Crate demes 

rust support for demes.

Introduction

This crate provides:

• Support for reading YAML descriptions of demes models. See loads and load.
• Support for building a demes model using rust code. See GraphBuilder.

The output of any of these operations is a fully-resolved Graph.

More information

• See here for an overview of demes.

Technical details

• YAML and GraphBuilder inputs support the Human Data Model (HDM) described in the demes specification
• A Graph is fully-resolved according to the Machine Data Model (MDM) described in the specification.

Features

The following cargo features are available:

• json: enables reading/writing a Graph in JSON format.

Modules

ffiffi

Define a foreign function interface (FFI) for this crate.

Structs

AsymmetricMigration

An asymmetric migration epoch.

CloningRate

The cloning rate of an Epoch.

Deme

A resolved deme.

DemeDefaults

Deme-level defaults

DemeSize

The size of a Deme at a given Time.

Epoch

A resolved epoch

GenerationTime

Generation time.

Graph

A resolved demes Graph.

GraphBuilder

This type allows building a Graph using code rather then using text input.

GraphDefaults

Top-level defaults

InputCloningRate

Input value for CloningRate, used when loading or building graphs.

InputDemeSize

Input value for DemeSize, used when loading or building graphs.

InputGenerationTime

Input value for GenerationTime, used when loading or building graphs.

InputMigrationRate

Input value for MigrationRate, used when loading or building graphs.

InputProportion

Input value for Proportion, used when loading or building graphs.

InputSelfingRate

Input value for SelfingRate, used when loading or building graphs.

InputTime

Input value for Time, used when loading or building graphs.

Metadata

Top-level metadata

MigrationRate

A migration rate.

Proportion

An ancestry proportion.

Pulse

A resolved Pulse event

SelfingRate

The selfing rate of an Epoch.

Time

Store time values.

TimeInterval

A half-open time interval [present, past).

TopLevelDemeDefaults

Top-level defaults for a Deme.

UnresolvedDemeHistory

HDM data for a Deme

UnresolvedEpoch

HDM representation of an epoch.

UnresolvedMigration

An unresolved migration epoch.

UnresolvedPulse

An unresolved Pulse event.

Enums

BuilderError

Error type raised by GraphBuilder

DemeId

A deme can be identified as an index or as a name

DemesError

Error type for this crate.

SizeFunction

Specify how deme sizes change during an Epoch.

TimeUnits

The time units of a graph

Functions

load

Build a Graph from a type implementing std::io::Read.

load_jsonjson

Load a Graph from a JSON reader.

loads

Build a Graph from an in-memory str.

loads_jsonjson

Generate a Graph from a JSON string.

round_time_to_integer_generations

Convert a time value into generations, rounding output to closest integer.

version

Return the package version given in the Cargo.toml file of this crate.