{ "info": { "author": "Simon J. Greenhill", "author_email": "simon@simon.net.nz", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "# RateCounter\n\n[![Build Status](https://travis-ci.org/SimonGreenhill/RateCounter.svg?branch=master)](https://travis-ci.org/SimonGreenhill/RateCounter)\n[![Coverage Status](https://coveralls.io/repos/github/SimonGreenhill/RateCounter/badge.svg?branch=master)](https://coveralls.io/github/SimonGreenhill/RateCounter?branch=master)\n[![DOI](https://zenodo.org/badge/DOI/10.3389/fpsyg.2018.00576.svg)](https://doi.org/10.3389/fpsyg.2018.00576)\n\n\n*RateCounter* is a python library and program for calculating the number of rate differences between taxa given a nexus file. \n\nIt is based on the method in:\n\n```\nGreenhill 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\n```\n\nPlease cite this paper if you find this software helpful.\n\n**Installation:**\n\n```shell\npip install RateCounter\n```\n\n**Usage:**\n\nAs a standalone program:\n\n```shell\n> ratecounter --help\n\nusage: ratecounter [-h] [-v] nexus taxon1 taxon2\n\nCalculate rates from the nexus for the two taxa\n\npositional arguments:\n nexus nexusfile\n taxon1 Taxon 1\n taxon2 Taxon 2\n\noptional arguments:\n -h, --help show this help message and exit\n -v, --verbose increases verbosity\n\n\n> ratecounter test.nex Taxon1 Taxon2\n GAIN A\t1\n GAIN B\t1\n LOSS A\t1\n LOSS B\t1\n TOTAL A\t2\n TOTAL B\t2\n ABSENCE\t1\n RETENTION\t1\n SHARED GAIN\t1\n SHARED LOSS\t1\n UNCOUNTABLE\t19\n TOTAL\t27\n```\n\nAs a python library\n\n```python\nfrom ratecounter.main import RateCounter\n\nrc = RateCounter(nexusfile=args.nexusfile)\nscores = rc.get_scores(Taxon1, Taxon2)\n```\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/SimonGreenhill/RateCounter", "keywords": "language-phylogenies", "license": "BSD", "maintainer": "", "maintainer_email": "", "name": "RateCounter", "package_url": "https://pypi.org/project/RateCounter/", "platform": "", "project_url": "https://pypi.org/project/RateCounter/", "project_urls": { "Homepage": "https://github.com/SimonGreenhill/RateCounter" }, "release_url": "https://pypi.org/project/RateCounter/1.1/", "requires_dist": null, "requires_python": "", "summary": "ratecounter - 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