In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

Introduction

ClinicoPathDescriptives provides a suite of functions for summarising and visualising clinicopathological data. This vignette showcases the main tools in the package with reproducible examples. The package ships with example data sets histopathology and treatmentResponse to illustrate typical workflows.

# install.packages("ClinicoPathDescriptives")
library(ClinicoPathDescriptives)

# Example data
data(histopathology)
head(histopathology)

Summaries of Continuous Variables

Use summarydata() to obtain descriptive statistics for numeric variables.

summarydata(data = histopathology, vars = vars(Age, TumorSize))

Summaries of Categorical Variables

reportcat() creates frequency tables and counts for categorical variables.

reportcat(data = histopathology, vars = vars(Sex, Grade))

Cross Tables

Generate cross tabulations with chi-square tests using crosstable().

crosstable(
  data = histopathology,
  vars = vars(Sex, Grade),
  group = "PreinvasiveComponent",
  sty = "nejm",
  excl = TRUE
)

Table One

tableone() produces formatted baseline characteristic tables for reports.

tableone(
  data = histopathology,
  vars = vars(Sex, PreinvasiveComponent, LVI, PNI, Grade, Age),
  sty = "t3",
  excl = TRUE
)

Visualisations

The package includes multiple plotting functions to explore data.

Age Pyramid

agepyramid(
  data = histopathology,
  age = "Age",
  gender = "Sex",
  female = "Female"
)

Alluvial Diagrams

alluvial(
  data = histopathology,
  vars = vars(Grade, LVI, PNI),
  fill = "first_variable"
)

Benford Analysis

benford(data = histopathology, var = "TumorSize")

Venn and Variable Trees

venn(data = histopathology, vars = vars(LVI, PNI, PreinvasiveComponent))
vartree(
  data = histopathology,
  vars = vars(Grade, LVI, PNI),
  percvar = "Grade",
  percvarLevel = "High"
)

Waterfall Plots

waterfall() visualises tumor response over time.

waterfall(
  data = treatmentResponse,
  patientID = "PatientID",
  responseVar = "Response",
  timeVar = "Month",
  inputType = "percentage",
  showWaterfallPlot = TRUE,
  showSpiderPlot = TRUE
)

Conclusion

These examples demonstrate the versatility of ClinicoPathDescriptives for summarising and visualising clinicopathological data. Explore the help pages of each function for additional options and customisation.

sbalci/ClinicoPathJamoviModule documentation built on June 13, 2025, 9:34 a.m.