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

• ffi
  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.