semvec/pypi-packages huggingface dataset:
RateCounter 1.1
ratecounter - Nexus file rate counter for language phylogenies
License: BSD
Keywords: language-phylogenies

# RateCounter

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[![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)
```