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Format a summariseCohortIntersect result into a visual table.

Source: R/tableSummarised.R
tableCohortIntersect.Rd

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

Usage

tableCohortIntersect(
  result,
  type = "gt",
  formatEstimateName = c(`N (%)` = "<count> (<percentage>%)", `Median [Q25 - Q75]` =
    "<median> [<q25> - <q75>]", `Mean (SD)` = "<mean> (<sd>)", Range = "<min> to <max>"),
  header = c("group"),
  split = c("group", "strata"),
  groupColumn = NULL,
  minCellCount = 5,
  excludeColumns = c("result_id", "estimate_type", "additional_name", "additional_level"),
  .options = list()
)

Arguments

result

A result from summariseCohortIntersect.

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::optionsTableCharacteristics() shows allowed arguments and their default values.

Value

A table with a formatted version of a summariseCohortIntersect result.

Examples

# \donttest{
library(PatientProfiles)

cdm <- mockPatientProfiles()

cdm$cohort1 |>
 summariseCohortIntersect(
  cohortIntersect = list(
    "Medications in the prior year" = list(
      targetCohortTable = "cohort2", value = "flag", window = c(-365, -1)
    )
   )
  ) |>
  tableCohortIntersect()
#> ℹ adding cohort intersect columns for table: cohort2
#> ℹ summarising data
#> ℹ The following estimates will be computed:
#> • flag_variable_00053_variable_00052: count, percentage
#> • flag_variable_00054_variable_00052: count, percentage
#> → Start summary of data, at 2024-05-11 12:04:50.879447
#> ✔ Summary finished, at 2024-05-11 12:04:51.37025
#> ✔ summariseCharacteristics finished!
#> ! Results have not been suppressed.
#> ℹ <median> [<q25> - <q75>] has not been formatted.
#> ℹ <mean> (<sd>) has not been formatted.
#> ℹ <min> to <max> has not been formatted.
#> <div id="ygftpbmcjf" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
#>   <style>#ygftpbmcjf 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;
#> }
#> 
#> #ygftpbmcjf thead, #ygftpbmcjf tbody, #ygftpbmcjf tfoot, #ygftpbmcjf tr, #ygftpbmcjf td, #ygftpbmcjf th {
#>   border-style: none;
#> }
#> 
#> #ygftpbmcjf p {
#>   margin: 0;
#>   padding: 0;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_caption {
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_bottom_border {
#>   border-bottom-style: solid;
#>   border-bottom-width: 2px;
#>   border-bottom-color: #D3D3D3;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_column_spanner_outer:first-child {
#>   padding-left: 0;
#> }
#> 
#> #ygftpbmcjf .gt_column_spanner_outer:last-child {
#>   padding-right: 0;
#> }
#> 
#> #ygftpbmcjf .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%;
#> }
#> 
#> #ygftpbmcjf .gt_spanner_row {
#>   border-bottom-style: hidden;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_from_md > :first-child {
#>   margin-top: 0;
#> }
#> 
#> #ygftpbmcjf .gt_from_md > :last-child {
#>   margin-bottom: 0;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_row_group_first td {
#>   border-top-width: 2px;
#> }
#> 
#> #ygftpbmcjf .gt_row_group_first th {
#>   border-top-width: 2px;
#> }
#> 
#> #ygftpbmcjf .gt_summary_row {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   text-transform: inherit;
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ygftpbmcjf .gt_first_summary_row {
#>   border-top-style: solid;
#>   border-top-color: #D3D3D3;
#> }
#> 
#> #ygftpbmcjf .gt_first_summary_row.thick {
#>   border-top-width: 2px;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_grand_summary_row {
#>   color: #333333;
#>   background-color: #FFFFFF;
#>   text-transform: inherit;
#>   padding-top: 8px;
#>   padding-bottom: 8px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_striped {
#>   background-color: rgba(128, 128, 128, 0.05);
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_footnote {
#>   margin: 0px;
#>   font-size: 90%;
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ygftpbmcjf .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;
#> }
#> 
#> #ygftpbmcjf .gt_sourcenote {
#>   font-size: 90%;
#>   padding-top: 4px;
#>   padding-bottom: 4px;
#>   padding-left: 5px;
#>   padding-right: 5px;
#> }
#> 
#> #ygftpbmcjf .gt_left {
#>   text-align: left;
#> }
#> 
#> #ygftpbmcjf .gt_center {
#>   text-align: center;
#> }
#> 
#> #ygftpbmcjf .gt_right {
#>   text-align: right;
#>   font-variant-numeric: tabular-nums;
#> }
#> 
#> #ygftpbmcjf .gt_font_normal {
#>   font-weight: normal;
#> }
#> 
#> #ygftpbmcjf .gt_font_bold {
#>   font-weight: bold;
#> }
#> 
#> #ygftpbmcjf .gt_font_italic {
#>   font-style: italic;
#> }
#> 
#> #ygftpbmcjf .gt_super {
#>   font-size: 65%;
#> }
#> 
#> #ygftpbmcjf .gt_footnote_marks {
#>   font-size: 75%;
#>   vertical-align: 0.4em;
#>   position: initial;
#> }
#> 
#> #ygftpbmcjf .gt_asterisk {
#>   font-size: 100%;
#>   vertical-align: 0;
#> }
#> 
#> #ygftpbmcjf .gt_indent_1 {
#>   text-indent: 5px;
#> }
#> 
#> #ygftpbmcjf .gt_indent_2 {
#>   text-indent: 10px;
#> }
#> 
#> #ygftpbmcjf .gt_indent_3 {
#>   text-indent: 15px;
#> }
#> 
#> #ygftpbmcjf .gt_indent_4 {
#>   text-indent: 20px;
#> }
#> 
#> #ygftpbmcjf .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 gt_spanner_row">
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="2" 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="2" colspan="1" style="text-align: center; font-weight: bold;" scope="col" id="Variable name">Variable name</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="2" colspan="1" style="text-align: center; font-weight: bold;" scope="col" id="Variable level">Variable level</th>
#>       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="2" colspan="1" style="text-align: center; font-weight: bold;" scope="col" id="Estimate name">Estimate name</th>
#>       <th class="gt_center gt_columns_top_border gt_column_spanner_outer" rowspan="1" colspan="1" style="background-color: #C8C8C8; text-align: center; font-weight: bold;" scope="col" id="Cohort name">
#>         <span class="gt_column_spanner">Cohort name</span>
#>       </th>
#>     </tr>
#>     <tr class="gt_col_headings">
#>       <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="Cohort 1">Cohort 1</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="Variable 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;">Medications in the prior year</td>
#> <td headers="Variable level" 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="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]Cohort name
#> [header_level]Cohort 1" class="gt_row gt_right" style="text-align: right;">2 (100.0%)</td></tr>
#>     <tr><td headers="CDM name" class="gt_row gt_left" style="text-align: left; border-top-width: 1px; border-top-style: hidden; border-top-color: #000000;"></td>
#> <td headers="Variable 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: hidden; border-top-color: #000000; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;"></td>
#> <td headers="Variable level" 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]Cohort name
#> [header_level]Cohort 1" class="gt_row gt_right" style="text-align: right;">1 (50.0%)</td></tr>
#>   </tbody>
#>   
#>   
#> </table>
#> </div>

CDMConnector::cdmDisconnect(cdm = cdm)
# }