ClinicoPathJamoviModule
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ClinicoPath jamovi Module
ClinicoPath
ClinicoPath jamovi Module π¬
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.
π¬πππππ¨πππβππΆππππ π¬π¬ππ΄ππ¨π» πΈπΊπππ¬πππ«πΈ
DOI 10.17605/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
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-library.png)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-0.0.2-released.gif)
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/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:
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-sideload.gif)
Screenshots of Module
Example Datasets
Using Example Datasets
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-example-datasets.gif)
Exploration
ClinicoPath Descriptives
TableOne
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-R-tableone.gif)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-tableone.gif)
Summary of Continuous Variables
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-write-summary-continuous-variables.gif)
Summary of Categorical Variables
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-R-report.gif)
Benford Analysis
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-BenfordAnalysis.gif)
ClinicoPath Descriptive Plots
Variable Tree
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-VariableTree.gif)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-VariableTree2.gif)
Alluvial Diagrams
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-easyalluvial.gif)
Age Pyramid
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-age-pyramid.png)
ClinicoPath Comparisons
Cross Tables
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-R-tangram.png)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-tangram-crosstable.gif)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-CrossTable-FinalFit.png)
Pairwise Chi-Square Tests
π¬π¬π¬π¬ UNDER CONSTRUCTION π βοΈβ οΈπ©
JJStatsPlot
Graphs and Plots
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-ggstatsplot-alluvial-plots.gif)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-R-ggstatsplot.png)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-ggstatsplot.gif)
Survival
jsurvival
Univariate Survival Analysis
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-survival-analysis-finalfit.png)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-survival-analysis-finalfit-2.png)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-survival-analysis-finalfit-3.png)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-KMunicate-survival.png)
Multivariate Survival Analysis
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-survival-analysis-multivariate-finalfit.png)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-multivariate-survival.gif)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-clinicopath-multivariate-survival.gif)
Univariate Survival Analysis for Continuous Explanatory Variable
Odds Ratio Table and Plot
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-oddsratio.gif)
Competing Survival
π¬π¬π¬π¬ UNDER CONSTRUCTION π βοΈβ οΈπ©
meddecide
Agreement
Interrater Reliability
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-clinicopath-kappa-irr.png)
ICC coefficients
π¬π¬π¬π¬ UNDER CONSTRUCTION π βοΈβ οΈπ©
Decision
Medical Decision
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-R-caret-from-data.png)
Decision Calculator
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-and-R-caret-user-input.png)
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-ClinicoPath-FaganNomogram.gif)
Decision Tree
explore
π¬π¬π¬π¬ UNDER CONSTRUCTION π βοΈβ οΈπ©
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-clinicopath-explore-decision-tree.png)
FFTrees
π¬π¬π¬π¬ UNDER CONSTRUCTION π βοΈβ οΈπ©
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-clinicopath-FFTrees-decision-tree.png)
rpart
π¬π¬π¬π¬ UNDER CONSTRUCTION π βοΈβ οΈπ©
![](https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/man/figures/jamovi-clinicopath-rpart-decision-tree.png)
ROC
π¬π¬π¬π¬ UNDER CONSTRUCTION π βοΈβ οΈπ©
Correlation
Correlation
π¬π¬π¬π¬ UNDER CONSTRUCTION π βοΈβ οΈπ©
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 BjΓΆrn Oettinghaus, and
- rstats community.
See https://github.com/ClinicoPath for forked packages.
Development Status
Check, CI
Recency, Updates
Webpage, Links, Size, Download