ClinicoPath jamovi Module
The umbrella jamovi module — and, contrary to how this page previously read, the primary product rather than a wrapper: it holds 388 analyses against 58 across all five sub-modules combined.
Purpose
Provide one implementation of each statistical analysis the group needs, exposed through a jamovi GUI so clinicians and trainees can run it without writing R. Stated rationale: lower friction than raw R, a reproducible analysis chain recorded in every jamovi file, each function implemented once and used everywhere, and publication-ready output.
Data used
Not a data project. Ships 929 bundled .rda datasets for examples and install verification; the documented smoke test is the Kaplan-Meier example on a bundled dataset.
Methods
Package ClinicoPath, version 1.0.1. 388 analyses (jamovi/*.a.yaml), each with a matching R backend (R/*.b.R), and 811 test files.
The correction that reorganises this page
This page previously described the module as an “umbrella over five focused sub-modules”. Read from source on 2026-07-26, that is misleading about where the capability lives:
| Module | Analyses |
|---|---|
| ClinicoPath (umbrella) | 388 |
| jjstatsplot | 18 |
| meddecide | 14 |
| ClinicoPathDescriptives | 14 |
| jsurvival | 8 |
| OncoPath | 4 |
| Five sub-modules combined | 58 |
Roughly 330 analyses exist only in the umbrella. The sub-modules are curated subsets for users who want a focused install, not the place the work lives. Every sub-module page in this repository previously described capabilities that are in fact only in the umbrella — each has been corrected, and the pattern is noted on all five.
Concretely, the umbrella is where these live: the advanced survival stack (flexmultistate, markovmultistate, curemodels, recurrentsurvival, finegray, landmarkanalysis, four frailty variants, robustaft, treatmentswitching, tumorgrowth), the ML layer (gradientboosting, lassocox, adaptivelasso, grouplasso, treeensemble, extratrees, highdimcox, ncvregcox), model evaluation (concordanceindex, brierscore, clinicalvalidation, aivalidation), interpretability (explainableai, biomarkerdiscovery, clinicalprediction), decision curves (decisioncurve, bayesdca, timedependentdca), oncology (stagemigration, jjoncoplot, circos, subgroupforest, groupedforest, jforester), plus mantelhaenszel, mixedmodelanova and optimalcutpoint.
Documentation convention versus reality
The stated convention is that every function has a vignette written by whoever adds it. Counting vignettes/*.Rmd against analyses:
| Module | Analyses | Vignettes |
|---|---|---|
| ClinicoPath (umbrella) | 388 | 32 |
| jjstatsplot | 18 | 63 |
| ClinicoPathDescriptives | 14 | 61 |
| meddecide | 14 | 55 |
| jsurvival | 8 | 35 |
| OncoPath | 4 | 7 |
The convention holds comfortably in the focused sub-modules — several vignettes per analysis — and does not hold in the umbrella, which is precisely where the 330 analyses that exist nowhere else are. That is the documentation gap worth naming: the least-documented code is the code with no other home.
Current state / open questions
Active. All six repositories are at version 1.0.1 and were last committed 2026-07-16, a coordinated release. Conventions: one function = one jamovi analysis panel = one documented example in the .yaml. WIP forks (ClinicoPathDescriptives-WIP, meddecide-WIP, jsurvival-WIP) exist and are explicitly not to be published from.
- With 388 analyses and 32 umbrella vignettes, is the vignette convention still intended to apply to umbrella-only functions, or has the umbrella become a different kind of artefact — a superset release — with documentation expected to live in the sub-modules? The answer decides whether the gap above is debt or design.
[unverified] - Is there a published mapping of which analyses belong to which sub-module? Working it out required listing
.a.yamlfiles across all six repositories, and it is the thing a user most needs in order to know which module to install. - 811 test files against 388 analyses, with no coverage figure recorded anywhere.
[unverified]
Related: the five sub-modules — ClinicoPathDescriptives, jsurvival, meddecide, jjstatsplot, OncoPath. Satellite/specialty modules named in the chapter: ClinicoPathShiny, ggstatsplot, vijPlots, conttablesplus, jPwrSS, jmvbaseR, gamlj, jamoviPsychoPDA, BrawStats-for-Jamovi-Full.
jamovi Module Development — how the declarative layer works, and why 388 analyses against 32 vignettes is a predictable outcome rather than an accident: the framework makes adding an analysis cheap and says nothing about explaining it.
ClinicoPath Org Collection — the reference library, where gamlj, vijPlots, jmvbaseR, jamoviPsychoPDA and BrawStats-for-Jamovi-Full named just above are all mirrored, alongside stale copies of this very module — check the warning at the top of that page before cloning anything named ClinicoPath from the org.
Derived from: repository working tree read 2026-07-26 — DESCRIPTION, the 388 jamovi/*.a.yaml analysis definitions, jamovi/concordanceindex.a.yaml, jamovi/multisurvival.a.yaml, data/, vignettes/, plus git ls-files/git log. Earlier content derived from jamovi/jamovi.qmd, onboarding.qmd, projects/projects.yml.