phytools (version 0.2-1)

pgls.Ives: Phylogenetic regression with intraspecific sampling error

Description

This function fits the phylogenetic regression model with within-species sampling error following Ives et al. (2007).

Usage

pgls.Ives(tree, X, y, Vx, Vy, Cxy, lower=c(1e-8,1e-8))

Arguments

tree

a phylogenetic tree in "phylo" format.

X

a named vector containing a single independent variable (multiple independent variables to be added).

y

vector the dependent variable.

Vx

sampling variances for X.

Vy

sampling variances for y.

Cxy

sampling covariances between X and y.

lower

vector specifying the lower bounds for estimation for sig2x and sig2y, respectively. (Must be >0.)

Value

• a list with the following components:
• beta
  a vector or matrix of regression coefficients.
• sig2x
  fitted BM rate for X.
• sig2y
  fitted BM rate for y.
• a
  fitted ancestral states for X and y.
• logL
  log-likelihood.
• convergence
  a value for convergence. convergence=0 is good; see optim for more details.
• message
  a message for convergence.

Details

Presently only the bivariate regression model is implemented. Uses optim(...,method="L-BFGS-B").

References

Ives, A. R., P. E. Midford, and T. Garland Jr. 2007. Within-species measurement error in phylogenetic comparative methods. Systematic Biology, 56, 252--270.

See Also

brownie.lite, phylosig, phyl.resid