ClinicoPathDescriptives

Descriptive statistics, Table 1, cross-tabulations, and stratified analysis for clinicopathological datasets

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What it does

The descriptive-statistics arm of the ClinicoPathJamoviModule. Produces the tables that appear on the first page of almost every clinicopathological paper:

• Table 1 — publication-ready baseline characteristics, auto-formatted.
• Categorical cross-tabs with chi-square / Fisher’s exact, and weighted / unweighted percentages.
• Stratified analysis (Mantel–Haenszel) for confounder adjustment in 2×2 tables.
• Mixed-model ANOVA for repeated-measures and nested designs.
• Missingness summaries — per variable and per pattern.

When to use

• You’re starting a new cohort analysis and need the baseline table.
• You want a reproducible alternative to hand-formatting Table 1 in Word.
• You need a consistent cross-tab style across every paper in the group.

Repo

• ClinicoPathDescriptives — the focused descriptives module.
• Shipped inside ClinicoPathJamoviModule — if you have the umbrella module installed, you already have this.

Quick start in jamovi

1. Open your dataset.
2. Analyses → ClinicoPath → Descriptives → Table 1.
3. Move baseline variables into the right-hand box.
4. Add the grouping variable (treatment arm, outcome, etc.).
5. Copy the output table straight into your manuscript.

Quick start in R

library(ClinicoPathDescriptives)
table1_result <- tableone_analysis(
  data = mydata,
  vars = c("age", "sex", "grade", "stage"),
  strata = "arm"
)

Pitfalls

• Don’t paste raw p-values across rows without adjusting for multiple comparisons — the module’s output includes an adjusted column; use it.
• For skewed continuous variables, confirm the module switched to median [IQR] — it does so automatically when normality fails, but verify in the footnote.
• Small-cell chi-square warnings are meaningful. Don’t silence them; switch to Fisher’s exact when flagged.