Analysis

Demographic reconstruction

This plots the distribution of demographic population sizes over time for a number of models (constant size, exponential growth & logistic growth) that are available in BEAST. This involves you selecting the traces for each parameter of the model. You should only select the model that was actually run under BEAST (e.g., if you ran an exponential growth model, you shouldn't plot the constant population size model).

Bayesian Skyline reconstruction

A Bayesian Skyline tutorial is available from BEAST tutorials.

Extended Bayesian Skyline reconstruction

GMRF Skyride reconstruction

SkyGrid reconstruction

Lineages through time

Conditional posterior

The purpose of finding conditional posterior distribution in Tracer is to provide:

1. fairly general solution to looking at conditional posterior distributions;
2. specifically, support for BSSVS forms of model averaging, in which some parameters are only in the likelihood when their submodel is "indicated" by some indicator function that is usually a discrete, integer or boolean variable. In that case the posterior of the parameter should not include the states when it was sampled only in the prior because the submodel it belonged to was "turned off". This is relevant for EBSP, Random Local Clocks model, microsatellite model averaging and relaxed clock model averaging methods all from my group in last couple of years. Also relevant for BSSVS in phylogeography as well depending on how the state is logged.