Format a summariseCohortTiming result into a visual table.
Source:R/tableSummarised.R
tableCohortTiming.Rd
`r lifecycle::badge("deprecated")`
Usage
tableCohortTiming(
result,
type = "gt",
formatEstimateName = c(N = "<count>", `Median [Q25 - Q75]` =
"<median> [<q25> - <q75>]", Range = "<min> - <max>"),
header = c("strata"),
split = c("group", "strata", "additional"),
groupColumn = NULL,
minCellCount = 5,
excludeColumns = c("result_id", "estimate_type", "variable_level"),
.options = list()
)
Arguments
- result
A summariseCohortTiming 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::optionsTableCohortTiming() shows allowed arguments and their default values.
Examples
# \donttest{
library(PatientProfiles)
cdm <- PatientProfiles::mockPatientProfiles()
timing <- summariseCohortTiming(cdm$cohort2)
#> ℹ The following estimates will be computed:
#> • days_between_cohort_entries: min, q25, median, q75, max
#> ! Table is collected to memory as not all requested estimates are supported on
#> the database side
#> → Start summary of data, at 2024-05-11 12:04:56.935375
#> ✔ Summary finished, at 2024-05-11 12:04:56.987158
tableCohortTiming(timing)
#> ! 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="Variable name">Variable 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="Estimate name">Estimate 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="Estimate value">Estimate value</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="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;">Number records</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="Estimate value" class="gt_row gt_left" style="text-align: left;">1</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="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: hidden; border-top-color: #000000; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;"></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: hidden; border-top-color: #000000; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;"></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;">Number subjects</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="Estimate value" class="gt_row gt_left" style="text-align: left;">1</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="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: hidden; border-top-color: #000000; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;"></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: hidden; border-top-color: #000000; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;"></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;">Days between cohort entries</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;">Median [Q25 - Q75]</td>
#> <td headers="Estimate value" class="gt_row gt_left" style="text-align: left;">147.00 [147.00 - 147.00]</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="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: hidden; border-top-color: #000000; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;"></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: hidden; border-top-color: #000000; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: #D3D3D3;"></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="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;">Range</td>
#> <td headers="Estimate value" class="gt_row gt_left" style="text-align: left;">147.00 - 147.00</td></tr>
#> </tbody>
#>
#>
#> </table>
#> </div>
CDMConnector::cdmDisconnect(cdm = cdm)
# }