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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.

🔬👀📑🗃📊🏨🗄📇📖⚗📝🎶📈📉📃🖍 🔬🔬🏋🚴🚙👨💻 📸📺🎛🔭🔬💊🔐🍫🌸

<!-- 🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩 -->

Download ClinicoPathJamoviModule <a href="https://www.buymeacoffee.com/bS0teIs" target="_blank">

DOI

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

<img src="man/figures/jamovi-library.png" align="center" width = 75% /> <img src="man/figures/jamovi-ClinicoPath-0.0.2-released.gif" align="center" width = 75% />

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

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/linux/R3.6.3/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/linux/R4.0.2/meddecide-0.0.1.0005.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")
<!-- #### c: For stable version --> <!-- - windows: https://library.jamovi.org/win64/R3.6.3/ClinicoPath-0.0.2.jmo --> <!-- - macOS: https://library.jamovi.org/macos/R3.6.3/ClinicoPath-0.0.2.jmo --> <!-- - linux: https://library.jamovi.org/linux/R3.6.3/ClinicoPath-0.0.2.jmo -->

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

<img src="man/figures/jamovi-sideload.gif" align="center" width = 75% />

Screenshots of Module

Example Datasets

Using Example Datasets

<img src="man/figures/jamovi-ClinicoPath-example-datasets.gif" align="center" width = 75% />

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
<img src="man/figures/jamovi-and-R-tableone.gif" align="center" width = 75% /> <img src="man/figures/jamovi-ClinicoPath-tableone.gif" align="center" width = 75% />
Summary of Continuous Variables
<img src="man/figures/jamovi-write-summary-continuous-variables.gif" align="center" width = 75% />
Summary of Categorical Variables
<img src="man/figures/jamovi-and-R-report.gif" align="center" width = 75% />
Benford Analysis
<img src="man/figures/jamovi-ClinicoPath-BenfordAnalysis.gif" align="center" width = 75% />

ClinicoPath Descriptive Plots

Variable Tree
<img src="man/figures/jamovi-ClinicoPath-VariableTree.gif" align="center" width = 75% /> <img src="man/figures/jamovi-ClinicoPath-VariableTree2.gif" align="center" width = 75% />
Alluvial Diagrams
<img src="man/figures/jamovi-ClinicoPath-easyalluvial.gif" align="center" width = 75% />
Age Pyramid
<img src="man/figures/jamovi-ClinicoPath-age-pyramid.png" align="center" width = 75% />

ClinicoPath Comparisons

Cross Tables
<img src="man/figures/jamovi-and-R-tangram.png" align="center" width = 75% /> <img src="man/figures/jamovi-and-tangram-crosstable.gif" align="center" width = 75% /> <img src="man/figures/jamovi-and-CrossTable-FinalFit.png" align="center" width = 75% />
Pairwise Chi-Square Tests

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

JJStatsPlot

Graphs and Plots

<img src="man/figures/jamovi-ClinicoPath-ggstatsplot-alluvial-plots.gif" align="center" width = 75% /> <img src="man/figures/jamovi-and-R-ggstatsplot.png" align="center" width = 75% /> <img src="man/figures/jamovi-and-ggstatsplot.gif" align="center" width = 75% />

Survival

jsurvival

Univariate Survival Analysis
<img src="man/figures/jamovi-and-survival-analysis-finalfit.png" align="center" width = 75% /> <img src="man/figures/jamovi-and-survival-analysis-finalfit-2.png" align="center" width = 75% /> <img src="man/figures/jamovi-and-survival-analysis-finalfit-3.png" align="center" width = 75% /> <img src="man/figures/jamovi-KMunicate-survival.png" align="center" width = 75% />
Multivariate Survival Analysis
<img src="man/figures/jamovi-and-survival-analysis-multivariate-finalfit.png" align="center" width = 75% /> <img src="man/figures/jamovi-and-multivariate-survival.gif" align="center" width = 75% /> <img src="man/figures/jamovi-clinicopath-multivariate-survival.gif" align="center" width = 75% />
Univariate Survival Analysis for Continuous Explanatory Variable
Odds Ratio Table and Plot
<img src="man/figures/jamovi-ClinicoPath-oddsratio.gif" align="center" width = 75% />
Competing Survival

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

meddecide

Agreement

Interrater Reliability
<img src="man/figures/jamovi-clinicopath-kappa-irr.png" align="center" width = 75% />
ICC coefficients

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

Decision

Medical Decision
<img src="man/figures/jamovi-and-R-caret-from-data.png" align="center" width = 75% />
Decision Calculator
<img src="man/figures/jamovi-and-R-caret-user-input.png" align="center" width = 75% /> <img src="man/figures/jamovi-ClinicoPath-FaganNomogram.gif" align="center" width = 75% />
Decision Tree
explore

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

<img src="man/figures/jamovi-clinicopath-explore-decision-tree.png" align="center" width = 75% />
FFTrees

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

<img src="man/figures/jamovi-clinicopath-FFTrees-decision-tree.png" align="center" width = 75% />
rpart

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

<img src="man/figures/jamovi-clinicopath-rpart-decision-tree.png" align="center" width = 75% />
ROC

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

Correlation

Correlation

🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩

Installation in R

<!-- You can install the released version of ClinicoPath from [CRAN](https://CRAN.R-project.org) with: --> <!-- ``` r --> <!-- install.packages("ClinicoPath") --> <!-- ``` -->

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

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

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Development Status

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Launch Rstudio Binder Gitpod Ready-to-Code Download ClinicoPathJamoviModule Project Status: Active – The project has reached a stable, usable state and is being actively developed.
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Code
Launch Rstudio Binder Gitpod Ready-to-Code Download ClinicoPathJamoviModule

Status
Project Status: Active – The project has reached a stable, usable state and is being actively developed.
lifecycle stability-unstable GitHub issues GitHub issues

Check, CI
R-CMD-check

Codacy Badge CodeFactor Coverage Status Build Status Build status codecov CircleCI GuardRails badge Maintainability Test Coverage

<!-- [![DepShield Badge](https://depshield.sonatype.org/badges/sbalci/ClinicoPathJamoviModule/depshield.svg)](https://depshield.github.io) -->

Recency, Updates
GitHub

<!-- [![GitHub version](https://img.shields.io/badge/GitHub-0.0.1.1000-orange.svg?style=flat-square)](https://github.com/sbalci/clinicopathjamovimodule/) -->

GitHub last commit Last-changedate GitHub Release Date GitHub commit activity

Webpage, Links, Size, Download
Website GitHub code size in bytes

Dependencies
minimal R version Libraries.io dependency status for GitHub repo Requirements Status

<!-- [![DepShield Badge](https://depshield.sonatype.org/badges/sbalci/clinicopathjamovimodule/depshield.svg)](https://depshield.github.io) -->

Interaction, Shares
GitHub forks GitHub forks GitHub stars Github Stars GitHub stars Twitter contributions welcome GitHub watchers

Videos

<iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLxRBOaoEoP4JfAMi7aIbkRXPXGUEwzTNv" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> </iframe>