brownie.lite | R Documentation |
This function takes an object of class "phylo"
or class "simmap"
with a mapped binary or multistate trait (see read.simmap
) and data for a single continuously valued character. It then fits the Brownian rate variation ("noncensored") model of O'Meara et al. (2006; Evolution). This is also the basic model implemented in Brian O'Meara's Brownie software.
brownie.lite(tree, x, maxit=2000, test="chisq", nsim=100, se=NULL, ...)
tree |
a phylogenetic tree either as an object of class |
x |
a vector of tip values for species. |
maxit |
an optional integer value indicating the maximum number of iterations for optimization - may need to be increased for large trees. |
test |
an optional string indicating the method for hypothesis testing - options are |
nsim |
number of simulations (only used if |
se |
a vector containing the standard errors for each estimated mean in |
... |
optional arguments. |
Sampling error in the estimation of species means can also be accounted for by assigning the vector se
with the species specific sampling errors for x
.
An object of class "brownie.lite"
containing the following components:
sig2.single |
is the rate, σ^2, for a single-rate model. This is usually the "null" model. |
a.single |
is the estimated state at the root node for the single rate model. |
var.single |
variance on the single rate estimator - obtained from the Hessian. |
logL1 |
log-likelihood of the single-rate model. |
k1 |
number of parameters in the single rate model (always 2). |
sig2.multiple |
is a length p (for p rates) vector of BM rates (σ_1^2, σ_2^2, and so on) from the multi-rate model. |
a.multiple |
is the estimated state at the root node for the multi-rate model. |
var.multiple |
p x p variance-covariance matrix for the p rates - the square-roots of the diagonals should give the standard error for each rate. |
logL.multiple |
log-likelihood of the multi-rate model. |
k2 |
number of parameters in the multi-rate model (p+1). |
P.chisq |
P-value for a likelihood ratio test against the χ^2 distribution; or |
P.sim |
P-value for a likelihood ratio test agains a simulated null distribution. |
convergence |
logical value indicating if the likelihood optimization converged. |
Liam Revell liam.revell@umb.edu
O'Meara, B. C., C. Ane, M. J. Sanderson, and P. C. Wainwright. (2006) Testing for different rates of continuous trait evolution using likelihood. Evolution, 60, 922-933.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
brownieREML
, evol.vcv
, ratebytree
## load data from Revell & Collar (2009) data(sunfish.tree) data(sunfish.data) ## extract character of interest buccal.length<-setNames(sunfish.data$buccal.length, rownames(sunfish.data)) ## fit model multiBM.fit<-brownie.lite(sunfish.tree, buccal.length) print(multiBM.fit)
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