plot_fit_1

object

An admix variable name (remember quotation marks).

resolution

Should the function plot the number of statistics where the graph fits
the data instead of the <code><a rd-options="" href="/link/cost_function?package=admixturegraph&version=1.0.2" data-mini-rdoc="admixturegraph::cost_function">cost_function</a></code>?

show_fit

If <code>show_fit</code> is <code>TRUE</code> then each statistic is considered fitted
if the difference between a prediction and the observation statistics is no
more than $D*\sigma/(2*Z)$. Notice that even when plotting the number of
fitted statistics, we have no guarantee that the chosen variables maximize
this number as the fitting function still optimizes 
<code><a rd-options="" href="/link/cost_function?package=admixturegraph&version=1.0.2" data-mini-rdoc="admixturegraph::cost_function">cost_function</a></code>.

sigma


A plot of the cost function with respect to one admix variable specified by the user.
Sorry about the name, all the good ones were taken and the fact that the word "graph" means
two different things doesn't help any.


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

plot_fit_1 function

Should the function plot the number of statistics where the graph fits
the data instead of the <code><a rd-options='' href='cost_function'>cost_function</a></code>?

If <code>show_fit</code> is <code>TRUE</code> then each statistic is considered fitted
if the difference between a prediction and the observation statistics is no
more than $D*\sigma/(2*Z)$. Notice that even when plotting the number of
fitted statistics, we have no guarantee that the chosen variables maximize
this number as the fitting function still optimizes 
<code><a rd-options='' href='cost_function'>cost_function</a></code>.

plot_fit_1: A plot of the cost function or number of fitted statistics.

Description

Usage

Arguments

Value

See Also