tree, estimateRoot, noCache, stdev, discreteRates, realRates, rateQuantiles, nBins, distr, clock.rate
| type: beast.base.evolution.tree.TreeInterface |
| (Species) tree to apply per-branch rates to. |
| Required input |
| type: java.lang.Boolean |
| Estimate rate of the root branch. |
| Optional input. Default: false |
| type: java.lang.Boolean |
| Always recalculate branch rates. |
| Optional input. Default: false |
| type: beast.base.inference.parameter.RealParameter |
| Standard deviation of the log-normal distribution for branch rates. If not supplied uses exponential. |
| Optional input |
| type: beast.base.inference.parameter.IntegerParameter |
| The rate categories associated with nodes in the species tree for sampling of individual rates among branches. |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| The real rates associated with nodes in the species tree for sampling of individual rates among branches. |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| The rate quantiles for sampling of individual rates among branches. |
| Optional input |
| type: java.lang.Integer |
| Number of discrete branch rate bins (default is equal to the number of estimated branch rates). Only used when branch rates are catrgories. |
| Optional input. Default: -1 |
| type: beast.base.inference.distribution.ParametricDistribution |
| the distribution governing the rates among branches, for quantiles only. Must have mean of 1. The clock.rate parameter can be used to change the mean rate. |
| Optional input |
| type: beast.base.core.Function |
| mean clock rate (defaults to 1.0) |
| Optional input |