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# ClinicoPath 0.0.2.0018
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-   added cumulative events and cumulative hazard plots to survival

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

-   added cox adjusted survival to multivariate survival
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Type: Package
Package: ClinicoPath
Title: Analysis for Clinicopathological Research
Version: 0.0.2.0017
Version: 0.0.2.0018
Date: 2020-07-03
Authors@R:
person(given = "Serdar",
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# ClinicoPath 0.0.2.0017

- added alluvial diagrams using easyalluvial package to Descriptives (under Explore menu)
https://github.com/sbalci/ClinicoPathJamoviModule/issues/19
https://github.com/erblast/easyalluvial/issues/19

- added easyalluvial as an option to Graphs and Plots (under JJStatsPlot menu) for repeated categorical measurements.

# 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)\
<https://github.com/sbalci/ClinicoPathJamoviModule/issues/19>\
<https://github.com/erblast/easyalluvial/issues/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/jjstatsplot/releases/>

- See: https://github.com/sbalci/ClinicoPath/releases/

- crosstable function partially resolves https://github.com/jamovi/jamovi/issues/443

- survival function resolves https://github.com/jonathon-love/deathwatch/issues/2

- added export html to crosstables to bypass https://github.com/jamovi/jamovi/issues/892
- See: <https://github.com/sbalci/ClinicoPath/releases/>

- crosstable function partially resolves
<https://github.com/jamovi/jamovi/issues/443>

- survival function resolves
<https://github.com/jonathon-love/deathwatch/issues/2>

- added export html to crosstables to bypass
<https://github.com/jamovi/jamovi/issues/892>

# ClinicoPath 0.0.2.0015

- Added tangram statistical results
- Added options to finalfit crosstables
fixes: https://github.com/sbalci/ClinicoPathJamoviModule/issues/24
Partially fixes: https://github.com/jamovi/jamovi/issues/901
fixes: https://github.com/ewenharrison/finalfit/issues/52
- Added tangram statistical results

- Added experimental biblometrics functions
- includes experimental changes
- Added options to finalfit crosstables fixes:
<https://github.com/sbalci/ClinicoPathJamoviModule/issues/24> Partially
fixes: <https://github.com/jamovi/jamovi/issues/901> fixes:
<https://github.com/ewenharrison/finalfit/issues/52>

- Added experimental biblometrics functions

- includes experimental changes

# ClinicoPath 0.0.2.0014

- Added footnote to arsenal crosstable


- 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 `.jmo`files 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
- 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 `.jmo`files 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/[email protected]` 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.

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


<img src="man/figures/jamovi-ClinicoPath-0.0.2-released.gif" 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
- version 0.0.2 is released
- works with jamovi latest release (\>=1.2.18)
<https://www.jamovi.org/download.html>

https://twitter.com/serdarbalci/status/1261256107919642629
![](man/figures/jamovi-ClinicoPath-0.0.2-released.gif){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

- #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/1261256107919642629>

https://twitter.com/serdarbalci/status/1261639212664840192
- \#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
- 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
<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

- #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>

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>

- With #ClinicoPath @jamovistats module it is easy to make crosstables.
uses #tangram package
#rstats #biostatistics #pathology #pathologists
- You can make different plots based on variable type via \#jamovi
\#ClinicoPath module. Using \#rstats [@jamovistats] \#ggstatsplot
\#ggalluvial \#easyalluvial packages \#pathology \#pathologists
\#datavisualisation

https://twitter.com/serdarbalci/status/1262691784574017536
<https://www.youtube.com/watch?v=m3uInetiC8w>

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

- You can make different plots based on variable type via #jamovi #ClinicoPath module. Using #rstats @jamovistats #ggstatsplot #ggalluvial #easyalluvial packages #pathology #pathologists #datavisualisation
- 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.youtube.com/watch?v=m3uInetiC8w
<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/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
<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."
"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
<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.”
"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
<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% …”
"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
<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.
"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
<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://twitter.com/serdarbalci/status/1264153711087140864>

https://github.com/sbalci/ClinicoPathJamoviModule
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>

<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>

<https://github.com/sbalci/ClinicoPathJamoviModule>

<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>

# 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.

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
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.
- removed 'frequencies'
- Documentations are being added.
- CI are being added.
- Badges, README are updated.

# ClinicoPath 0.0.1.1000

## Functions work as defaults
## 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.
- 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:
### For descriptive analysis:

* TableOne
* WriteSummary
* Report General Features
* Frequencies
- TableOne
- WriteSummary
- Report General Features
- Frequencies

### For comparing variables:

* CrossTable
* GGStatsPlot2
- CrossTable
- GGStatsPlot2

### For survival analysis

* FinalFit
* FinalFit Multivariate Survival
- FinalFit
- FinalFit Multivariate Survival

### For medical decision tests:

* Medical Decision
* Decision Calculator
- Medical Decision
- Decision Calculator

### For correlation analysis:

* Correlation
- Correlation

### For inter and intra observer agreement

* Interrater Intrarater Reliability
- Interrater Intrarater Reliability

### Decision tree and cluster analysis sections.

* Not active yet.
- Not active yet.

# ClinicoPath 0.0.1-beta

* First Pre-release
- First Pre-release

* https://github.com/sbalci/ClinicoPathJamoviModule/releases/tag/0.0.1-beta
- <https://github.com/sbalci/ClinicoPathJamoviModule/releases/tag/0.0.1-beta>
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