Changelog

Source: NEWS.md

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: https://github.com/sbalci/ClinicoPathJamoviModule/issues/38

saving calculated variables to Data

ClinicoPath 0.0.2.0064

ClinicoPath 0.0.2.0048

ClinicoPath 0.0.2.0046

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: https://github.com/sbalci/ClinicoPathJamoviModule/issues/28

ClinicoPath 0.0.2.0037

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 0.0.2.0034

  • 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 0.0.2.0025

  • 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 0.0.2.0019

  • 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

ClinicoPath 0.0.2.0015

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

{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

https://github.com/sbalci/ClinicoPathJamoviModule

https://github.com/sbalci/ClinicoPathJamoviModule/releases/tag/v0.0.1

ClinicoPath 0.0.1.1001

  • removed ‘frequencies’
  • Documentations are being added.
  • CI are being added.
  • Badges, README are updated.

ClinicoPath 0.0.1.1000

Functions work as defaults

  • Divided module into 2 windows: ClinicoPath1 and ClinicoPath2
  • Removed unnecessary outputs.
  • Added ToDo section and a warning that still in development
  • Updated Readme file
  • Currently functions are working. But only in defaults.

For descriptive analysis:

  • TableOne
  • WriteSummary
  • Report General Features
  • Frequencies

For comparing variables:

  • CrossTable
  • GGStatsPlot2

For survival analysis

  • FinalFit
  • FinalFit Multivariate Survival

For medical decision tests:

  • Medical Decision
  • Decision Calculator

For correlation analysis:

  • Correlation

For inter and intra observer agreement

  • Interrater Intrarater Reliability

Decision tree and cluster analysis sections.

  • Not active yet.