Crate forrustts[−][src]

Rust library for forward time population genetic simulation with tree sequence recording.

Overview

This package is a port of many ideas from fwdpp from C++ to rust.

Currently, this should be viewed as experimental.

The tables model differs from tskit in some important ways:

Time moves from the past to the present. Thus, child nodes have time values greater than those of their parents.
The data layout is “array of structures” while tskit is a “structure of arrays”.
Metadata is not part of the tables. Often, what one thinks of as metadata is data used during the simulation. Thus, it is not part of a TableCollection and is something that would only be useful to write when transfering final results to a tskit::TableCollection.
Mutation table data are different. See MutationRecord.
Time is measured as an integer (see Time), as are genomic locations (see Position). In tskit, both are C double, the equivalent of f64.

In the examples/ directory of the project repository.

nested_forward_list	Compact representation of multiple forward linked lists.
tskit_tools	Data interchange to `tskit` format using `tskit`.

Edge	An Edge is a transmission event
MutationRecord	A MutationRecord is the minimal information needed about a mutation to track it on a tree sequence.
Node	A Node of a tree sequence
SamplesInfo	Information about samples used for table simpilfication.
Segment	A segment is a half-open interval of `crate::Position`s associated with a `crate::Node`.
SimplificationBuffers	Holds internal memory used by simplification machinery.
SimplificationFlags	Boolean flags affecting simplification behavior.
SimplificationOutput	Useful information output by table simplification.
Site	A Site is the location and ancestral state of a tables::MutationRecord
TableCollection	A collection of node, edge, site, and mutation tables.
TableSortingFlags	Modifies behavior of `TableCollection::sort_tables`
TableValidationFlags	Modifies behavior of `TableCollection::validate`

ForrusttsError	Primary error type.
TablesError	Error type related to `TableCollection`

Equals -1 (minus one). Primary use is to indicate a null Node id.

simplify_from_edge_buffer	Simplify a `TableCollection` from an `EdgeBuffer`.
simplify_tables	Simplify a `TableCollection`.
simplify_tables_without_state	Simplify a `TableCollection`.
validate_edge_table	Perform a data integrity check on an `EdgeTable`.
version	Get the forrustts version number.

EdgeBuffer	Data type used for edge buffering. Simplification of simulated data happens via `crate::simplify_from_edge_buffer()`.
EdgeTable	An edge table
IdType	Integer type used to refer to Node objects.
MutationTable	A Mutation table
NodeTable	A node table
Position	Integer type used to refer to a genomic coordinate/position
SiteTable	A site table
TablesResult	Result type for operations on tables
Time	Time is recorded as a discrete, signed integer.