edge_optimisation_function

data

The Cholesky decomposition of the inverted covariance matrix.

concentration

A full edge optimisation matrix (typically given by the
function <code><a rd-options="" href="/link/build_edge_optimisation_matrix?package=admixturegraph&version=1.0.2" data-mini-rdoc="admixturegraph::build_edge_optimisation_matrix">build_edge_optimisation_matrix</a></code>).

matrix

graph

In case one wants to tweak something in the graph.

parameters

Given to <code><a rd-options="" href="/link/mynonneg?package=admixturegraph&version=1.0.2" data-mini-rdoc="admixturegraph::mynonneg">mynonneg</a></code>.

iteration_multiplier


Returning the cost, an example edge solution of an optimal fit, and linear
relations describing the set of all edge solutions. Operating with the full
edge optimisation matrix, not the column reduced one.


Implements tools for building and visualising admixture graphs
and for extracting equations from them. These equations can be compared to f-
statistics obtained from data to test the consistency of a graph against data --
for example by comparing the sign of f_4-statistics with the signs predicted by
the graph -- and graph parameters (edge lengths and admixture proportions) can
be fitted to observed statistics.

Thomas Mailund

admixturegraph

Admixture Graph Manipulation and Fitting

edge_optimisation_function function

A full edge optimisation matrix (typically given by the
function <code><a rd-options='' href='build_edge_optimisation_matrix'>build_edge_optimisation_matrix</a></code>).

Given to <code><a rd-options='' href='mynonneg'>mynonneg</a></code>.

edge_optimisation_function: More detailed edge fitting than mere cost_function.

Description

Usage

Arguments

Value

See Also