In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

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ClinicoPath

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ClinicoPath jamovi Module 🔬

A jamovi Module that contains main analysis used in ClinicoPathological research. ClinicoPath help researchers to generate natural language summaries of their dataset, generate cross tables with statistical tests, and survival analysis with survival tables, survival curves, and natural language summaries.

🔬👀📑🗃📊🏨🗄📇📖⚗📝🎶📈📉📃🖍 🔬🔬🏋🚴🚙👨💻 📸📺🎛🔭🔬💊🔐🍫🌸

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https://zenodo.org/account/settings/github/repository/sbalci/ClinicoPathJamoviModule

DOI 10.17605/OSF.IO/9SZUD

https://osf.io/9szud/

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Installation in jamovi

You can install this module after installing jamovi version >= 1.2.19 from here: https://www.jamovi.org/download.html

Then you can install the submodules directly inside the jamovi, using library.

Submodules are:

• ClinicoPathDescriptives
• jsurvival
• meddecide
• jjstatsplot

Installation via sideload jamovi

Step 1:

Download and install jamovi.

Step 2:

Download the relevant jmo file for your operating system from

a: For development version

• releases
• sourceforge.

b: For smaller modules

ClinicoPathDescriptives

ClinicoPathDescriptives functions are separately added to jamovi library under Exploration menu

ClinicoPathDescriptives module can be downloaded inside jamovi (click Modules and jamovi library)

https://github.com/sbalci/ClinicoPathDescriptives/

https://github.com/sbalci/ClinicoPathDescriptives/releases/

https://library.jamovi.org/win64/R4.0.5/ClinicoPathDescriptives-0.0.2.02.jmo

https://library.jamovi.org/macos/R4.0.5/ClinicoPathDescriptives-0.0.2.02.jmo

remotes::install_github("sbalci/ClinicoPathDescriptives")

- name: ClinicoPathDescriptives
  url: https://github.com/sbalci/ClinicoPathDescriptives.git
  commit: c425bb0021a097b76666006c19b3b87fa137264e
  platforms:
    - win64
    - macos

ClinicoPathLinuxDescriptives

ClinicoPath Descriptives functions for Linux

https://github.com/sbalci/ClinicoPathLinuxDescriptives/

https://github.com/sbalci/ClinicoPathLinuxDescriptives/releases/

https://library.jamovi.org/linux/R4.0.5/ClinicoPathLinuxDescriptives-0.0.2.0084.jmo

remotes::install_github("sbalci/ClinicoPathLinuxDescriptives")

- name: ClinicoPathDescriptives
  url: https://github.com/sbalci/ClinicoPathLinuxDescriptives.git
  commit: 0bac188199fda2e8397f09a1416e162c18f6c85d
  platforms:
    - linux

JJStatsPlot

GGStatsPlot functions are separately added to jamovi library under jjstatsplot menu

JJStastPlot module can be downloaded inside jamovi (click Modules and jamovi library)

https://library.jamovi.org/win64/R4.0.5/jjstatsplot-0.0.2.02.jmo

https://library.jamovi.org/macos/R4.0.5/jjstatsplot-0.0.2.02.jmo

https://github.com/sbalci/jjstatsplot

https://github.com/sbalci/jjstatsplot/releases/

remotes::install_github("sbalci/jjstatsplot")

- name: jjstatsplot
  url: https://github.com/sbalci/jjstatsplot.git
  commit: b26c2c37f02b25ff3c3d32391a5cc7f413373a9d
  platforms:
    - win64
    - macos

jsurvival

https://github.com/sbalci/jsurvival

https://github.com/sbalci/jsurvival/releases/

https://library.jamovi.org/macos/R4.0.5/jsurvival-0.0.2.02.jmo

https://library.jamovi.org/win64/R4.0.5/jsurvival-0.0.2.02.jmo

remotes::install_github("sbalci/jsurvival")

- name: jsurvival
  url: https://github.com/sbalci/jsurvival.git
  commit: 080034635c3f0173e5a22ddd2614d0af90504763
  platforms:
    - win64
    - macos

meddecide

https://github.com/sbalci/meddecide/

https://github.com/sbalci/meddecide/releases/

https://library.jamovi.org/win64/R4.0.5/meddecide-0.0.2.04.jmo

https://library.jamovi.org/macos/R4.0.5/meddecide-0.0.2.04.jmo

remotes::install_github("sbalci/meddecide")

- name: meddecide
  url: https://github.com/sbalci/meddecide.git
  commit: 2bda14af05d8dafe33d9d137705f9fb8ac527279
  platforms:
    - win64
    - macos

jbbplot

https://github.com/sbalci/jbbplot/

https://github.com/sbalci/jbbplot/releases/

remotes::install_github("sbalci/jbbplot")

Step 3: And install using side-load as shown below:

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Screenshots of Module

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Example Datasets

Using Example Datasets

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https://cloud.jamovi.org/?open=https://raw.githubusercontent.com/sbalci/ClinicoPathJamoviModule/master/data/histopathology.csv

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https://cloud.jamovi.org/?open=https://raw.githubusercontent.com/sbalci/ClinicoPathJamoviModule/master/data/histopathology.omv

https://cloud.jamovi.org/?open=https://docs.google.com/spreadsheets/d/e/2PACX-1vST3kwze9bNUSEr0eijs_81F6hXBrDZ-2Zt97ez-fbpXMELKGFHJNuQHSP2Oxars2C6F3n50KzT1-zD/pub?output=csv

Exploration

ClinicoPath Descriptives

TableOne

Summary of Continuous Variables

Summary of Categorical Variables

Benford Analysis

ClinicoPath Descriptive Plots

Variable Tree

Alluvial Diagrams

Age Pyramid

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ClinicoPath Comparisons

Cross Tables

Pairwise Chi-Square Tests

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

JJStatsPlot

Graphs and Plots

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Survival

jsurvival

Univariate Survival Analysis

Multivariate Survival Analysis

Univariate Survival Analysis for Continuous Explanatory Variable

Odds Ratio Table and Plot

Competing Survival

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

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meddecide

Agreement

Interrater Reliability

ICC coefficients

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

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Decision

Medical Decision

Decision Calculator

Decision Tree

explore

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

FFTrees

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

rpart

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

ROC

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

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Correlation

Correlation

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

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Installation in R

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("sbalci/ClinicoPathJamoviModule")

Current Package Versions:

R: 4.0.5

MRAN: https://cran.microsoft.com/snapshot/2020-08-24

Acknowledgement {#acknowledgement}

Made possible via the codes, help, and guidence of

• jamovi developer Jonathon Love,
• finalfit developer Ewen Harrison,
• ggstatsplot developer Indrajeet Patil,
• tangram developer Shawn Garbett,
• easystats developers ,
• report ,
• tableone,
• survival,
• survminer,
• vtree developer Nick Barrowman,
• easyalluvial, developer Björn Oettinghaus, and
• rstats community.

See https://github.com/ClinicoPath for forked packages.

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Development Status

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sbalci/ClinicoPathJamoviModule documentation built on Feb. 25, 2025, 6:34 a.m.