RateCounter 1.1

ratecounter - Nexus file rate counter for language phylogenies

# RateCounter

[](https://travis-ci.org/SimonGreenhill/RateCounter)
[](https://coveralls.io/github/SimonGreenhill/RateCounter?branch=master)
[](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)
```