In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

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

This vignette focuses on the functions that generate tables and textual summaries.

Continuous Variables

summarydata() provides descriptive statistics (mean, median, quartiles) for numeric variables.

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

Categorical Variables

reportcat() summarises categorical variables with counts and percentages.

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

Cross Tables

Use crosstable() to create cross tabulations with statistical tests. The group argument defines the column variable.

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

Table One for Publications

tableone() creates publication-ready tables of baseline characteristics.

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

These functions output results objects that contain tables which can be converted to data frames for further customisation.

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