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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r global options, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# ClinicoPath
---
## ClinicoPath [jamovi](https://www.jamovi.org) Module 🔬
A [jamovi](https://www.jamovi.org) 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 🛠⛔️⚠️🔩 -->
---
[](https://sourceforge.net/projects/clinicopathjamovimodule/files/latest/download)
<a href="https://www.buymeacoffee.com/bS0teIs" target="_blank">
https://zenodo.org/account/settings/github/repository/sbalci/ClinicoPathJamoviModule
DOI 10.17605/OSF.IO/9SZUD
https://osf.io/9szud/
---
## Installation in [jamovi](https://www.jamovi.org)
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](https://www.jamovi.org)
### Step 1:
**Download and install [jamovi](https://www.jamovi.org).**
### Step 2:
**Download the relevant `jmo` file for your operating system from**
#### a: For development version
- [releases](https://github.com/sbalci/ClinicoPathJamoviModule/releases/)
- [sourceforge](https://sourceforge.net/projects/clinicopathjamovimodule/files/latest/download).
#### 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
```r
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
```r
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/linux/R3.6.3/jjstatsplot-0.0.2.0038.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/
```r
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
<!-- https://library.jamovi.org/linux/R4.0.5/jsurvival-0.0.2.02.jmo -->
```r
remotes::install_github("sbalci/jsurvival")
```
- name: jsurvival
url: https://github.com/sbalci/jsurvival.git
commit: 080034635c3f0173e5a22ddd2614d0af90504763
platforms:
- win64
- macos
<!-- - linux -->
##### 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/linux/R4.0.5/meddecide-0.0.1.0005.jmo -->
https://library.jamovi.org/macos/R4.0.5/meddecide-0.0.2.04.jmo
```r
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/
```r
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](https://github.com/) with:
``` r
# 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](https://www.jamovi.org/) developer [Jonathon Love](https://github.com/jonathon-love),
- [finalfit](https://finalfit.org/) developer [Ewen Harrison](https://github.com/ewenharrison),
- [ggstatsplot](https://indrajeetpatil.github.io/ggstatsplot/) developer [Indrajeet Patil](https://github.com/IndrajeetPatil),
- [tangram](https://github.com/spgarbet/tangram) developer [Shawn Garbett](https://github.com/spgarbet),
- [easystats](https://easystats.github.io/blog/) developers ,
- [report](https://easystats.github.io/report/) ,
- [tableone](https://github.com/kaz-yos/tableone),
- [survival](https://github.com/therneau/survival),
- [survminer](https://github.com/kassambara/survminer),
- [vtree](https://github.com/nbarrowman/vtree) developer [Nick Barrowman](https://github.com/nbarrowman),
- [easyalluvial](https://github.com/erblast/easyalluvial), developer [Björn Oettinghaus](https://github.com/erblast), and
- [rstats community](https://twitter.com/search?q=%23rstats&src=savs).
See https://github.com/ClinicoPath for forked packages.
---
<a class="twitter-follow-button" data-show-count="false" href="https://twitter.com/serdarbalci">Follow @serdarbalci</a><script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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https://paypal.me/serdarbalci
---
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[](https://saythanks.io/to/sbalci)
## Development Status
<!-- badges: start -->
[](https://mybinder.org/v2/gh/sbalci/ClinicoPathJamoviModule/master?urlpath=rstudio)
[](https://gitpod.io/#https://github.com/sbalci/ClinicoPathJamoviModule)
[](https://sourceforge.net/projects/clinicopathjamovimodule/files/latest/download)
[](https://www.repostatus.org/#active)
[](https://www.tidyverse.org/lifecycle/)
[](https://github.com/joethorley/stability-badges#unstable)
[](https://github.com/sbalci/clinicopathjamovimodule/issues)
[](https://www.codacy.com/manual/drserdarbalci/ClinicoPathJamoviModule?utm_source=github.com&utm_medium=referral&utm_content=sbalci/ClinicoPathJamoviModule&utm_campaign=Badge_Grade)
[](https://www.codefactor.io/repository/github/sbalci/clinicopathjamovimodule)
[](https://coveralls.io/github/sbalci/ClinicoPathJamoviModule?branch=master)
[](https://travis-ci.com/sbalci/ClinicoPathJamoviModule)
[](https://ci.appveyor.com/project/sbalci/clinicopathjamovimodule)
[](https://codecov.io/gh/sbalci/ClinicoPathJamoviModule)
[](https://circleci.com/gh/sbalci/ClinicoPathJamoviModule)
[](https://dashboard.guardrails.io/gh/sbalci/33943)
[](https://codeclimate.com/github/sbalci/ClinicoPathJamoviModule/maintainability)
[](https://codeclimate.com/github/sbalci/ClinicoPathJamoviModule/test_coverage)
[](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
[)`-yellowgreen.svg)](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
[](https://sbalci.github.io/ClinicoPathJamoviModule/)
[](https://github.com/sbalci/ClinicoPathJamoviModule)
[](https://cran.r-project.org/)
[](https://libraries.io/github/sbalci/clinicopathjamovimodule)
[](https://requires.io/github/sbalci/ClinicoPathJamoviModule/requirements/?branch=gh-pages)
[](https://github.com/sbalci/clinicopathjamovimodule/network)
[](https://github.com/sbalci/clinicopathjamovimodule/stargazers)
[](https://github.com/sbalci/clinicopathjamovimodule)
[](https://github.com/sbalci/clinicopathjamovimodule/issues)
[](https://codecov.io/gh/sbalci/ClinicoPathJamoviModule?branch=master)
<!-- badges: end -->
**Code**
[](https://mybinder.org/v2/gh/sbalci/ClinicoPathJamoviModule/master?urlpath=rstudio)
[](https://gitpod.io/#https://github.com/sbalci/ClinicoPathJamoviModule)
[](https://sourceforge.net/projects/clinicopathjamovimodule/files/latest/download)
**Status**
[](https://www.repostatus.org/#active)
[](https://www.tidyverse.org/lifecycle/)
[](https://github.com/joethorley/stability-badges#unstable)
[](https://github.com/sbalci/clinicopathjamovimodule/issues)
**Check, CI**
[](https://www.codacy.com/manual/drserdarbalci/ClinicoPathJamoviModule?utm_source=github.com&utm_medium=referral&utm_content=sbalci/ClinicoPathJamoviModule&utm_campaign=Badge_Grade)
[](https://www.codefactor.io/repository/github/sbalci/clinicopathjamovimodule)
[](https://coveralls.io/github/sbalci/ClinicoPathJamoviModule?branch=master)
[](https://travis-ci.com/sbalci/ClinicoPathJamoviModule)
[](https://ci.appveyor.com/project/sbalci/clinicopathjamovimodule)
[](https://codecov.io/gh/sbalci/ClinicoPathJamoviModule)
[](https://circleci.com/gh/sbalci/ClinicoPathJamoviModule)
[](https://dashboard.guardrails.io/gh/sbalci/33943)
[](https://codeclimate.com/github/sbalci/ClinicoPathJamoviModule/maintainability)
[](https://codeclimate.com/github/sbalci/ClinicoPathJamoviModule/test_coverage)
<!-- [](https://depshield.github.io) -->
**Recency, Updates**
<!-- [](https://github.com/sbalci/clinicopathjamovimodule/) -->
[](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
[)`-yellowgreen.svg)](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
**Webpage, Links, Size, Download**
[](https://sbalci.github.io/ClinicoPathJamoviModule/)
[](https://github.com/sbalci/ClinicoPathJamoviModule)
**Dependencies**
[](https://cran.r-project.org/)
[](https://libraries.io/github/sbalci/clinicopathjamovimodule)
[](https://requires.io/github/sbalci/ClinicoPathJamoviModule/requirements/?branch=gh-pages)
<!-- [](https://depshield.github.io) -->
**Interaction, Shares**
[](https://github.com/sbalci/clinicopathjamovimodule/network)
[](https://github.com/sbalci/clinicopathjamovimodule/stargazers)
[](https://github.com/sbalci/clinicopathjamovimodule)
[](https://twitter.com/intent/tweet?text=A%20@jamovistats%20module%20for%20%23histopathology%20%23clinicopathology%20%23pathology%20%23research%20using%20various%20%23rstats%20packages%20📦.%20@serdarbalci&url=https%3A%2F%2Fsbalci.github.io%2ClinicoPathJamoviModule%2)
[](https://github.com/sbalci/clinicopathjamovimodule/issues)
## 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>