sbalci / clinicopathjamovimodule

ClinicoPath jamovi Module

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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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/R4.0.2/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:

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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: 4.0.2

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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Follow @serdarbalci

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Buy me a coffee

https://paypal.me/serdarbalci

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Development Status

Code

Status

Check, CI

Recency, Updates

Webpage, Links, Size, Download

Dependencies

Interaction, Shares

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>

clinicopathjamovimodule's Issues

ICC coefficient

Decision Tree

• options will be added
• two word variable names are causing problems. consider adding trimws()

add functions from DescTools package

https://github.com/AndriSignorell/DescTools
https://cloud.r-project.org/web/packages/DescTools/index.html

separate menu for Graphs

https://www.r-graph-gallery.com/

https://www.data-to-viz.com/

easyalluvial options

add summarytools functions to descriptives

https://github.com/dcomtois/summarytools

add time interval function to jsurvival

.b.R

            if (! is.null(self$options$resids)) {
                calculatedtime <- as.vector(calculatedtime)
                calculatedtime <- jmvcore::toNumeric(calculatedtime)
            }

            if ( ! is.null(self$options$resids)) {
                self$results$resids$setValues(calculatedtime)
            }

.a.yaml

    - name: resids
      title: Residuals
      type: Output

    - name: resids2
      title: Residuals2
      type: Output

.u.yaml

  - type: VariableSupplier
    persistentItems: false
    stretchFactor: 1
    children:
      - type: TargetLayoutBox
        label: Residuals
        children:
          - type: VariablesListBox
            name: resids
            maxItemCount: 1
            isTarget: true
      - type: TargetLayoutBox
        label: Residuals2
        children:
          - type: VariablesListBox
            name: resids2
            maxItemCount: 1
            isTarget: true

include The proportional hazards (PH) assumption

by rabouqal » Sun Nov 08, 2020 6:55 pm
Hello,
It is possible to include The proportional hazards (PH) assumption in the Clinicopath survival module.
thank you for your very useful modules in clinical research.
Redouane

https://forum.jamovi.org/viewtopic.php?f=11&t=1485

add eurostats function

gifs describing functions

• The new version of #ClinicoPath @jamovistats module is on the jamovi library.
  Requires #jamovi 1.2.18 #rstats #biostatistics #pathology #pathologists

https://twitter.com/serdarbalci/status/1261256107919642629

• #ClinicoPath #jamovi module comes with example datasets as with other #jamovi modules. Use them as example to prepare your data.

https://twitter.com/serdarbalci/status/1261639212664840192

• You can easily make 'Table One' for reports/manuscripts via #ClinicoPath
  @jamovistats module. Uses #tableone, #arsenal, #gtsummary, and #janitor packages. #rstats #biostatistics #pathology #pathologists

https://twitter.com/serdarbalci/status/1262083972328230912

• #jamovi has very nice tables. Sometimes I prefer to read the tables automatically via #ClinicoPath @jamovistats module. Using #easystats #report package.
  #naturallanguage #data #summary
  #rstats #biostatistics #pathology #pathologists

https://twitter.com/serdarbalci/status/1262354990787694599

tangram recent version is not working

See spgarbet/tangram#64

See spgarbet/tangram#38

arguments for jsurvival

jamovi/jamovi#935 (comment)

Coefficient plots

Coefficient plots:
https://rawcdn.githack.com/RPanczak/R_alike/f481a22c3ed3fd9038e928a80f94311e81a93786/docs/03_coeff-plots.html

find >1 cut-off in continuous explanatory variable in survival analysis

Extracting dataframes with statistical details from ggstatsplot

Extracting dataframes with statistical details from ggstatsplot
https://indrajeetpatil.github.io/ggstatsplot/reference/extract_stats.html

add examples to functions

use preformatted instead of html outputs

ROC options

add options to ROC function

Problem on Interrater Reliability calculation with meddecide

Hello!
First of all, I'm new in the GitHub world so I don't know if this is the right place to put this issue. I'm a Radiologist from Brazil who is taking its first steps in statistics and the use of software to do it. I needed to do some Interrater Reliability calculation using the Cohen's Kappa and was literally searching on google how to do it when I came across with the Jamovi software and the ClinicoPath Module.

I've installed the submodule "meddecide" to use the Interrater Reliability calculation but I'm facing some problems. When I put the data and try to calculate the Cohen Kappa the following message appears: DLL 'IpSolve' not found: maybe not installed for this architecture?.

Is there something I'm doing wrong?
Thank you in advance for the help.

OBS:
I'm using Jamovi Version 1.2.25.0 for Windows

Combining and arranging multiple plots in a grid

Combining and arranging multiple plots in a grid
https://indrajeetpatil.github.io/ggstatsplot/reference/combine_plots.html

Parsnip wrappers for survival models

Parsnip wrappers for survival models
https://github.com/tidymodels/censored

`ggstatsplot` next release removes helper message functions

If I am not mistaken, this module currently uses normality_message and bartlett_message functions exported from ggstatsplot.

But these functions will be removed in the next release (IndrajeetPatil/ggstatsplot#417)

If you want to use them, feel free to copy the code from here and implement it internally in this module:
https://github.com/cran/ipmisc/blob/master/R/helpers_messages.R

add calculated cut-off to data in survival analysis of continious predictor

forest_model: Produce a forest plot based on a regression model

forest_model: Produce a forest plot based on a regression model
https://rdrr.io/cran/forestmodel/man/forest_model.html

venn diagrams

https://github.com/gaospecial/ggVennDiagram

correlation natural language reports will be added

add exampless to vignette

add p.adjust options to pairwise survival

#37 (reply in thread)

add ggplot2 extensions

ggplot2 extensions - gallery exts.ggplot2.tidyverse.org
https://exts.ggplot2.tidyverse.org/gallery/

grouped_ variant of ggstatsplot functions

grouped_ variant of ggstatsplot functions:

https://indrajeetpatil.github.io/ggstatsplot/index.html

https://twitter.com/giladfeldman/status/1263336491629121538

https://twitter.com/giladfeldman/status/1263336846567837698

separate menu for ggstatsplot

enhance tables

https://twitter.com/statistishdan/status/1303705152797519872

https://themockup.blog/posts/2020-09-04-10-table-rules-in-r/

on windows survival analysis gives error

• tidyselect version:

• invalid argument to unary operator

Not working

The module doesn't seem to be working on the new Jamovi 1.29. It crashes and doesn't show all the options in the module as well

Variable Tree is not displaying correctly

add Predictive Power Score

https://github.com/paulvanderlaken/ppsr

clintools monitor

https://github.com/lilleoel/clintools

pairwise chi-square

crosstables html output issues

• See about improving the export of html content jamovi/jamovi#892

• ClinicoPath / Crosstabs jamovi/jamovi#901

statsplot requires more explanation and test referrals

adjusted survival plot with more than one variable

#37 (reply in thread)

Update variable tree arguments

https://twitter.com/nbarrowman/status/1297257354338226178

https://nbarrowman.github.io/vtree

add paired samples style to a new jjwithinstats2 function

Competing Survival

In survival analysis for cancer we sometimes use more than 2 levels. DOD (dead of disease), DOOC (dead of other causes), AWD (alive with disease), AWOD (alive without disease). And these different levels are grouped differently depending on analysis (see https://finalfit.org/articles/survival.html#death-status). Not all are mandatory, so I want optional one to have default NULL level.

property allowNone to the LevelSelector control. This will allow the user to select None from the listbox. It will be in the next release and will need an updated compilor as well.

add ggridges plots

https://wilkelab.org/ggridges/articles/introduction.html

add forester package style forest plots

https://github.com/rdboyes/forester

Extending ggstatsplot functions with purrr

Maybe I should try to implement these as well:
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/purrr_examples.html

add hypothesis test names to crosstable

add hypothesis test names to crosstable ewenharrison/finalfit#52 (comment)

fork packages used in the module

See https://github.com/ClinicoPath

Add Bibliometrics analysis

datawizard: Easy Data Wrangling

datawizard: Easy Data Wrangling
https://easystats.github.io/datawizard/