picx: Estimate the extended phylogenetic independent contrast....

In caseywdunn/hutan: A Collection of Tools for Phylogenetic Tree Manipulation

Description

Estimate the extended phylogenetic independent contrast. Rather than normalize differences across nodes by branch lengths, differences are normalized be the expected difference obtained from replicate simulations. This allows for greater model flexibility.

Usage

picx(
  x,
  phy,
  var.contrasts = FALSE,
  model_method = "BM",
  model_parameters = NA,
  n_replicates = 200
)

Arguments

x	A numeric vector with one trait value per tip
phy	An ape::phylo object
var.contrasts	logical, indicates whether the expected variances of the contrasts should be returned
model_method	The model of trait evolution. Can be one of c("BM", "OU")
model_parameters	Model parameters from fitContinuous. Will estimate if not provided.
n_replicates	The number of simulations used to estimate the expected differences

Value

A vector of phylogenetically independent contrasts

caseywdunn/hutan documentation built on June 12, 2020, 3:12 a.m.