pgls.Ives | R Documentation |
Phylogenetic regression 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),
fixed.b1=NULL)
pgls.SEy(model, data, corClass=corBrownian, tree,
se=NULL, method=c("REML","ML"), interval=c(0,1000), ...)
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 |
fixed.b1 |
fixed regression slope, |
model |
model to fit. (For |
data |
data frame. (For |
corClass |
correlation structure. (For |
se |
vector of standard errors in y. (For |
method |
optimization method. (For |
interval |
interval over which to perform optimization. (For |
... |
optional arguments. (For |
pgls.Ives
fits the phylogenetic regression model with within-species sampling error following Ives et al. (2007).
pgls.SEy
fits a simpler model in which only sampling error in y
is taken into account. This function uses gls
from the nlme package internally for optimization and returns an object of class "gls"
that is compatible with all methods for that object class.
In the case of pgls.Ives
, only the bivariate regression model is implemented. 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.
In the case of pgls.SEy
the user can (theoretically) specify any class of linear model permitted by gls
.
In the case of pgls.Ives
, an object of class "pgls.Ives"
with the following elements:
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. |
In the case of pgls.SEy
, an object of class "gls"
.
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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
brownie.lite
, phylosig
, phyl.resid
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