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)
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.
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.
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.