argile
argile (formerly terracotta) is a Python package for estimating migration surfaces and the locations of genetic ancestors from gene trees. The latest release is available either here on GitHub or through PyPI. See example_dataset/ for details about file formats.
Estimate the most likely migration surface
import argile
result, loglikelihood = argile.run(
demes_path="example_dataset/demes.tsv",
connections_path="example_dataset/connections.tsv",
samples_path="example_dataset/samples.tsv",
trees_dir_path="example_dataset/trees",
output_file="output.tsv"
)
argile.run() estimates the most likely migration surface using the L-BFGS-B algorithm. It estimates values for the coefficient (the default migration rate) and any migration rate modifier variables (here r0, r1, and r2). These variables will be automatically included in this search if present in connections.tsv. This fucntion takes the paths to the files as input rather than loading the world map prior.
Loading the world map
import pandas as pd
import argile
demes = pd.read_csv("example_dataset/demes.tsv", sep="\t")
connections = pd.read_csv("example_dataset/connections.tsv", sep="\t")
samples = pd.read_csv("example_dataset/samples.tsv", sep="\t")
world_map = argile.WorldMap(demes, connections, samples)
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Metadata
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Release files for argile 0.0.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| argile-0.0.1.tar.gz | 13.7 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| argile-0.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 28.4 kB
Release files / argile-0.0.1.tar.gz
| Download URL | argile-0.0.1.tar.gz |
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| Size | 13.7 kB |
| Tags | Source |
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Release files / argile-0.0.1-py3-none-any.whl
| Download URL | argile-0.0.1-py3-none-any.whl |
|---|---|
| Size | 14.7 kB |
| Tags | Python 3 |
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