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=NULL, Vy=NULL, Cxy=NULL, lower=c(1e-8,1e-8))

Arguments

tree

a phylogenetic tree in "phylo" format.

a named vector containing a single independent variable (multiple independent variables to be added). X can contain the species means, or a single long vector containing the sample of values for each species. In the latter case the <

vector the dependent variable. Can be species means or individual values, as for X.

sampling variances for X. If NULL, then the within-species variance is computed from the data assuming that individual samples, not species means, have been provided in X.

sampling variances for y. If NULL, then the within-species variance is computed from the data assuming that individual samples, not species means, have been provided in y.

Cxy

sampling covariances between X and y. This will also be computed from the data if Cxy==NULL. Note than in this case - but not for the calculation of Vx and Vy, the same number of observation

lower

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

Value

a list with the following components:
betaa vector or matrix of regression coefficients.
sig2xfitted BM rate for X.
sig2yfitted BM rate for y.
afitted ancestral states for X and y.
logLlog-likelihood.
convergencea value for convergence. convergence=0 is good; see optim for more details.
messagea 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.