Skip to main content

ratecounter - Nexus file rate counter for language phylogenies

Project description

# 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)
```

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
RateCounter-1.1-py2.py3-none-any.whl (10.3 kB) Copy SHA256 hash SHA256 Wheel 3.7
RateCounter-1.1.tar.gz (7.5 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page