nexusmaker 2.0.7

nexusmaker - Nexus file maker for language phylogenies

NexusMaker

Simply Generate Nexus Files

from nexusmaker import NexusMaker, Record


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

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

maker = NexusMaker(data)

maker = NexusMakerAscertained(data)  # adds Ascertainment bias character

maker = NexusMakerAscertainedWords(data)  # adds Ascertainment character per word

# generate
nex = maker.make()
maker.write(nex, filename="output.nex")


# remove combining cognates:
#    If a language has multiple cognates for a parameter, then this will filter
#    the cognates to a maximum of `keep`, i.e. if a language has cognate sets
#    "a, b, c" for the word `hand`, then `keep=2` will leave the top 2 cognates
#    (="a, b"), while `keep=1` will leave the top cognate set (="a").
maker = remove_combining_cognates(NexusMaker(data), keep=2)
nex = maker.make()

Version History:

• 2.0.6: allow different ID columns in load_cldf
• 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.