ClinicoPath 0.0.2.0072

calculated cut-off groups in continuous survival can be added to data

ClinicoPath 0.0.2.0069

optional padjustement to pairwise survival fixes: #38

saving calculated variables to Data

ClinicoPath 0.0.2.0064

added ggvenn function fixed yanlinlin82/ggvenn#16
deleted some functions, will add as updated

ClinicoPath 0.0.2.0048

started adding arguments of ggstatsplot fixed: sbalci/jjstatsplot#3

ClinicoPath 0.0.2.0046

use x and y instead of main and condition arguments for ggpiestats and ggbarstats
partially fixed: sbalci/jjstatsplot#1
add point.path argument in grouped_ggwithinstats partially fixed: sbalci/jjstatsplot#2
waiting for update in jamovi mran version. current ggstatsplot dependencies are not up to date in jamovi's library

ClinicoPath 0.0.2.0044

fixed multivariate survival to work without continuous explanatory

ClinicoPath 0.0.2.0043

added jsurvival to linux
added some functions of descriptives to linux

ClinicoPath 0.0.2.0041

updated jsurvival
added more controls under collapse boxes
advanced outcome: users can select more than one outcome level depending on their analysis (event free or overall survival). Competing risk survival will also be added in the future.
advanced survival: users can use dates to calculate survival time. the date type should be defined. many variations for date types are given.
Cumulative events, cumulative survival and KMunicate style Kaplan-Meier curves are added.
A separate function for continuous explanatory variable is added. The optimal cut-off based on survival outcome is defined and after cut-off definition other univariate survival analysis are performed.
under multivariate analysis users can now generate Kaplan-Meier curves upto two explanatory variables.
an adjusted survival curve is also added, though it requires further management.

ClinicoPath 0.0.2.0040

separating univariate continuous survival from categorical

ClinicoPath 0.0.2.0039

added options to vartree

fixes: #28

ClinicoPath 0.0.2.0038

fixes #20

ClinicoPath 0.0.2.0037

added Survival Analysis for Continuous Explanatory
added vtree package functions to vartree function
fixes #9

ClinicoPath 0.0.2.0036

added Benford Analysis
added interactive size to jjbarstats

.init = function() {
            deplen <- length(self$options$dep)
            self$results$plot$setSize(400, deplen*300)
        }

ClinicoPath 0.0.2.0035

meddecide has been added to jamovi library

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

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

https://library.jamovi.org/win64/R3.6.3/meddecide-0.0.1.0005.jmo

https://library.jamovi.org/linux/R3.6.3/meddecide-0.0.1.0005.jmo

https://library.jamovi.org/macos/R3.6.3/meddecide-0.0.1.0005.jmo

ClinicoPath 0.0.2.0034

added metrics to survival functions
updating survival options (continuous explanatory, cut-off, two categorical explanatory, multiple outcome options, elapsed time calculation from dates)
added KMunicate type survival curve
added Fagan's nomogram

ClinicoPath 0.0.2.0027

temporarily added many functions from various packages to update functions and arguments

ClinicoPath 0.0.2.0026

jsurvival has been added to jamovi library

https://github.com/sbalci/jsurvival

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

https://library.jamovi.org/macos/R3.6.3/jsurvival-0.0.2.0026.jmo

https://library.jamovi.org/win64/R3.6.3/jsurvival-0.0.2.0026.jmo

ClinicoPath 0.0.2.0025

ClinicoPath as a combined module has been taken down from jamovi library.
Users are adviced to install submodules.
ClinicoPathDescriptives, jsurvival, and meddecide tables have been updated to look more jamovian :)

ClinicoPath 0.0.2.0024

ClinicoPathDescriptives functions are separately added to jamovi library under Exploration menu

ClinicoPathDescriptives module can be downloaded inside jamovi (click Modules and jamovi library)

https://library.jamovi.org/win64/R3.6.3/ClinicoPathDescriptives-0.0.2.0019.jmo

https://library.jamovi.org/linux/R3.6.3/ClinicoPathDescriptives-0.0.2.0019.jmo

https://library.jamovi.org/macos/R3.6.3/ClinicoPathDescriptives-0.0.2.0019.jmo

ClinicoPath 0.0.2.0023

added Age Pyramid
survival status can be selected from levels
WIP decisioncalculator

ClinicoPath 0.0.2.0022

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/macos/R3.6.3/jjstatsplot-0.0.1.0001.jmo

https://library.jamovi.org/win64/R3.6.3/jjstatsplot-0.0.1.0001.jmo

https://library.jamovi.org/linux/R3.6.3/jjstatsplot-0.0.1.0001.jmo

ClinicoPath 0.0.2.0021

updating jjstatsplot for release

ClinicoPath 0.0.2.0020

made submodules:
ClinicoPathDescriptives

https://github.com/sbalci/ClinicoPathDescriptives/

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

JJStatsPlot:

https://github.com/sbalci/jjstatsplot

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

jsurvival:

https://github.com/sbalci/jsurvival

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

meddecide

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

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

ClinicoPath 0.0.2.0019

rewrote summary of categorical values to decrease dependencies

ClinicoPath 0.0.2.0018

added cumulative events and cumulative hazard plots to survival

https://rpkgs.datanovia.com/survminer/survminer_cheatsheet.pdf

added cox adjusted survival to multivariate survival

ClinicoPath 0.0.2.0017

added alluvial diagrams using easyalluvial package to Descriptives (under Explore menu)
#19
erblast/easyalluvial#19
added easyalluvial as an option to Graphs and Plots (under JJStatsPlot menu) for repeated categorical measurements.

ClinicoPath 0.0.2.0016

See: https://github.com/sbalci/jjstatsplot/releases/
See: https://github.com/sbalci/ClinicoPath/releases/
crosstable function partially resolves jamovi/jamovi#443
survival function resolves jonathon-love/deathwatch#2
added export html to crosstables to bypass jamovi/jamovi#892

ClinicoPath 0.0.2.0015

Added tangram statistical results
Added options to finalfit crosstables fixes: #24 Partially fixes: jamovi/jamovi#901 fixes: ewenharrison/finalfit#52
Added experimental biblometrics functions
includes experimental changes

ClinicoPath 0.0.2.0014

Added footnote to arsenal crosstable

ClinicoPath 0.0.2.0012

jjstatsplot is the wrapper functions for using ggstatsplot in jamovi.
I thought it might be a nice separate module too. I have prepared it to ask opinions.
Use attached .jmofiles to install via side load in jamovi.
Requires latest jamovi >=1.2.22 https://www.jamovi.org/download.html
tangram error is fixed, but it does not reveal statistical test results.
arsenal's footnote is not visible in Html output

ClinicoPath 0.0.2.0004

Using spgarbet/tangram@0.3.2 until the bug is fixed.

ClinicoPath 0.0.2.0003

Added arsenal, finalfit, and gtsummary to crosstable function. gtsummary gives different results, due to nonparametric tests. Should add options and documentation. tangram still not functioning.

ClinicoPath 0.0.2

version 0.0.2 is released
works with jamovi latest release (>=1.2.18) https://www.jamovi.org/download.html

{align="center" width="75%"}

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

With #ClinicoPath [@jamovistats] module it is easy to make crosstables. uses #tangram package #rstats #biostatistics #pathology #pathologists

https://twitter.com/serdarbalci/status/1262691784574017536

You can make different plots based on variable type via #jamovi #ClinicoPath module. Using #rstats [@jamovistats] #ggstatsplot #ggalluvial #easyalluvial packages #pathology #pathologists #datavisualisation

https://www.youtube.com/watch?v=m3uInetiC8w

https://twitter.com/serdarbalci/status/1263191858454413312

Some examples of survival analysis via [@jamovistats] #ClinicoPath module. Using #rstats #finalfit by [@ewenharrison] #survival #survminer #ggstatsplot in #jamovi #biostatistics #pathology #pathologists https://www.youtube.com/watch?v=gIPf4xIKAOU

https://www.linkedin.com/pulse/survival-analysis-via-jamovi-clinicopath-module-serdar-balc%25C4%25B1 #datavisualisation #datascience #patoloji #analysis #datascientist #data #clinicaltrials #clinicalstudies #clinicaltrial #clinicalresearch

https://twitter.com/serdarbalci/status/1264153665386004480

It is generating natural language summaries to make easy to read the tables: "Median Survival: When LVI is Absent, median survival is 26 [20.1 - 32.3,"95% CI] months. When LVI is Present, median survival is 9.3 [8.8 - 10.6, 95% CI] months."

https://twitter.com/serdarbalci/status/1264153686508478465

"Hazard: When LVI is Present, there is 2.55 (1.85-3.51, p<0.001) times risk than when LVI is Absent."

https://twitter.com/serdarbalci/status/1264153695715053568

"1, 3, 5-yr Survival: When LVI Absent, 12 month survival is 70.9% [63.36%-79.3%, 95% CI]. When LVI Absent, 24 month survival is 54.2% [45.85%-64.1%, When LVI Present, 12 month survival is 28.4% [20.03%-40.3%, 95% CI]. When LVI Present, 24 month survival is 14.4% ..."

https://twitter.com/serdarbalci/status/1264153698764312577

"pairwise comparison of Grade: The comparison between Grade 2 and Grade 1 has a p-value of 0.87." Note for myself: The wording should be better.

https://twitter.com/serdarbalci/status/1264153700114862080

You can do multivariate survival analysis

https://twitter.com/serdarbalci/status/1264153711087140864

And also make Odds Ratio Tables and Plots. When you change the order of variables in jamovi data, the analysis also changes.

https://twitter.com/serdarbalci/status/1264153752015122432

https://github.com/sbalci/ClinicoPathJamoviModule

ClinicoPath 0.0.1.0001

Added multivariate survival, and comparison plots.

ClinicoPath v0.0.1

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.

You may install using side load: windows: https://library.jamovi.org/win64/R3.6.1/ClinicoPath-0.0.1.jmo macOS: https://library.jamovi.org/macos/R3.6.1/ClinicoPath-0.0.1.jmo