makeBD : function

collection: diversificationModels

Overview

makeBD is a function for setting up a birth-death model in Arbor. Use in conjunction with fitBD.

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