nexusmaker


Namenexusmaker JSON
Version 2.0.5 PyPI version JSON
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home_pagehttps://github.com/SimonGreenhill/NexusMaker
Summarynexusmaker - Nexus file maker for language phylogenies
upload_time2023-01-11 01:01:42
maintainer
docs_urlNone
authorSimon J. Greenhill
requires_python>=3.7
licenseBSD-2-Clause
keywords language-phylogenies phylolinguistics
VCS
bugtrack_url
requirements python-nexus
Travis-CI
coveralls test coverage
            # NexusMaker

## Simply Generate Nexus Files

```
from nexusmaker import NexusMaker, Record


data = [
    Record(Language="A", Word="eye", Item="", Cognate="1"),
    Record(Language="A", Word="leg", Item="", Cognate="1"),
    Record(Language="A", Word="arm", Item="", Cognate="1"),
    
    Record(Language="B", Word="eye", Item="", Cognate="1"),
    Record(Language="B", Word="leg", Item="", Cognate="2"),
    Record(Language="B", Word="arm", Item="", Cognate="2"),
    
    Record(Language="C", Word="eye", Item="", Cognate="1"),
    # No ReCord for C 'leg'
    Record(Language="C", Word="arm", Item="", Cognate="3"),

    Record(Language="D", Word="eye", Item="", Cognate="1", loan=True),
    Record(Language="D", Word="leg", Item="", Cognate="1"),
    Record(Language="D", Word="leg", Item="", Cognate="2"),
    Record(Language="D", Word="arm", Item="", Cognate="2,3"),
]

maker = NexusMaker(data)

maker = NexusMakerAscertained(data)  # adds Ascertainment bias character

maker = NexusMakerAscertainedWords(data)  # adds Ascertainment character per word
nex = maker.make()
maker.write(nex, filename="output.nex")


```

### Version History:

* 2.0.4: add `unique_ids` parameter 
* 2.0.3: handle CLDF datasets
* 2.0.2: add tool to filter combining cognates
* 2.0.1: minor bugfixes.
* 2.0: major refactor of testing and other components.
* 1.5: do more validation of cognate sets to detect possibly broken combined cognate sets.
* 1.4: normalise order of cognates (i.e. so 1,54 == 54,1).
* 1.3: handle cognates of form '1a'.
* 1.2: initial release.

            

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