brownie.lite | R Documentation |
Fits a multi-rate Brownian motion evolution model using maximum likelihood.
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. |
This function takes an object of class "phylo"
or class "simmap"
with a mapped binary or multi-state 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.
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 elements:
sig2.single |
is the rate, |
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 ( |
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 |
P.sim |
P-value for a likelihood ratio test against 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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.