #ynegttjhan .gt_indent_1 {
#>   text-indent: 5px;
#> }
#> 
#> #ynegttjhan .gt_indent_2 {
#>   text-indent: 10px;
#> }
#> 
#> #ynegttjhan .gt_indent_3 {
#>   text-indent: 15px;
#> }
#> 
#> #ynegttjhan .gt_indent_4 {
#>   text-indent: 20px;
#> }
#> 
#> #ynegttjhan .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" style="text-align: center; font-weight: bold;" scope="col" id="CDM name">CDM name</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="text-align: center; font-weight: bold;" scope="col" id="Cohort name reference">Cohort name reference</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="text-align: center; font-weight: bold;" scope="col" id="Cohort name comparator">Cohort name comparator</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" style="text-align: center; font-weight: bold;" scope="col" id="Estimate name">Estimate name</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="background-color: #E1E1E1; text-align: center; font-weight: bold;" scope="col" id="Comparator">Comparator</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="background-color: #E1E1E1; text-align: center; font-weight: bold;" scope="col" id="Overlap">Overlap</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" style="background-color: #E1E1E1; text-align: center; font-weight: bold;" scope="col" id="Reference">Reference</th>
#>     </tr>
#>   </thead>
#>   <tbody class="gt_table_body">
#>     <tr><td headers="CDM name" class="gt_row gt_left" style="text-align: left;">PP_MOCK</td>
#> <td headers="Cohort name reference" class="gt_row gt_left" style="text-align: left; border-left-width: 1px; border-left-style: solid; border-left-color: #D3D3D3; border-right-width: 1px; border-right-style: solid; border-right-color: #D3D3D3; border-top-width: 1px; border-top-style: solid; border-top-color: #D3D3D3; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;">Cohort 1</td>
#> <td headers="Cohort name comparator" class="gt_row gt_left" style="text-align: left; border-left-width: 1px; border-left-style: solid; border-left-color: #D3D3D3; border-right-width: 1px; border-right-style: solid; border-right-color: #D3D3D3; border-top-width: 1px; border-top-style: solid; border-top-color: #D3D3D3; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;">Cohort 2</td>
#> <td headers="Estimate name" class="gt_row gt_left" style="text-align: left; border-left-width: 1px; border-left-style: solid; border-left-color: #D3D3D3; border-right-width: 1px; border-right-style: solid; border-right-color: #D3D3D3; border-top-width: 1px; border-top-style: solid; border-top-color: #D3D3D3; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;">N (%)</td>
#> <td headers="[header_level]Comparator" class="gt_row gt_right" style="text-align: right; border-left-width: 1px; border-left-style: solid; border-left-color: #D3D3D3; border-right-width: 1px; border-right-style: solid; border-right-color: #D3D3D3; border-top-width: 1px; border-top-style: solid; border-top-color: #D3D3D3; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;">0 (0.00%)</td>
#> <td headers="[header_level]Overlap" class="gt_row gt_right" style="text-align: right; border-left-width: 1px; border-left-style: solid; border-left-color: #D3D3D3; border-right-width: 1px; border-right-style: solid; border-right-color: #D3D3D3; border-top-width: 1px; border-top-style: solid; border-top-color: #D3D3D3; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;">1 (100.00%)</td>
#> <td headers="[header_level]Reference" class="gt_row gt_right" style="text-align: right;">0 (0.00%)</td></tr>
#>   </tbody>
#>   
#>   
#> </table>
#> </div>
CDMConnector::cdmDisconnect(cdm = cdm)
# }