dist2root {aphylo}

Pointer to pruner

Description

Creates an external pointer to an object of class aphylo_pruner. This is mostly used to compute the model's likelihood function faster by reusing underlying C++ class objects to store probability matrices and data. This is intended for internal use only.

Usage

dist2root(ptr)

get_postorder(ptr)

new_aphylo_pruner(x, ...)

Arguments

ptr

An object of class aphylo_pruner.

x

An object of class aphylo or multiAphylo.

...

Further arguments passed to the method

Details

The underlying implementation of the pruning function is based on the pruner C++ library that implements Felsenstein's tree pruning algorithm. See https://github.com/USCbiostats/pruner.

Value

dist2root: An integer vector with the number of steps from each node (internal or not) to the root node.

get_postorder: An integer vector with the postorder sequence for pruning the tree (indexed from 0).

The function new_aphylo_pruner returns an object of class aphylo_pruner or multiAphylo_pruner, depending on the class of x.

Examples

set.seed(1)
x  <- raphylo(20) 
pruner <- new_aphylo_pruner(x)

# Computing loglike
LogLike(
  pruner,
  psi  = c(.10, .20),
  mu_d = c(.90, .80),
  mu_s = c(.10, .05),
  Pi   = .05,
  eta  = c(.90, .80)
  )
  
dist2root(pruner)
get_postorder(pruner)