add_an_admixture2

graph

admixture_variable_name

An optional parameter for the preferred outgroup.

outgroup


Given an admixture graph, selects a child edge and two parent edges, disconnects the child edge
from its original parent node and connects it to the two parent edges with an admixture event,
if possible. Thus, contrary to <code><a rd-options="" href="/link/add_an_admixture?package=admixturegraph&version=1.0.2" data-mini-rdoc="admixturegraph::add_an_admixture">add_an_admixture</a></code>, the resulting graph need not be an
extension of the input graph in the sense that erasing one of the admixture edges we get
the original admixture graph. In practice, we know that when fitting data to admixture graphs,
the best graph with $k$ admixture events is not always an extension like that from the best
graph with $k - 1$ admixture events. Most likely it doesn't need to be an extension like
this (the two new admixture edges can both go where ever) either.


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

add_an_admixture2 function


Given an admixture graph, selects a child edge and two parent edges, disconnects the child edge
from its original parent node and connects it to the two parent edges with an admixture event,
if possible. Thus, contrary to <code><a rd-options='' href='add_an_admixture'>add_an_admixture</a></code>, the resulting graph need not be an
extension of the input graph in the sense that erasing one of the admixture edges we get
the original admixture graph. In practice, we know that when fitting data to admixture graphs,
the best graph with $k$ admixture events is not always an extension like that from the best
graph with $k - 1$ admixture events. Most likely it doesn't need to be an extension like
this (the two new admixture edges can both go where ever) either.


add_an_admixture2: Adds a new admixture event to a graph.

Description

Usage

Arguments

Value

See Also