ClinicoPath

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.

🔬👀📑🗃📊🏨🗄📇📖⚗📝🎶📈📉📃🖍 🔬🔬🏋🚴🚙👨💻 📸📺🎛🔭🔬💊🔐🍫🌸

DOI 10.17605/OSF.IO/9SZUD

https://osf.io/9szud/

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/R4.0.2/ClinicoPathDescriptives-0.0.2.0039.jmo

https://library.jamovi.org/macos/R4.0.2/ClinicoPathDescriptives-0.0.2.0039.jmo

remotes::install_github("sbalci/ClinicoPathDescriptives")

- name: ClinicoPathDescriptives
  url: https://github.com/sbalci/ClinicoPathDescriptives.git
  commit: 190b914807518bf0e9139bc282eabcf3883a9e72
  platforms:
    - win64
    - macos

ClinicoPathLinuxDescriptives

ClinicoPathDescriptives functions for Linux

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

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

https://library.jamovi.org/linux/R4.0.2/ClinicoPathDescriptives-0.0.2.0041.jmo

remotes::install_github("sbalci/ClinicoPathDescriptives")

- name: ClinicoPathDescriptives
  url: https://github.com/sbalci/ClinicoPathLinuxDescriptives.git
  commit: cc63b37bd0a639194baf5a35db72783e05336027
  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/R4.0.2/jjstatsplot-0.0.2.0038.jmo

https://library.jamovi.org/macos/R4.0.2/jjstatsplot-0.0.2.0038.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: c49c23de8b9ff8a1569da4ee1b6f4fcc8cf61d1f
  platforms:
    - win64
    - macos

jsurvival

https://github.com/sbalci/jsurvival

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

https://library.jamovi.org/macos/R4.0.2/jsurvival-0.0.2.0044.jmo

https://library.jamovi.org/win64/R4.0.2/jsurvival-0.0.2.0044.jmo

https://library.jamovi.org/linux/R4.0.2/jsurvival-0.0.2.0044.jmo

remotes::install_github("sbalci/jsurvival")

- name: jsurvival
  url: https://github.com/sbalci/jsurvival.git
  commit: 9c57e504ddc0ceb42681f92b63ec0c0adf294436
  platforms:
    - win64
    - macos
    - linux

meddecide

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

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

https://library.jamovi.org/win64/R4.1.2/meddecide-0.0.2.07.jmo

https://library.jamovi.org/macos/R4.1.2/meddecide-0.0.2.07.jmo

remotes::install_github("sbalci/meddecide")

- name: meddecide
  url: https://github.com/sbalci/meddecide.git
  commit: 38aaf74a807241def57c23b99cc89a31a1ed5123

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:

Screenshots of Module

Example Datasets

Using Example Datasets

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

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

ClinicoPath Comparisons

Cross Tables

Pairwise Chi-Square Tests

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

JJStatsPlot

Graphs and Plots

Survival

jsurvival

Univariate Survival Analysis

Multivariate Survival Analysis

Univariate Survival Analysis for Continuous Explanatory Variable

Odds Ratio Table and Plot

Competing Survival

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

meddecide

Agreement

Interrater Reliability

ICC coefficients

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

Decision

Medical Decision

Decision Calculator

Decision Tree

explore

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

FFTrees

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

rpart

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

ROC

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

Correlation

Correlation

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

Installation in R

You can install the development version from GitHub with:

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

Current Package Versions:

R: 4.0.2

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

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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