bisseMLE
: function
Overview
bisseMLE is a function for finding the maximum-likelihood parameter estimates for a BiSSE model.
Example
From the docs page, get anolis.phy and anolis.csv.
Load these files into Arbor, and …
Arguments
- table: A data table including species names
- tree: A phylogenetic tree
- column: The name of the column to analyze
- type: The character type
- discrete: a character with a discrete number of states
- continuous: a continuously varying character
- fromData: will attempt to determine the data type from the data itself
- method: specifies the method used to reconstruct ancestral character states
- marginal: marginal ancestral state reconstructions, which reconstruct each node integrating over all possibilities at all other nodes in the tree; this is typically the method used in the literature to reconstruce ACEs
- joint: joint ancestral reconstructions, which give the configuration of ancestral states that together maximize the likelihood of the data given model parameters
- mcmc: reconstruct ancestral states using Bayesian MCMC. Note that the discrete version of this doesn’t seem to work, and even if it did work it is not a full MCMC ancestral state method
- stochastic: create stochastic character map
Outputs
References