Metadata-Version: 1.1
Name: RateCounter
Version: 1.1
Summary: ratecounter - Nexus file rate counter for language phylogenies
Home-page: https://github.com/SimonGreenhill/RateCounter
Author: Simon J. Greenhill
Author-email: simon@simon.net.nz
License: BSD
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)
        ```
        
Keywords: language-phylogenies
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
