pgls.Ives {phytools} | R Documentation |
This function fits the phylogenetic regression model with within-species sampling error following Ives et al. (2007).
pgls.Ives(tree, X, y, Vx=NULL, Vy=NULL, Cxy=NULL, lower=c(1e-8,1e-8))
tree |
a phylogeny as an object of class |
X |
a named vector containing a single independent variable (multiple independent variables to be added in future). |
y |
vector the dependent variable. Can be species means or individual values, as for |
Vx |
sampling variances for |
Vy |
sampling variances for |
Cxy |
sampling covariances between |
lower |
vector specifying the lower bounds for estimation for |
Presently only the bivariate regression model is implemented. Uses optim(...,method="L-BFGS-B")
for optimization. Note that some problems have been reported with the optimization algorithm for this model, which is simple and thus may fail to find the ML solution.
A list with the following components:
beta |
a vector or matrix of regression coefficients. |
sig2x |
fitted BM rate for |
sig2y |
fitted BM rate for |
a |
fitted ancestral states for |
logL |
log-likelihood. |
convergence |
a value for convergence. |
message |
a message for convergence. |
Liam Revell liam.revell@umb.edu
Ives, A. R., P. E. Midford, and T. Garland Jr. (2007) Within-species measurement error in phylogenetic comparative methods. Systematic Biology, 56, 252-270.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
brownie.lite
, phylosig
, phyl.resid