ClinicoPathDescriptives
The descriptive-statistics sub-module — Table 1 and cross-tabs as advertised, plus a data-quality and visualisation layer, including Benford analysis, that this page had never mentioned.
Purpose
Produce the tables that appear on the first page of almost every clinicopathological paper, reproducibly and in a consistent house style.
Data used
Any cohort dataset opened in jamovi. No project-specific data.
Methods
Package ClinicoPathDescriptives, version 1.0.1, 14 analyses, 61 vignettes.
| Analysis | What it is |
|---|---|
tableone |
Table One |
crosstable |
Cross Tables |
chisqposttest |
Chi-Square Post-Hoc Tests |
summarydata |
Summary of Continuous Variables |
reportcat |
Summary of Categorical Variables |
categorize |
Categorize Continuous Variables |
checkdata |
Single Variable Quality Check |
dataquality |
Multi-Variable Visual Quality |
outlierdetection |
Outlier Detection |
benford |
Benford Analysis |
vartree |
Variable Tree |
alluvial |
Alluvial Diagrams |
agepyramid |
Age Pyramid |
venn |
Venn Diagram |
Correction: two claimed methods are in the umbrella
Mantel-Haenszel stratified analysis and mixed-model ANOVA were both listed here. Neither is in this repository — they are mantelhaenszel and mixedmodelanova in ClinicoPath jamovi Module. A focused install of this module gets neither.
The half of the module that was undocumented
Six of the fourteen analyses are a data-quality and integrity layer that no page mentioned, and it is arguably the more interesting half:
benford— Benford’s law analysis. This is a data-integrity check: digit distributions that deviate from Benford’s expectation are a classic signal of fabricated or mishandled numeric data. Having it in the standard descriptive toolkit is a research-integrity capability that nothing in this wiki records the group as having.checkdata,dataquality,outlierdetection— single-variable and multi-variable quality screening before analysis begins.vartree,alluvial,agepyramid,venn— cohort structure and flow visualisation.
The claimed “missingness summaries per variable and per pattern” is plausibly checkdata and dataquality rather than a dedicated missingness analysis; the umbrella additionally has a missingdataexplorer. [unverified] which the chapter meant.
Current state / open questions
Active; last commit 2026-07-16 at version 1.0.1, in step with the other five. Shipped inside ClinicoPath jamovi Module and also available as a focused module.
Documented pitfalls: don’t paste raw p-values across rows without using the module’s adjusted column; verify in the footnote that the module switched to median [IQR] for skewed continuous variables; small-cell chi-square warnings are meaningful — switch to Fisher’s exact rather than silencing them.
categorizeis where continuous-variable categorisation lives, not OncoPath as Biomarker Cut Points previously stated. The ROC-derived and validated cut-point procedures areoptimalcutpointin the umbrella. That page is corrected.- Has
benfordever been run on a group dataset? A data-integrity screen that exists and is never used is worth either adopting into the standard intake or noting as unused.[unverified] - Does the group’s Table 1 house style live in this module’s defaults, or in per-paper configuration? The claim of a consistent house style across papers implies the former and nothing records it.
[unverified]
Related: ClinicoPath jamovi Module — the umbrella, which holds Mantel-Haenszel and mixed-model ANOVA. Descriptive Tables — the method page this module implements. Biomarker Cut Points — corrected to point at categorize here and optimalcutpoint in the umbrella.
Derived from: repository working tree read 2026-07-26 — DESCRIPTION, the 14 jamovi/*.a.yaml files, vignettes/, plus git ls-files/git log; and the umbrella’s analysis inventory for the correction. Earlier content derived from jamovi/ClinicoPathDescriptives.qmd.