https://github.com/walterxie/beast2stats

Basic statistics of BEAST2 development
https://github.com/walterxie/beast2stats

beast2

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Basic statistics of BEAST2 development

• Host: GitHub
• URL: https://github.com/walterxie/beast2stats
• Owner: walterxie
• License: mit
• Created: 2018-08-07T22:40:12.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2022-05-30T05:38:40.000Z (over 2 years ago)
• Last Synced: 2024-10-19T09:33:41.747Z (3 months ago)
• Topics: beast2
• Language: HTML
• Homepage: https://walterxie.github.io/beast2stats/
• Size: 2.52 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
## Basic statistics

Do you know how the BEAST 2 project was going since 2014? 

Here is the answer:

![Basic statistics](figures/beast2-stats-every6m.svg)

The three lines are:

1. the lines of Java code of BEAST 2 core as a function of time (per month) since 2014;

2. the lines of Java code of other packages excluding BEAST 2 core as a function of time (per month) since 2014;

3. the number of other packages created during the period.

The vertical lines are major releases of BEAST 2 core.

The data was collected at the first day of each month. 

But there were two packages not included in this summary because the source code was not available by then.

## The detail

### BEAST 2 core 

![BEAST 2 core](figures/beast2.svg)

### Other packages excluding BEAST 2 core

The released packages in [CBAN for BEAST 2.6](https://github.com/CompEvol/CBAN/raw/master/packages2.6.xml) 

were chosen in this summary.

The livetime summary of all BEAST 2 packages are also available from BEAST 2 

[Package Viewer](https://compevol.github.io/CBAN/).

Because the first release date of packages was not easy to access, 

I used the date when the package started to have a LoC (lines of Java code) record, 

and adjusted the data according to the history of CBAN XML in this summary.

The bar charts:

![packages LoC](figures/other-packages-LoC.svg)

![packages NoP](figures/other-packages-NoP.svg)

The 3D interactive view is also [available](https://walterxie.github.io/beast2stats/3d) using Safari or Chrome.

## Pipeline

```bash

# source code has to be ready before analysis

cd ~/WorkSpace

git clone https://github.com/CompEvol/beast2.git

ls

# check out beast2stats project

git clone https://github.com/walterxie/beast2stats.git

# start pipeline

cd ~/WorkSpace/beast2stats

# save code stats to *.txt in tmp-yyyy-mm-dd

PACKAGE_DIR="beast2"

./createStats.sh $PACKAGE_DIR

# create *.svg in figures

Rscript beast2Stats.R

# other packages: check out code, calculate stats and create fig

Rscript packagesStats.R

```