R: Phylogenetic regression with intraspecific sampling error

pgls.Ives {phytools}

R Documentation

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 phylogeny as an object of class `"phylo"`.
`X`	a named vector containing a single independent variable (multiple independent variables to be added in future). `X` can contain the species means, or a single long vector containing the sample of values for each species. In the latter case the `names(X)` will be repeating - all samples from the same species should have the same name.
`y`	vector the dependent variable. Can be species means or individual values, as for `X`.
`Vx`	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`.
`Vy`	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 observations and the same ordering must be provided for `X` and `y`. If this is not the case, then it is assumed that different individuals have been sampled for `X` and `y` and thus `Cxy` is assumed to be zero for all species.
`lower`	vector specifying the lower bounds for estimation for `sig2x` and `sig2y`, respectively. (Must be >0.)

Details

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.

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.

Author(s)

Liam Revell liam.revell@umb.edu

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.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.