cost_function

data

The Cholesky decomposition of the inverted covariance
matrix.

concentration

A column reduced 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


We want Nelder-Mead to run fast so the cost function operates with the column
reduced edge optimisation matrix and does not give any extra information about
the fit. For the details, use <code><a rd-options="" href="/link/edge_optimisation_function?package=admixturegraph&version=1.0.2" data-mini-rdoc="admixturegraph::edge_optimisation_function">edge_optimisation_function</a></code> instead.


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

cost_function function

A column reduced 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>.


We want Nelder-Mead to run fast so the cost function operates with the column
reduced edge optimisation matrix and does not give any extra information about
the fit. For the details, use <code><a rd-options='' href='edge_optimisation_function'>edge_optimisation_function</a></code> instead.


cost_function: The cost function fed to Nelder-Mead.

Description

Usage

Arguments

Value

See Also