apragsdale/demes.jl

Demes.jl

A Julia package for working with demes demographic models.

Usage

Demographic models written in the demes standard can be loaded as

using Demes
graph = Demes.loadGraph("test/gutenkunst_ooa.yaml")

This imports a demes-specified demographic model, which is used in downstream population genetics simulation software.

demes.jl's Issues

Fix broken tests from checking against demes-spec

• Pulse edge cases (popsim-consortium/demes-spec#132)
• Valid identifiers
• Migration overlaps for the same pair of demes
• Migrations into a deme must always sum to <= 1

Make error messages more helpful

Error messages should point to the invalid deme/epoch/migration/etc more specifically.

Test loaded models against resolved models

The demes-spec repo has a number of examples, e.g. with defaults, along with their expected resolved data. These need to be tested against.

Fully test getDiscreteDemographicEvents

Equality checks from #2 will be needed to finalize such tests.

Add functions for checking equality

Graph, Deme, Epoch, Migration, and discrete demographic events are defined as mutable structs. For these, we need to implement functions to manually check equality.

Function names do not follow Julia style guide

They shouldn't be camel case. See https://docs.julialang.org/en/v1/manual/style-guide/

Implement a prune function

Given sampled demes, we can imagine pruning demes that do not interact in any way with ancestry of the given samples. This can be used to simplify demographic models for a given sample set, reducing runtime in simulation applications.

Implement a slice function

See popsim-consortium/demes-python#332