Expand description
rust support for demes.
Example of YAML input
let yaml = "
description: The Gutenkunst et al. (2009) OOA model.
doi:
- https://doi.org/10.1371/journal.pgen.1000695
time_units: years
generation_time: 25
demes:
- name: ancestral
description: Equilibrium/root population
epochs:
- {end_time: 220e3, start_size: 7300}
- name: AMH
description: Anatomically modern humans
ancestors: [ancestral]
epochs:
- {end_time: 140e3, start_size: 12300}
- name: OOA
description: Bottleneck out-of-Africa population
ancestors: [AMH]
epochs:
- {end_time: 21.2e3, start_size: 2100}
- name: YRI
description: Yoruba in Ibadan, Nigeria
ancestors: [AMH]
epochs:
- start_size: 12300
- name: CEU
description: Utah Residents (CEPH) with Northern and Western European Ancestry
ancestors: [OOA]
epochs:
- {start_size: 1000, end_size: 29725}
- name: CHB
description: Han Chinese in Beijing, China
ancestors: [OOA]
epochs:
- {start_size: 510, end_size: 54090}
migrations:
- {demes: [YRI, OOA], rate: 25e-5}
- {demes: [YRI, CEU], rate: 3e-5}
- {demes: [YRI, CHB], rate: 1.9e-5}
- {demes: [CEU, CHB], rate: 9.6e-5}
";
let graph = match demes::loads(yaml) {
Ok(graph) => graph,
Err(e) => panic!("{}", e),
};
{
// round trip back into yaml
let yaml_from_graph = serde_yaml::to_string(&graph).unwrap();
let roundtripped_graph = demes::loads(&yaml_from_graph).unwrap();
assert_eq!(graph, roundtripped_graph);
}
for deme in graph.demes() {
println!("{} {} {} {} {}",
deme.name(),
deme.start_time(),
deme.end_time(),
deme.start_size(),
deme.end_size());
// A HashMap maps ancestor name -> ancestor Deme
for ancestor in deme.ancestors().keys() {
println!("{} is an ancestor of {}", ancestor, deme.name());
}
// Ref<'_, [String]> of ancestor names
for ancestor in deme.ancestor_names().iter() {
println!("{} is an ancestor of {}", ancestor, deme.name());
}
}
for m in graph.migrations() {
println!("{} -> {} at rate {} from: {}, to: {}",
m.source(),
m.dest(),
m.rate(),
m.start_time(),
m.end_time());
}Modules
Implement the demes technical specification in terms of rust structs.