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ratecounter

Phylogenetic Rate Counter

https://github.com/simongreenhill/ratecounter

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: frontiersin.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.3%) to scientific vocabulary

Keywords

cultural-phylogeny language-phylogeny phylogenetics
Last synced: 9 months ago · JSON representation

Repository

Phylogenetic Rate Counter

Basic Info
  • Host: GitHub
  • Owner: SimonGreenhill
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Size: 129 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
cultural-phylogeny language-phylogeny phylogenetics
Created about 9 years ago · Last pushed over 7 years ago

https://github.com/SimonGreenhill/RateCounter/blob/master/ 

# RateCounter

[![Build Status](https://travis-ci.org/SimonGreenhill/RateCounter.svg?branch=master)](https://travis-ci.org/SimonGreenhill/RateCounter)
[![Coverage Status](https://coveralls.io/repos/github/SimonGreenhill/RateCounter/badge.svg?branch=master)](https://coveralls.io/github/SimonGreenhill/RateCounter?branch=master)
[![DOI](https://zenodo.org/badge/DOI/10.3389/fpsyg.2018.00576.svg)](https://doi.org/10.3389/fpsyg.2018.00576)


*RateCounter* is a python library and program for calculating the number of rate differences between taxa given a nexus file. 

It is based on the method in:

```
Greenhill SJ, Hua X, Welsh CF, Schneemann H & Bromham L. 2018. [Population Size and the Rate of Language Evolution: A Test across Indo-European, Austronesian and Bantu Languages](https://www.frontiersin.org/articles/10.3389/fpsyg.2018.00576/abstract). Frontiers in Psychology doi: 10.3389/fpsyg.2018.00576
```

Please cite this paper if you find this software helpful.

**Installation:**

```shell
pip install RateCounter
```

**Usage:**

As a standalone program:

```shell
> ratecounter --help

usage: ratecounter [-h] [-v] nexus taxon1 taxon2

Calculate rates from the nexus for the two taxa

positional arguments:
  nexus          nexusfile
  taxon1         Taxon 1
  taxon2         Taxon 2

optional arguments:
  -h, --help     show this help message and exit
  -v, --verbose  increases verbosity


> ratecounter test.nex Taxon1 Taxon2
              GAIN A	1
              GAIN B	1
              LOSS A	1
              LOSS B	1
             TOTAL A	2
             TOTAL B	2
             ABSENCE	1
           RETENTION	1
         SHARED GAIN	1
         SHARED LOSS	1
         UNCOUNTABLE	19
               TOTAL	27
```

As a python library

```python
from ratecounter.main import RateCounter

rc = RateCounter(nexusfile=args.nexusfile)
scores = rc.get_scores(Taxon1, Taxon2)
```

Owner

  • Name: Simon J Greenhill
  • Login: SimonGreenhill
  • Kind: user
  • Location: Jena, Canberra, Auckland
  • Company: @shh-dlce @eva-dlce

I study how languages and cultures evolve. Scientist at the University of Auckland, and the Max Planck Institute for Evolutionary Anthropology

GitHub Events

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Last Year

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 33
  • Total Committers: 1
  • Avg Commits per committer: 33.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
SimonGreenhill s****n@s****z 33
Committer Domains (Top 20 + Academic)
simon.net.nz: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 24 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 1
pypi.org: ratecounter

ratecounter - Nexus file rate counter for language phylogenies

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 24 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Average: 28.7%
Forks count: 29.8%
Stargazers count: 38.8%
Downloads: 43.2%
Maintainers (1)
SimonGreenhill
Last synced: 10 months ago

Dependencies

requirements.txt pypi
  • python-nexus *
setup.py pypi
  • python-nexus >=1.4