# Create a sample data frame for a clinical cohort
set.seed(123)
n_patients <- 100
brca_data <- data.frame(
AgeAtDiagnosis = as.integer(rnorm(n_patients, mean = 62, sd = 12)),
TumorSize_mm = rlnorm(n_patients, meanlog = 3, sdlog = 0.5), # Log-normal (skewed)
Ki67_Index = runif(n_patients, min = 5, max = 80)
)
head(brca_data)
#> AgeAtDiagnosis TumorSize_mm Ki67_Index
#> 1 55 14.08058 78.95407
#> 2 59 22.83837 15.28006
#> 3 80 17.75477 72.89822
#> 4 62 16.88167 48.22264
#> 5 63 12.48079 34.65866
#> 6 82 19.63839 38.73519Vignette: Descriptive Analysis of Continuous Variables in Clinical Data
2025-06-03
Source:vignettes/summarydata.qmd
# This code simulates how the jamovi module would be called in an R environment.
# You would need the ClinicoPathDescriptives package installed.
# Load the library
library(ClinicoPathDescriptives)
#> Registered S3 method overwritten by 'future':
#> method from
#> all.equal.connection parallelly
#> Warning: replacing previous import 'dplyr::select' by 'jmvcore::select' when
#> loading 'ClinicoPathDescriptives'
# Run the summarydata analysis with distribution diagnostics enabled
results <- summarydata(
data = brca_data,
vars = c("AgeAtDiagnosis", "TumorSize_mm", "Ki67_Index"),
distr = TRUE
)
#>
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#> [1] "Mean of <strong>AgeAtDiagnosis</strong> is: 62.6 ± 11. (Median: 62 [Min: 34 - Max: 88]) <br><br><em>Distribution Diagnostics for AgeAtDiagnosis:</em> Shapiro-Wilk p-value = 0.92; Skewness = 0.07; Kurtosis = 2.84 (Data appears to be normally distributed).<br><br>"
#> [1] "Mean of <strong>TumorSize_mm</strong> is: 21.7 ± 13.3. (Median: 17.9 [Min: 7.2 - Max: 101.5]) <br><br><em>Distribution Diagnostics for TumorSize_mm:</em> Shapiro-Wilk p-value = 0; Skewness = 2.89; Kurtosis = 15.31 (Data does not appear to be normally distributed. Please use relevant visualisation and tests to verify the characteristics of distribution.).<br><br>"
#> [1] "Mean of <strong>Ki67_Index</strong> is: 41.4 ± 21.7. (Median: 39.6 [Min: 5 - Max: 79.7]) <br><br><em>Distribution Diagnostics for Ki67_Index:</em> Shapiro-Wilk p-value = 0.001; Skewness = 0.13; Kurtosis = 1.77 (Data does not appear to be normally distributed. Please use relevant visualisation and tests to verify the characteristics of distribution.).<br><br>"
#>
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#> <td headers="name" class="gt_row gt_left" style="font-weight: bold;">AgeAtDiagnosis</td>
#> <td headers="value" class="gt_row gt_center"><?xml version='1.0' encoding='UTF-8' ?><svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' width='141.73pt' height='34.02pt' viewBox='0 0 141.73 34.02'><g class='svglite'><defs> <style type='text/css'><![CDATA[ .svglite line, .svglite polyline, .svglite polygon, .svglite path, .svglite rect, .svglite circle { fill: none; stroke: #000000; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; } .svglite text { white-space: pre; } .svglite g.glyphgroup path { fill: inherit; stroke: none; } ]]></style></defs><rect width='100%' height='100%' style='stroke: none; fill: none;'/><defs> <clipPath id='cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg=='> <rect x='0.00' y='0.00' width='141.73' height='34.02' /> </clipPath></defs><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'></g><defs> <clipPath id='cpMS4wMHwxNDAuNzR8MS4wMHwyMy41Ng=='> <rect x='1.00' y='1.00' width='139.74' height='22.56' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8MS4wMHwyMy41Ng==)'><rect x='7.35' y='23.56' width='12.70' height='0.00' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='20.05' y='21.59' width='12.70' height='1.96' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='32.76' y='19.63' width='12.70' height='3.92' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='45.46' y='15.71' width='12.70' height='7.85' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='58.16' y='1.00' width='12.70' height='22.56' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='70.87' y='2.96' width='12.70' height='20.60' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='83.57' y='5.90' width='12.70' height='17.66' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='96.27' y='10.80' width='12.70' height='12.75' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='108.98' y='16.69' width='12.70' height='6.87' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='121.68' y='19.63' width='12.70' height='3.92' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><circle cx='19.41' cy='22.57' r='0.46' style='stroke-width: 0.71; stroke: none;' /><circle cx='19.41' cy='22.57' r='0.46' style='stroke-width: 0.71; stroke: none;' /><line x1='78.46' y1='23.56' x2='78.46' y2='1.00' style='stroke-width: 1.07; stroke-linecap: butt;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><polyline points='1.00,23.56 140.74,23.56 ' style='stroke-width: 0.75;' /><polyline points='20.53,26.39 20.53,23.56 ' style='stroke-width: 0.75;' /><polyline points='132.25,26.39 132.25,23.56 ' style='stroke-width: 0.75;' /><text x='20.53' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='25.16px' lengthAdjust='spacingAndGlyphs'>34 auto</text><text x='132.25' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='25.16px' lengthAdjust='spacingAndGlyphs'>88 auto</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right">0.0%</td>
#> <td headers="Mean" class="gt_row gt_right">62.6</td>
#> <td headers="Median" class="gt_row gt_right">62.0</td>
#> <td headers="SD" class="gt_row gt_right">11.0</td></tr>
#> <tr><td headers="type" class="gt_row gt_left gt_striped"><svg aria-hidden="true" role="img" viewBox="0 0 640 512" style="height:20px;width:25px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#f18e2c;overflow:visible;position:relative;"><path d="M576 0c17.7 0 32 14.3 32 32V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V32c0-17.7 14.3-32 32-32zM448 96c17.7 0 32 14.3 32 32V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V128c0-17.7 14.3-32 32-32zM352 224V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V224c0-17.7 14.3-32 32-32s32 14.3 32 32zM192 288c17.7 0 32 14.3 32 32V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V320c0-17.7 14.3-32 32-32zM96 416v64c0 17.7-14.3 32-32 32s-32-14.3-32-32V416c0-17.7 14.3-32 32-32s32 14.3 32 32z"/></svg></td>
#> <td headers="name" class="gt_row gt_left gt_striped" style="font-weight: bold;">TumorSize_mm</td>
#> <td headers="value" class="gt_row gt_center gt_striped"><?xml version='1.0' encoding='UTF-8' ?><svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' width='141.73pt' height='34.02pt' viewBox='0 0 141.73 34.02'><g class='svglite'><defs> <style type='text/css'><![CDATA[ .svglite line, .svglite polyline, .svglite polygon, .svglite path, .svglite rect, .svglite circle { fill: none; stroke: #000000; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; } .svglite text { white-space: pre; } .svglite g.glyphgroup path { fill: inherit; stroke: none; } ]]></style></defs><rect width='100%' height='100%' style='stroke: none; fill: none;'/><defs> <clipPath id='cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg=='> <rect x='0.00' y='0.00' width='141.73' height='34.02' /> </clipPath></defs><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'></g><defs> <clipPath id='cpMS4wMHwxNDAuNzR8MS4wMHwyMy41Ng=='> <rect x='1.00' y='1.00' width='139.74' height='22.56' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8MS4wMHwyMy41Ng==)'><rect x='7.35' y='22.72' width='6.35' height='0.84' style='stroke-width: 1.07; 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#> <td headers="n_missing" class="gt_row gt_right gt_striped">0.0%</td>
#> <td headers="Mean" class="gt_row gt_right gt_striped">21.7</td>
#> <td headers="Median" class="gt_row gt_right gt_striped">17.9</td>
#> <td headers="SD" class="gt_row gt_right gt_striped">13.3</td></tr>
#> <tr><td headers="type" class="gt_row gt_left"><svg aria-hidden="true" role="img" viewBox="0 0 640 512" style="height:20px;width:25px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#f18e2c;overflow:visible;position:relative;"><path d="M576 0c17.7 0 32 14.3 32 32V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V32c0-17.7 14.3-32 32-32zM448 96c17.7 0 32 14.3 32 32V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V128c0-17.7 14.3-32 32-32zM352 224V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V224c0-17.7 14.3-32 32-32s32 14.3 32 32zM192 288c17.7 0 32 14.3 32 32V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V320c0-17.7 14.3-32 32-32zM96 416v64c0 17.7-14.3 32-32 32s-32-14.3-32-32V416c0-17.7 14.3-32 32-32s32 14.3 32 32z"/></svg></td>
#> <td headers="name" class="gt_row gt_left" style="font-weight: bold;">Ki67_Index</td>
#> <td headers="value" class="gt_row gt_center"><?xml version='1.0' encoding='UTF-8' ?><svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' width='141.73pt' height='34.02pt' viewBox='0 0 141.73 34.02'><g class='svglite'><defs> <style type='text/css'><![CDATA[ .svglite line, .svglite polyline, .svglite polygon, .svglite path, .svglite rect, .svglite circle { fill: none; stroke: #000000; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; } .svglite text { white-space: pre; } .svglite g.glyphgroup path { fill: inherit; stroke: none; } ]]></style></defs><rect width='100%' height='100%' style='stroke: none; fill: none;'/><defs> <clipPath id='cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg=='> <rect x='0.00' y='0.00' width='141.73' height='34.02' /> </clipPath></defs><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'></g><defs> <clipPath id='cpMS4wMHwxNDAuNzR8MS4wMHwyMy41Ng=='> <rect x='1.00' y='1.00' width='139.74' height='22.56' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8MS4wMHwyMy41Ng==)'><rect x='7.35' y='21.75' width='21.17' height='1.80' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='28.52' y='1.00' width='21.17' height='22.56' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='49.69' y='5.51' width='21.17' height='18.05' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='70.87' y='7.31' width='21.17' height='16.24' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='92.04' y='3.70' width='21.17' height='19.85' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='113.21' y='11.82' width='21.17' height='11.73' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><circle cx='23.87' cy='22.65' r='0.46' style='stroke-width: 0.71; stroke: none;' /><circle cx='23.87' cy='22.65' r='0.46' style='stroke-width: 0.71; stroke: none;' /><line x1='72.80' y1='23.56' x2='72.80' y2='1.00' style='stroke-width: 1.07; stroke-linecap: butt;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><polyline points='1.00,23.56 140.74,23.56 ' style='stroke-width: 0.75;' /><polyline points='24.90,26.39 24.90,23.56 ' style='stroke-width: 0.75;' /><polyline points='128.30,26.39 128.30,23.56 ' style='stroke-width: 0.75;' /><text x='24.90' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='21.56px' lengthAdjust='spacingAndGlyphs'>5 auto</text><text x='128.30' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='25.16px' lengthAdjust='spacingAndGlyphs'>80 auto</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right">0.0%</td>
#> <td headers="Mean" class="gt_row gt_right">41.4</td>
#> <td headers="Median" class="gt_row gt_right">39.6</td>
#> <td headers="SD" class="gt_row gt_right">21.7</td></tr>
#> </tbody>
#>
#>
#> </table>
#> </div>
#>
|
| | 0%
|
|......................................................................| 100%
# The results are HTML outputs that render directly in jamovi.
# In R, you would access them like this:
results$text # (for the text summary)
#>
#> Mean of AgeAtDiagnosis is: 62.6 ± 11. (Median: 62 [Min: 34 - Max: 88])
#>
#> *Distribution Diagnostics for AgeAtDiagnosis:* Shapiro-Wilk p-value =
#> 0.92; Skewness = 0.07; Kurtosis = 2.84 (Data appears to be normally
#> distributed).
#>
#> Mean of TumorSize_mm is: 21.7 ± 13.3. (Median: 17.9 [Min: 7.2 - Max:
#> 101.5])
#>
#> *Distribution Diagnostics for TumorSize_mm:* Shapiro-Wilk p-value = 0;
#> Skewness = 2.89; Kurtosis = 15.31 (Data does not appear to be normally
#> distributed. Please use relevant visualisation and tests to verify the
#> characteristics of distribution.).
#>
#> Mean of Ki67_Index is: 41.4 ± 21.7. (Median: 39.6 [Min: 5 - Max:
#> 79.7])
#>
#> *Distribution Diagnostics for Ki67_Index:* Shapiro-Wilk p-value =
#> 0.001; Skewness = 0.13; Kurtosis = 1.77 (Data does not appear to be
#> normally distributed. Please use relevant visualisation and tests to
#> verify the characteristics of distribution.).
results$text1 # (for the visual summary table)
#>
#> <table class="gt_table" data-quarto-disable-processing="false"
#> data-quarto-bootstrap="false">
#>
#> <tr class="gt_heading">
#> <td colspan="7" class="gt_heading gt_title gt_font_normal" style>.
#>
#> <tr class="gt_heading">
#> <td colspan="7" class="gt_heading gt_subtitle gt_font_normal
#> gt_bottom_border" style>100 rows x 3 cols
#>
#> <tr class="gt_col_headings">
#> <th class="gt_col_heading gt_columns_bottom_border gt_left"
#> rowspan="1" colspan="1" scope="col" id="type">
#> <th class="gt_col_heading gt_columns_bottom_border gt_left"
#> rowspan="1" colspan="1" scope="col" id="name">Column
#> <th class="gt_col_heading gt_columns_bottom_border gt_center"
#> rowspan="1" colspan="1" scope="col" id="value">Plot Overview
#> <th class="gt_col_heading gt_columns_bottom_border gt_right"
#> rowspan="1" colspan="1" scope="col" id="n_missing">Missing
#> <th class="gt_col_heading gt_columns_bottom_border gt_right"
#> rowspan="1" colspan="1" scope="col" id="Mean">Mean
#> <th class="gt_col_heading gt_columns_bottom_border gt_right"
#> rowspan="1" colspan="1" scope="col" id="Median">Median
#> <th class="gt_col_heading gt_columns_bottom_border gt_right"
#> rowspan="1" colspan="1" scope="col" id="SD">SD
#>
#>
#> <tbody class="gt_table_body">
#> <td headers="type" class="gt_row gt_left"><svg aria-hidden="true"
#> role="img" viewBox="0 0 640 512"
#> style="height:20px;width:25px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#f18e2c;overflow:visible;position:relative;"><path
#> d="M576 0c17.7 0 32 14.3 32 32V480c0 17.7-14.3 32-32
#> 32s-32-14.3-32-32V32c0-17.7 14.3-32 32-32zM448 96c17.7 0 32 14.3 32
#> 32V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V128c0-17.7 14.3-32
#> 32-32zM352 224V480c0 17.7-14.3 32-32 32s-32-14.3-32-32V224c0-17.7
#> 14.3-32 32-32s32 14.3 32 32zM192 288c17.7 0 32 14.3 32 32V480c0
#> 17.7-14.3 32-32 32s-32-14.3-32-32V320c0-17.7 14.3-32 32-32zM96
#> 416v64c0 17.7-14.3 32-32 32s-32-14.3-32-32V416c0-17.7 14.3-32 32-32s32
#> 14.3 32 32z"/>
#> <td headers="name" class="gt_row gt_left" style="font-weight:
#> bold;">AgeAtDiagnosis
#> <td headers="value" class="gt_row gt_center"><?xml version='1.0'
#> encoding='UTF-8' ?><svg xmlns='http://www.w3.org/2000/svg'
#> xmlns:xlink='http://www.w3.org/1999/xlink' width='141.73pt'
#> height='34.02pt' viewBox='0 0 141.73 34.02'><g class='svglite'> <style
#> type='text/css'><![CDATA[ .svglite line, .svglite polyline, .svglite
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