jamovi — Overview

The group’s statistical backbone: ClinicoPath + focused sub-modules, all behind a jamovi GUI

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Repo	Use for
template	Generic Quarto + R scaffold for a new study
histopathology-template	Case-series / clinical-study scaffold

JamoviTest | Quick jamovi-module sanity check |

• MyRCodesForDataAnalysis — snippets used across studies.

• histopatoloji-calismalarinda-biyoistatistik-icin-veri-hazirlama — data-preparation helpers (TR).

• clinicopathological — shared clinicopathological data helpers.

• New case series or study? Clone histopathology-template.

• New statistical function? Add it to ClinicoPathJamoviModule

Why jamovi

• Lower friction for clinicians and trainees than raw R.
• Reproducible: every jamovi file records the full analysis chain.
• Each function is implemented once, used everywhere.
• Output is publication-ready — Table 1, KM curves, decision curves, forest plots.

Modules in the sidebar

Page	Scope
ClinicoPathDescriptives	Table 1, cross-tabs, stratified descriptives
jsurvival	Kaplan–Meier, Cox, competing risks, cure models, ML survival
meddecide	Diagnostic test evaluation, decision curves, agreement
jjstatsplot	Publication-ready statistical plots
OncoPath	Oncology-specific templates (staging, response, biomarkers)

Install order

1. ClinicoPathJamoviModule — always first.
2. Install the submodule(s) you need from the same sideload folder.
3. Verify the install by running the Kaplan–Meier example on the bundled dataset.

Satellite / specialty modules

• ClinicoPathShiny — Shiny web version.
• ggstatsplot, vijPlots — plot building blocks.
• conttablesplus, jPwrSS, jmvbaseR, gamlj, jamoviPsychoPDA, BrawStats-for-Jamovi-Full.

Work-in-progress (do not publish from)

• ClinicoPathDescriptives-WIP
• meddecide-WIP
• jsurvival-WIP

Conventions

• One function, one jamovi analysis panel, one documented example in the .yaml.
• Every function has a vignette — if you add a function, you write the vignette.
• Use ClinicoPathJamoviModule rather than reinventing analyses in raw R. Consistency across papers matters more than per-paper novelty.

How to contribute

1. Clone ClinicoPathJamoviModule and get devtools::load_all() green on your machine.
2. Pick a “good first issue” labeled in the repo.
3. Add a failing test, make it pass, write the vignette, open a PR.

In the research wiki

• ClinicoPath jamovi Module — the umbrella module read at source: the analysis count, and the rule that anything not listed on a sub-module page lives here.
• jamovi Module Development — how any of it is built — an R package with a declarative layer, where the GUI, the R API and the validation are generated from a YAML description.
• ClinicoPath Org Collection — the 205-repository organisation behind the modules, including the caution that its copies of these modules are stale mirrors.
• Descriptive Tables — the analysis these modules are used for most often.
• Survival Analysis Workflow — the second most common, and the one with the most ways to go wrong.