General 02: Getting Started with Statistical Analysis for Pathologists
ClinicoPath Development Team
2025-06-30
Source:vignettes/general-03-getting-started-alt.Rmd
general-03-getting-started-alt.RmdIntroduction
ClinicoPathDescriptives is a comprehensive R package designed for descriptive analysis in clinicopathological research. It provides both programmatic R functions and a graphical user interface through jamovi, making advanced statistical analysis accessible to researchers with varying levels of programming experience.
Key Features
- Descriptive Statistics: Generate comprehensive “Table One” summaries
-
Cross-tabulations: Create contingency tables with
appropriate statistical tests
- Visualization Tools: Age pyramids, alluvial diagrams, Venn diagrams, and more
- Treatment Response Analysis: Waterfall and swimmer plots for oncology research
- Data Quality Assessment: Benford’s law analysis for fraud detection
- Dual Interface: Use in R or through jamovi’s point-and-click interface
Installation
Install from GitHub
# Install development version
if (!require("remotes")) install.packages("remotes")
remotes::install_github("sbalci/ClinicoPathDescriptives")Install as jamovi Module
Download the .jmo file from Releases
and install in jamovi via:
jamovi menu > Modules > Install from file
Example Dataset
The package includes a comprehensive histopathology dataset with 250 cancer patients and 38 variables including demographics, pathological features, biomarkers, and outcomes.
# Load the example dataset
data(histopathology)
# Examine the structure
str(histopathology, give.attr = FALSE)
#> spc_tbl_ [250 × 38] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
#> $ ID : num [1:250] 1 2 3 4 5 6 7 8 9 10 ...
#> $ Name : chr [1:250] "Tonisia" "Daniyah" "Naviana" "Daerion" ...
#> $ Sex : chr [1:250] "Male" "Female" "Male" "Male" ...
#> $ Age : num [1:250] 27 36 65 51 58 53 33 26 25 68 ...
#> $ Race : chr [1:250] "White" "White" "White" "White" ...
#> $ PreinvasiveComponent: chr [1:250] "Present" "Absent" "Absent" "Absent" ...
#> $ LVI : chr [1:250] "Present" "Absent" "Absent" "Present" ...
#> $ PNI : chr [1:250] "Absent" "Absent" "Absent" "Absent" ...
#> $ LastFollowUpDate : chr [1:250] "2019.10.22 00:00:00" "2019.06.22 00:00:00" "2019.08.22 00:00:00" "2019.03.22 00:00:00" ...
#> $ Death : chr [1:250] "YANLIŞ" "DOĞRU" "DOĞRU" "YANLIŞ" ...
#> $ Group : chr [1:250] "Control" "Treatment" "Control" "Treatment" ...
#> $ Grade : num [1:250] 2 2 1 3 2 2 1 2 3 3 ...
#> $ TStage : num [1:250] 4 4 4 4 1 4 2 3 4 4 ...
#> $ Anti-X-intensity : num [1:250] 3 2 2 3 3 3 2 2 1 2 ...
#> $ Anti-Y-intensity : num [1:250] 1 1 2 3 3 2 2 2 1 3 ...
#> $ LymphNodeMetastasis : chr [1:250] "Present" "Absent" "Absent" "Absent" ...
#> $ Valid : chr [1:250] "YANLIŞ" "DOĞRU" "YANLIŞ" "DOĞRU" ...
#> $ Smoker : chr [1:250] "YANLIŞ" "YANLIŞ" "DOĞRU" "YANLIŞ" ...
#> $ Grade_Level : chr [1:250] "high" "low" "low" "high" ...
#> $ SurgeryDate : chr [1:250] "2019.07.08 00:00:00" "2019.03.18 00:00:00" "2019.05.18 00:00:00" "2018.10.24 00:00:00" ...
#> $ DeathTime : chr [1:250] "Within1Year" "Within1Year" "Within1Year" "Within1Year" ...
#> $ int : chr [1:250] "2019-07-08 UTC--2019-10-22 UTC" "2019-03-18 UTC--2019-06-22 UTC" "2019-05-18 UTC--2019-08-22 UTC" "2018-10-24 UTC--2019-03-22 UTC" ...
#> $ OverallTime : num [1:250] 3.5 3.1 3.1 4.9 3.3 9.3 6.3 9 5.8 9.9 ...
#> $ Outcome : num [1:250] 0 1 1 0 0 0 1 1 1 0 ...
#> $ Mortality5yr : chr [1:250] "Alive" "Dead" "Dead" "Alive" ...
#> $ Rater 1 : num [1:250] 0 1 1 0 0 0 1 1 1 0 ...
#> $ Rater 2 : num [1:250] 0 0 0 0 0 0 0 0 0 0 ...
#> $ Rater 3 : num [1:250] 1 1 1 0 1 1 1 1 1 1 ...
#> $ Rater A : num [1:250] 3 2 3 3 2 3 1 1 2 1 ...
#> $ Rater B : num [1:250] 3 2 3 3 2 3 1 1 2 1 ...
#> $ New Test : num [1:250] 0 0 0 0 0 0 1 0 0 0 ...
#> $ Golden Standart : num [1:250] 0 0 0 0 0 0 0 0 0 0 ...
#> $ MeasurementA : num [1:250] -1.63432 0.37071 0.01585 -1.23584 -0.00141 ...
#> $ MeasurementB : num [1:250] 0.611 0.554 0.742 0.622 0.527 ...
#> $ Disease Status : chr [1:250] "Ill" "Ill" "Healthy" "Ill" ...
#> $ Measurement1 : num [1:250] 0.387 0.829 0.159 2.447 0.847 ...
#> $ Measurement2 : num [1:250] 1.8654 0.5425 0.0701 2.4071 0.5564 ...
#> $ Outcome2 : chr [1:250] "DOD" "DOOC" "AWD" "AWOD" ...
# Quick overview of key variables
histopathology %>%
select(Age, Sex, Grade, TStage, Group, Outcome, OverallTime) %>%
head(10)
#> # A tibble: 10 × 7
#> Age Sex Grade TStage Group Outcome OverallTime
#> <dbl> <chr> <dbl> <dbl> <chr> <dbl> <dbl>
#> 1 27 Male 2 4 Control 0 3.5
#> 2 36 Female 2 4 Treatment 1 3.1
#> 3 65 Male 1 4 Control 1 3.1
#> 4 51 Male 3 4 Treatment 0 4.9
#> 5 58 Female 2 1 Treatment 0 3.3
#> 6 53 Female 2 4 Treatment 0 9.3
#> 7 33 Male 1 2 Treatment 1 6.3
#> 8 26 Male 2 3 Treatment 1 9
#> 9 25 Female 3 4 Treatment 1 5.8
#> 10 68 Female 3 4 Control 0 9.9Basic Descriptive Analysis
Table One
Generate a comprehensive descriptive summary table - the cornerstone of clinical research manuscripts:
# Basic Table One
tableone(
data = histopathology,
vars = c("Age", "Sex", "Grade", "TStage", "LVI", "PNI")
)
#>
#> TABLE ONE
#>
#> character(0)
#>
#> Overall
#> n 250
#> Age (mean (SD)) 49.44 (13.81)
#> Sex = Male (%) 128 (51.4)
#> Grade (mean (SD)) 2.10 (0.83)
#> TStage (mean (SD)) 3.05 (1.02)
#> LVI = Present (%) 106 (42.6)
#> PNI = Present (%) 83 (33.3)Continuous Variables Summary
Generate detailed summaries for continuous variables:
summarydata(
data = histopathology,
vars = c("Age", "OverallTime", "MeasurementA"),
date_vars = NULL,
grvar = "Grade"
)
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#> <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;">Age</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='20.48' width='15.88' height='3.08' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='23.23' y='3.05' width='15.88' height='20.51' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='39.11' y='5.61' width='15.88' height='17.94' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='54.99' y='1.00' width='15.88' height='22.56' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='70.87' y='2.02' width='15.88' height='21.53' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='86.75' y='5.61' width='15.88' height='17.94' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='102.63' y='1.51' width='15.88' height='22.05' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='118.50' y='21.50' width='15.88' height='2.05' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><circle cx='18.68' cy='23.04' r='0.46' style='stroke-width: 0.71; stroke: none;' /><circle cx='18.68' cy='23.04' r='0.46' style='stroke-width: 0.71; stroke: none;' /><line x1='69.63' y1='23.56' x2='69.63' 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='19.68,26.39 19.68,23.56 ' style='stroke-width: 0.75;' /><polyline points='119.58,26.39 119.58,23.56 ' style='stroke-width: 0.75;' /><text x='19.68' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='25.16px' lengthAdjust='spacingAndGlyphs'>25 auto</text><text x='119.58' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='25.16px' lengthAdjust='spacingAndGlyphs'>73 auto</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right">0.4%</td>
#> <td headers="Mean" class="gt_row gt_right">49.4</td>
#> <td headers="Median" class="gt_row gt_right">49.0</td>
#> <td headers="SD" class="gt_row gt_right">13.8</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;">OverallTime</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='23.56' width='10.59' height='0.00' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='17.93' y='1.00' width='10.59' height='22.56' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='28.52' y='1.89' width='10.59' height='21.67' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='39.11' y='19.40' width='10.59' height='4.16' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='49.69' y='16.73' width='10.59' height='6.83' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='60.28' y='18.51' width='10.59' height='5.05' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='70.87' y='18.81' width='10.59' height='4.75' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='81.45' y='20.88' width='10.59' height='2.67' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='92.04' y='22.37' width='10.59' height='1.19' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='102.63' y='22.37' width='10.59' height='1.19' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='113.21' y='20.88' width='10.59' height='2.67' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='123.80' y='22.67' width='10.59' height='0.89' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><circle cx='17.37' cy='23.26' r='0.46' style='stroke-width: 0.71; stroke: none;' /><circle cx='17.37' cy='23.26' r='0.46' style='stroke-width: 0.71; stroke: none;' /><line x1='33.10' y1='23.56' x2='33.10' 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='18.49,26.39 18.49,23.56 ' style='stroke-width: 0.75;' /><polyline points='129.94,26.39 129.94,23.56 ' style='stroke-width: 0.75;' /><text x='18.49' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='21.56px' lengthAdjust='spacingAndGlyphs'>3 auto</text><text x='129.94' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='25.16px' lengthAdjust='spacingAndGlyphs'>58 auto</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right gt_striped">0.8%</td>
#> <td headers="Mean" class="gt_row gt_right gt_striped">16.5</td>
#> <td headers="Median" class="gt_row gt_right gt_striped">10.1</td>
#> <td headers="SD" class="gt_row gt_right gt_striped">13.5</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;">MeasurementA</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='23.02' width='9.07' height='0.54' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='16.42' y='23.56' width='9.07' height='0.00' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='25.50' y='23.02' width='9.07' height='0.54' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='34.57' y='16.04' width='9.07' height='7.52' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='43.64' y='14.42' width='9.07' height='9.13' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='52.72' y='9.59' width='9.07' height='13.97' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='61.79' y='3.68' width='9.07' height='19.87' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='70.87' y='1.00' width='9.07' height='22.56' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='79.94' y='3.14' width='9.07' height='20.41' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='89.01' y='5.29' width='9.07' height='18.26' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='98.09' y='11.74' width='9.07' height='11.82' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='107.16' y='19.26' width='9.07' height='4.30' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='116.24' y='18.72' width='9.07' height='4.83' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><rect x='125.31' y='23.02' width='9.07' height='0.54' style='stroke-width: 1.07; stroke: #FFFFFF; stroke-linecap: butt; stroke-linejoin: miter; fill: #F8BB87;' /><circle cx='15.23' cy='23.02' r='0.46' style='stroke-width: 0.71; stroke: none;' /><circle cx='15.23' cy='23.02' r='0.46' style='stroke-width: 0.71; stroke: none;' /><line x1='77.68' y1='23.56' x2='77.68' 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='16.36,26.39 16.36,23.56 ' style='stroke-width: 0.75;' /><polyline points='129.56,26.39 129.56,23.56 ' style='stroke-width: 0.75;' /><text x='16.36' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='32.34px' lengthAdjust='spacingAndGlyphs'>-2.5 auto</text><text x='129.56' y='33.36' text-anchor='middle' style='font-size: 6.00px; font-weight: 0; font-family: "Courier";' textLength='28.75px' lengthAdjust='spacingAndGlyphs'>2.3 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">0.1</td>
#> <td headers="Median" class="gt_row gt_right">0.1</td>
#> <td headers="SD" class="gt_row gt_right">0.9</td></tr>
#> <tr><td headers="type" class="gt_row gt_left gt_striped"><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:20px;width:20px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#4e79a7;overflow:visible;position:relative;"><path d="M40 48C26.7 48 16 58.7 16 72v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V72c0-13.3-10.7-24-24-24H40zM192 64c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zM16 232v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V232c0-13.3-10.7-24-24-24H40c-13.3 0-24 10.7-24 24zM40 368c-13.3 0-24 10.7-24 24v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V392c0-13.3-10.7-24-24-24H40z"/></svg></td>
#> <td headers="name" class="gt_row gt_left gt_striped" style="font-weight: bold;"><div style='max-width: 150px;'>
#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>Grade</summary>
#> 3, 2 and 1
#> </details></div></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='cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ=='> <rect x='1.00' y='2.99' width='139.74' height='20.62' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ==)'><rect x='99.21' y='3.93' width='41.53' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #DDEAF7;' /><rect x='56.56' y='3.93' width='42.65' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #91B4DA;' /><rect x='1.00' y='3.93' width='55.56' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #3181BD;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><text x='1.00' y='30.18' style='font-size: 8.00px; font-family: "Arial";' textLength='43.61px' lengthAdjust='spacingAndGlyphs'>3 categories</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right gt_striped">0.4%</td>
#> <td headers="Mean" class="gt_row gt_right gt_striped">—</td>
#> <td headers="Median" class="gt_row gt_right gt_striped">—</td>
#> <td headers="SD" class="gt_row gt_right gt_striped">—</td></tr>
#> </tbody>
#>
#>
#> </table>
#> </div>
#>
#> SUMMARY OF CONTINUOUS VARIABLES
#>
#> character(0)
#>
#> *Group: 1*
#> Mean of Age is: 50.2 ± 14.5. (Median: 46.5 [Min: 26 - Max: 73])
#>
#> *Group: 1*
#> Mean of OverallTime is: 17 ± 14.1. (Median: 10.1 [Min: 3 - Max: 58.2])
#>
#> *Group: 1*
#> Mean of MeasurementA is: 0.1 ± 0.8. (Median: 0.2 [Min: -1.7 - Max:
#> 2.1])
#>
#> *Group: 2*
#> Mean of Age is: 47.6 ± 13. (Median: 48 [Min: 26 - Max: 70])
#>
#> *Group: 2*
#> Mean of OverallTime is: 15.8 ± 14.7. (Median: 9.4 [Min: 3.1 - Max:
#> 57.7])
#>
#> *Group: 2*
#> Mean of MeasurementA is: 0 ± 0.9. (Median: 0.1 [Min: -2 - Max: 2.3])
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#> Mean of Age is: 50 ± 13.7. (Median: 50 [Min: 25 - Max: 73])
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#> Mean of OverallTime is: 16.6 ± 12.1. (Median: 11.4 [Min: 2.9 - Max:
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#> *Group: 3*
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#> <td headers="SD" class="gt_row gt_right gt_striped">—Categorical Variables Summary
Analyze categorical variables with counts and percentages:
reportcat(
data = histopathology,
vars = c("Sex", "Grade", "TStage", "LVI", "PNI")
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#> <td headers="n_missing" class="gt_row gt_right">0.4%</td></tr>
#> <tr><td headers="type" class="gt_row gt_left gt_striped"><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:20px;width:20px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#4e79a7;overflow:visible;position:relative;"><path d="M40 48C26.7 48 16 58.7 16 72v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V72c0-13.3-10.7-24-24-24H40zM192 64c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zM16 232v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V232c0-13.3-10.7-24-24-24H40c-13.3 0-24 10.7-24 24zM40 368c-13.3 0-24 10.7-24 24v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V392c0-13.3-10.7-24-24-24H40z"/></svg></td>
#> <td headers="name" class="gt_row gt_left gt_striped" style="font-weight: bold;"><div style='max-width: 150px;'>
#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>Grade</summary>
#> 3, 2 and 1
#> </details></div></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='cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ=='> <rect x='1.00' y='2.99' width='139.74' height='20.62' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ==)'><rect x='99.21' y='3.93' width='41.53' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #DDEAF7;' /><rect x='56.56' y='3.93' width='42.65' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #91B4DA;' /><rect x='1.00' y='3.93' width='55.56' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #3181BD;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><text x='1.00' y='30.18' style='font-size: 8.00px; font-family: "Arial";' textLength='43.61px' lengthAdjust='spacingAndGlyphs'>3 categories</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right gt_striped">0.4%</td></tr>
#> <tr><td headers="type" class="gt_row gt_left"><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:20px;width:20px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#4e79a7;overflow:visible;position:relative;"><path d="M40 48C26.7 48 16 58.7 16 72v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V72c0-13.3-10.7-24-24-24H40zM192 64c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zM16 232v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V232c0-13.3-10.7-24-24-24H40c-13.3 0-24 10.7-24 24zM40 368c-13.3 0-24 10.7-24 24v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V392c0-13.3-10.7-24-24-24H40z"/></svg></td>
#> <td headers="name" class="gt_row gt_left" style="font-weight: bold;"><div style='max-width: 150px;'>
#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>TStage</summary>
#> 4, 3, 2 and 1
#> </details></div></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='cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ=='> <rect x='1.00' y='2.99' width='139.74' height='20.62' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ==)'><rect x='127.27' y='3.93' width='13.47' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #DDEAF7;' /><rect x='98.65' y='3.93' width='28.62' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #ABC6E4;' /><rect x='63.29' y='3.93' width='35.36' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #75A3D0;' /><rect x='1.00' y='3.93' width='62.29' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #3181BD;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><text x='1.00' y='30.18' style='font-size: 8.00px; font-family: "Arial";' textLength='43.61px' lengthAdjust='spacingAndGlyphs'>4 categories</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right">0.4%</td></tr>
#> <tr><td headers="type" class="gt_row gt_left gt_striped"><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:20px;width:20px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#4e79a7;overflow:visible;position:relative;"><path d="M40 48C26.7 48 16 58.7 16 72v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V72c0-13.3-10.7-24-24-24H40zM192 64c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zM16 232v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V232c0-13.3-10.7-24-24-24H40c-13.3 0-24 10.7-24 24zM40 368c-13.3 0-24 10.7-24 24v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V392c0-13.3-10.7-24-24-24H40z"/></svg></td>
#> <td headers="name" class="gt_row gt_left gt_striped" style="font-weight: bold;"><div style='max-width: 150px;'>
#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>LVI</summary>
#> Absent and Present
#> </details></div></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='cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ=='> <rect x='1.00' y='2.99' width='139.74' height='20.62' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ==)'><rect x='81.25' y='3.93' width='59.49' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #DDEAF7;' /><rect x='1.00' y='3.93' width='80.25' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #3181BD;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><text x='1.00' y='30.18' style='font-size: 8.00px; font-family: "Arial";' textLength='43.61px' lengthAdjust='spacingAndGlyphs'>2 categories</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right gt_striped">0.4%</td></tr>
#> <tr><td headers="type" class="gt_row gt_left"><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:20px;width:20px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#4e79a7;overflow:visible;position:relative;"><path d="M40 48C26.7 48 16 58.7 16 72v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V72c0-13.3-10.7-24-24-24H40zM192 64c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zM16 232v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V232c0-13.3-10.7-24-24-24H40c-13.3 0-24 10.7-24 24zM40 368c-13.3 0-24 10.7-24 24v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V392c0-13.3-10.7-24-24-24H40z"/></svg></td>
#> <td headers="name" class="gt_row gt_left" style="font-weight: bold;"><div style='max-width: 150px;'>
#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>PNI</summary>
#> Absent and Present
#> </details></div></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='cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ=='> <rect x='1.00' y='2.99' width='139.74' height='20.62' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ==)'><rect x='94.16' y='3.93' width='46.58' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #DDEAF7;' /><rect x='1.00' y='3.93' width='93.16' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #3181BD;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><text x='1.00' y='30.18' style='font-size: 8.00px; font-family: "Arial";' textLength='43.61px' lengthAdjust='spacingAndGlyphs'>2 categories</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right">0.4%</td></tr>
#> </tbody>
#>
#>
#> </table>
#> </div>
#>
#> SUMMARY OF CATEGORICAL VARIABLES
#>
#> character(0)
#>
#> Sex has 250 observations and 2 levels.
#> Female: n = 121, 48.6% of valid cases.
#> Male: n = 128, 51.4% of valid cases.
#> Missing values: 1.
#>
#> Grade has 250 observations and 3 levels.
#> 1: n = 74, 29.72% of valid cases.
#> 2: n = 76, 30.52% of valid cases.
#> 3: n = 99, 39.76% of valid cases.
#> Missing values: 1.
#>
#> TStage has 250 observations and 4 levels.
#> 1: n = 24, 9.6% of valid cases.
#> 2: n = 51, 20.5% of valid cases.
#> 3: n = 63, 25.3% of valid cases.
#> 4: n = 111, 44.6% of valid cases.
#> Missing values: 1.
#>
#> LVI has 250 observations and 2 levels.
#> Absent: n = 143, 57% of valid cases.
#> Present: n = 106, 43% of valid cases.
#> Missing values: 1.
#>
#> PNI has 250 observations and 2 levels.
#> Absent: n = 166, 67% of valid cases.
#> Present: n = 83, 33% of valid cases.
#> Missing values: 1.
#>
#> <table class="gt_table" data-quarto-disable-processing="false"
#> data-quarto-bootstrap="false">
#>
#> <tr class="gt_heading">
#> <td colspan="4" class="gt_heading gt_title gt_font_normal" style>.
#>
#> <tr class="gt_heading">
#> <td colspan="4" class="gt_heading gt_subtitle gt_font_normal
#> gt_bottom_border" style>250 rows x 5 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
#>
#>
#> <tbody class="gt_table_body">
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#> bold;"><div style='max-width: 150px;'>
#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>Sex
#> Male and Female
#>
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#> <td headers="n_missing" class="gt_row gt_right">0.4%
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#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>Grade
#> 3, 2 and 1
#>
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#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>TStage
#> 4, 3, 2 and 1
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#> <td headers="n_missing" class="gt_row gt_right">0.4%
#> <td headers="type" class="gt_row gt_left gt_striped"><svg
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#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>LVI
#> Absent and Present
#>
#> <td headers="value" class="gt_row gt_center gt_striped"><?xml
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#> <td headers="n_missing" class="gt_row gt_right gt_striped">0.4%
#> <td headers="type" class="gt_row gt_left"><svg aria-hidden="true"
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#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>PNI
#> Absent and Present
#>
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#> <td headers="n_missing" class="gt_row gt_right">0.4%Cross-tabulation Analysis
Create contingency tables with appropriate statistical tests:
crosstable(
data = histopathology,
vars = "Grade",
group = "Group"
)
#>
#> CROSS TABLE
#>
#> character(0)
#>
#> character(0)
#>
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#> Verdana, "Verdana Ref", sans-serif;
#> font-size: 66%;
#> -webkit-print-color-adjust: exact;
#> }
#>
#> #tbl3 .figure { margin-left: auto;
#> margin-right: auto;
#> }
#> #tbl3 .caption { text-align: left;
#> text-indent: 2em;
#> padding: 0.5em 0 0.5em 0;
#> font-weight: bold;
#> background-color: #f7f4ef !important;
#> border: 1px solid black;
#> }
#>
#> #tbl3 .figbody {
#> text-align: center;
#> border: 1px solid black
#> }
#>
#> #tbl3 .figbody table {
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#>
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#> }
#>
#> #tbl3 .figbody thead tr td
#> {
#> font-weight: bold;
#> }
#>
#> #tbl3 .figbody tbody tr:nth-child(odd) {background: #fffbed
#> !important;}
#>
#> #tbl3 .header td {text-align: center;}
#>
#> #tbl3 .subheader { font-size: smaller; }
#> #tbl3 .subheader td { text-align: center; /* border-bottom: 1pt solid
#> black; */ }
#>
#> #tbl3 .subheader em {font-style: normal;}
#>
#> #tbl3 tbody .variable {
#> float: left;
#> text-align: left;
#> padding-left: 0.5em;
#> }
#>
#> #tbl3 .units {
#> float: right;
#> font-size: x-small;
#> text-align: right;
#> padding-left: 1em;
#> vertical-align: text-bottom; /* FIXME why doesn't this work */
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#> #tbl3 .statistics {padding-right: 0.5em;}
#> <div class="caption">Cross Table for Dependent group<div
#> class="figbody"><table class="tangram">
#> <th class="header even tg-label"><span class="variable"><th
#> class="header even tg-label"><span class="variable">N<th class="header
#> even tg-label"><span class="variable">Control<th class="header even
#> tg-label"><span class="variable">Treatment<th class="header even
#> tg-label"><span class="variable">Test Statistic<tr
#> class="subheaderrow"><th class="subheader header even tg-label"><span
#> class="variable"><th class="subheader header even tg-label"><span
#> class="variable"><th class="subheader header even data N"><span
#> class="N">(N=120)<th class="subheader header even data N"><span
#> class="N">(N=129)<th class="subheader header even tg-label"><span
#> class="variable">
#> <td class="header odd tg-label"><span class="variable">Grade<td
#> class="odd data N"><span class="N">249<td class="odd">1.0 2.0 3.0<td
#> class="odd">1.0 2.0 3.0<td class="statistics odd">F1,246=0.74, P=0.393
#> <div class="footnote">N is the number of non-missing value.
#> 1Kruskal-Wallis. 2Pearson. 3Wilcoxon.
# Multiple variables cross-tabulation
crosstable(
data = histopathology,
vars = c("Grade", "TStage"),
group = "LymphNodeMetastasis"
)
#>
#> CROSS TABLE
#>
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#>
#> character(0)
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#> Sans", "DejaVu Sans", "Bitstream Vera Sans", "Liberation Sans",
#> Verdana, "Verdana Ref", sans-serif;
#> font-size: 66%;
#> -webkit-print-color-adjust: exact;
#> }
#>
#> #tbl3 .figure { margin-left: auto;
#> margin-right: auto;
#> }
#> #tbl3 .caption { text-align: left;
#> text-indent: 2em;
#> padding: 0.5em 0 0.5em 0;
#> font-weight: bold;
#> background-color: #f7f4ef !important;
#> border: 1px solid black;
#> }
#>
#> #tbl3 .figbody {
#> text-align: center;
#> border: 1px solid black
#> }
#>
#> #tbl3 .figbody table {
#> margin: 0;
#> width: 100%;
#> }
#>
#> #tbl3 .figbody td {
#> padding: 0.2em 0.5em 0.2em 0.5em;
#> }
#>
#> #tbl3 .figbody thead tr td
#> {
#> font-weight: bold;
#> }
#>
#> #tbl3 .figbody tbody tr:nth-child(odd) {background: #fffbed
#> !important;}
#>
#> #tbl3 .header td {text-align: center;}
#>
#> #tbl3 .subheader { font-size: smaller; }
#> #tbl3 .subheader td { text-align: center; /* border-bottom: 1pt solid
#> black; */ }
#>
#> #tbl3 .subheader em {font-style: normal;}
#>
#> #tbl3 tbody .variable {
#> float: left;
#> text-align: left;
#> padding-left: 0.5em;
#> }
#>
#> #tbl3 .units {
#> float: right;
#> font-size: x-small;
#> text-align: right;
#> padding-left: 1em;
#> vertical-align: text-bottom; /* FIXME why doesn't this work */
#> }
#>
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#> display: inline-block;
#> margin: 0 auto;
#> }
#>
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#> white-space: nowrap;
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#> #tbl3 .statistics {padding-right: 0.5em;}
#> <div class="caption">Cross Table for Dependent
#> lymph_node_metastasis<div class="figbody"><table class="tangram">
#> <th class="header even tg-label"><span class="variable"><th
#> class="header even tg-label"><span class="variable">N<th class="header
#> even tg-label"><span class="variable">Absent<th class="header even
#> tg-label"><span class="variable">Present<th class="header even
#> tg-label"><span class="variable">Test Statistic<tr
#> class="subheaderrow"><th class="subheader header even tg-label"><span
#> class="variable"><th class="subheader header even tg-label"><span
#> class="variable"><th class="subheader header even data N"><span
#> class="N">(N=153)<th class="subheader header even data N"><span
#> class="N">(N=96)<th class="subheader header even tg-label"><span
#> class="variable">
#> <td class="header odd tg-label"><span class="variable">Grade<td
#> class="odd data N"><span class="N">249<td class="odd">1.0 2.0 3.0<td
#> class="odd">1.0 2.0 3.0<td class="statistics odd">F1,246=0.66, P=0.423
#> <td class="header even tg-label"><span class="variable">TStage<td
#> class="even data N"><span class="N">249<td class="even">2.0 3.0 4.0<td
#> class="even">2.0 3.0 4.0<td class="statistics even">F1,246=0.54,
#> P=0.463
#> <div class="footnote">N is the number of non-missing value.
#> 1Kruskal-Wallis. 2Pearson. 3Wilcoxon.Data Visualization
Age Pyramid
Visualize age and sex distribution:
agepyramid(
data = histopathology,
age = "Age",
gender = "Sex",
female = "Female"
)
#>
#> AGE PYRAMID
#>
#> Population Data
#> ────────────────────────────────
#> Population Female Male
#> ────────────────────────────────
#> (70,73] 8 5
#> (65,70] 17 11
#> (60,65] 16 10
#> (55,60] 14 17
#> (50,55] 8 11
#> (45,50] 8 15
#> (40,45] 19 14
#> (35,40] 13 15
#> (30,35] 6 13
#> (25,30] 10 17
#> (20,25] 1 0
#> ────────────────────────────────
Alluvial Diagrams
Show relationships between categorical variables:
alluvial(
data = histopathology,
vars = c("Grade", "TStage", "LymphNodeMetastasis", "Outcome"),
condensationvar = "Outcome"
)
#>
#> ALLUVIAL DIAGRAMS
#>
#> character(0)
#> [1] "Number of flows: 49"
#> [1] "Original Dataframe reduced to 19.6 %"
#> [1] "Maximum weight of a single flow 5.6 %"
Venn Diagrams
Analyze overlap between sets:
# Create binary indicators for Venn diagram
histopathology_venn <- histopathology %>%
mutate(
LVI_present = ifelse(LVI == "Present", 1, 0),
PNI_present = ifelse(PNI == "Present", 1, 0),
LN_positive = ifelse(LymphNodeMetastasis == "Present", 1, 0)
)
venn(
data = histopathology_venn,
var1 = "LVI_present",
var1true = 1,
var2 = "PNI_present",
var2true = 1,
var3 = "LN_positive",
var3true = 1,
var4 = NULL,
var4true = NULL
)
#>
#> VENN DIAGRAM
#>
#> character(0)
Data Quality Assessment
Benford’s Law Analysis
Assess data quality using Benford’s law - useful for detecting fabricated data:
# Analyze first digits of continuous measurements
benford(
data = histopathology,
var = "MeasurementA"
)
#>
#> BENFORD ANALYSIS
#>
#> See
#> <a href = 'https://github.com/carloscinelli/benford.analysis'>Package
#> documentation for interpratation.
#>
#> Benford object:
#>
#> Data: var
#> Number of observations used = 135
#> Number of obs. for second order = 134
#> First digits analysed = 2
#>
#> Mantissa:
#>
#> Statistic Value
#> Mean 0.506
#> Var 0.108
#> Ex.Kurtosis -1.514
#> Skewness -0.037
#>
#>
#> The 5 largest deviations:
#>
#> digits absolute.diff
#> 1 52 4.88
#> 2 17 4.65
#> 3 66 4.12
#> 4 13 3.66
#> 5 16 3.55
#>
#> Stats:
#>
#> Pearson's Chi-squared test
#>
#> data: var
#> X-squared = 137.97, df = 89, p-value = 0.0006808
#>
#>
#> Mantissa Arc Test
#>
#> data: var
#> L2 = 0.058715, df = 2, p-value = 0.000361
#>
#> Mean Absolute Deviation (MAD): 0.008005873
#> MAD Conformity - Nigrini (2012): Nonconformity
#> Distortion Factor: NaN
#>
#> Remember: Real data will never conform perfectly to Benford's Law. You should not focus on p-values! MeasurementA
#> <num>
#> 1: 0.0176978
#> 2: 1.7391655
#> 3: 0.5256537
#> 4: 1.7557878
#> 5: 0.5239132
#> 6: 0.1729459
#> 7: 0.1769035
#> 8: 0.5289038
#> 9: 0.5236107
#> 10: 1.7691411
#> 11: 0.5241260
#> 12: 0.5263020
#> 13: 1.7349714
#> 14: 0.1749262
#> $xlog
#> [1] FALSE
#>
#> $ylog
#> [1] FALSE
#>
#> $adj
#> [1] 0.5
#>
#> $ann
#> [1] TRUE
#>
#> $ask
#> [1] FALSE
#>
#> $bg
#> [1] "transparent"
#>
#> $bty
#> [1] "o"
#>
#> $cex
#> [1] 0.66
#>
#> $cex.axis
#> [1] 1
#>
#> $cex.lab
#> [1] 1
#>
#> $cex.main
#> [1] 1.2
#>
#> $cex.sub
#> [1] 1
#>
#> $col
#> [1] "black"
#>
#> $col.axis
#> [1] "black"
#>
#> $col.lab
#> [1] "black"
#>
#> $col.main
#> [1] "black"
#>
#> $col.sub
#> [1] "black"
#>
#> $crt
#> [1] 0
#>
#> $err
#> [1] 0
#>
#> $family
#> [1] ""
#>
#> $fg
#> [1] "black"
#>
#> $fig
#> [1] 0.6666667 1.0000000 0.0000000 0.5000000
#>
#> $fin
#> [1] 7 5
#>
#> $font
#> [1] 1
#>
#> $font.axis
#> [1] 1
#>
#> $font.lab
#> [1] 1
#>
#> $font.main
#> [1] 2
#>
#> $font.sub
#> [1] 1
#>
#> $lab
#> [1] 5 5 7
#>
#> $las
#> [1] 0
#>
#> $lend
#> [1] "round"
#>
#> $lheight
#> [1] 1
#>
#> $ljoin
#> [1] "round"
#>
#> $lmitre
#> [1] 10
#>
#> $lty
#> [1] "solid"
#>
#> $lwd
#> [1] 1
#>
#> $mai
#> [1] 1.02 0.82 0.82 0.42
#>
#> $mar
#> [1] 5.1 4.1 4.1 2.1
#>
#> $mex
#> [1] 1
#>
#> $mfcol
#> [1] 1 1
#>
#> $mfg
#> [1] 1 1 1 1
#>
#> $mfrow
#> [1] 1 1
#>
#> $mgp
#> [1] 3 1 0
#>
#> $mkh
#> [1] 0.001
#>
#> $new
#> [1] TRUE
#>
#> $oma
#> [1] 0 0 0 0
#>
#> $omd
#> [1] 0 1 0 1
#>
#> $omi
#> [1] 0 0 0 0
#>
#> $pch
#> [1] 1
#>
#> $pin
#> [1] 5.76 3.16
#>
#> $plt
#> [1] 0.08857143 0.91142857 0.18400000 0.81600000
#>
#> $ps
#> [1] 12
#>
#> $pty
#> [1] "m"
#>
#> $smo
#> [1] 1
#>
#> $srt
#> [1] 0
#>
#> $tck
#> [1] NA
#>
#> $tcl
#> [1] -0.5
#>
#> $usr
#> [1] 0.568 1.432 0.568 1.432
#>
#> $xaxp
#> [1] 0 1 5
#>
#> $xaxs
#> [1] "r"
#>
#> $xaxt
#> [1] "s"
#>
#> $xpd
#> [1] FALSE
#>
#> $yaxp
#> [1] 0 1 5
#>
#> $yaxs
#> [1] "r"
#>
#> $yaxt
#> [1] "s"
#>
#> $ylbias
#> [1] 0.2Variable Tree Summary
Get a hierarchical overview of your dataset:
# Variable tree visualization example
# Note: vartree requires specific parameter configuration for optimal results
# This is a demonstration of the function call structure
vartree_result <- vartree(
data = histopathology,
vars = c("Grade", "TStage", "LVI", "PNI"),
percvar = NULL,
percvarLevel = NULL,
summaryvar = NULL,
prunebelow = NULL,
pruneLevel1 = NULL,
pruneLevel2 = NULL,
follow = NULL,
followLevel1 = NULL,
followLevel2 = NULL,
excl = FALSE,
vp = TRUE,
horizontal = FALSE,
sline = TRUE,
varnames = FALSE,
nodelabel = TRUE,
pct = FALSE
)
# For detailed vartree examples, see the vartree-specific vignette
cat("Variable tree visualization complete. See vartree documentation for advanced usage.")Working with Treatment Response Data
Load the treatment response dataset for oncology-specific analyses:
# Load treatment response data
data(treatmentResponse)
if(exists("treatmentResponse")) {
head(treatmentResponse)
} else {
cat("treatmentResponse dataset not found. Using histopathology dataset instead.\n")
head(histopathology)
}
#> PatientID ResponseValue
#> 1 PT0001 63.5
#> 2 PT0002 -100.0
#> 3 PT0003 -20.5
#> 4 PT0004 55.1
#> 5 PT0005 -60.5
#> 6 PT0006 -93.6Waterfall Plot
Visualize individual patient treatment responses:
# Waterfall plot example (requires proper treatmentResponse dataset)
if(exists("treatmentResponse") && "PatientID" %in% names(treatmentResponse)) {
waterfall(
data = treatmentResponse,
patientID = "PatientID",
responseVar = "ResponseValue",
timeVar = NULL,
showWaterfallPlot = TRUE
)
} else {
cat("Waterfall plot requires treatmentResponse dataset with PatientID and ResponseValue columns.\n")
cat("See waterfall vignette for detailed examples with proper data structure.\n")
}Integration with jamovi
All functions in this package are also available through jamovi’s graphical interface:
- Install the module in jamovi
-
Navigate to:
Exploration > ClinicoPath Descriptives - Select your analysis function
- Configure options through the GUI
- Generate results with point-and-click ease
Next Steps
This vignette covered the basic functionality of ClinicoPathDescriptives. For more advanced usage, see:
- Clinical Workflow Vignette: Complete analysis workflows for clinical research
-
Treatment Response Analysis: Advanced oncology
analysis techniques
- Data Quality and Exploration: Comprehensive data assessment methods
- Visualization Gallery: Advanced plotting techniques and customization
Citation
citation("ClinicoPathDescriptives")