Defines an uncorrelated relaxed molecular clock.
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biol 4(5): e88
doi:10.1371/journal.pbio.0040088
distr, rateCategories, numberOfDiscreteRates, rateQuantiles, rates, tree, normalize, clock.rate
| type: beast.math.distributions.ParametricDistribution |
| the distribution governing the rates among branches. Must have mean of 1. The clock.rate parameter can be used to change the mean rate. |
| Required input |
| type: beast.core.parameter.IntegerParameter |
| the rate categories associated with nodes in the tree for sampling of individual rates among branches. |
| Optional input |
| type: java.lang.Integer |
| the number of discrete rates to approximate the rate distribution by. With category parameterisation, a value <= 0 will cause the number of categories to be set equal to the number of branches in the tree. With quantile paramterisation, a value <= 1 will calculate rates for every quantile, a value > 1 will approximate the distribution piecewise linearly with specified number of rates. (default = -1) |
| Optional input. Default: -1 |
| type: beast.core.parameter.RealParameter |
| the rate quantiles associated with nodes in the tree for sampling of individual rates among branches. |
| Optional input |
| type: beast.core.parameter.RealParameter |
| the rates associated with nodes in the tree for sampling of individual rates among branches. |
| Optional input |
| type: beast.evolution.tree.Tree |
| the tree this relaxed clock is associated with. |
| Required input |
| type: java.lang.Boolean |
| Whether to normalize the average rate (default false). |
| Optional input. Default: false |
| type: beast.core.parameter.RealParameter |
| mean clock rate (defaults to 1.0) |
| Optional input |