Description Usage Arguments Details Value Note Author(s) References See Also Examples
Creates a phylogenetic tree with branch lengths and a diagonal matrix to represent a (generalized) 3point structured covariance matrix from a trait evolution model on a known tree.
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phy 
a phylogenetic tree of type phylo with branch lengths. 
model 
a phylogenetic model. Default is "BM", for Brownian motion. Alternatives are "OU", "lambda", "kappa", "delta", "EB" and "trend". 
parameters 
List of parameters for the model (see Note). 
check.pruningwise 
if FALSE, the tree is assumed to be in pruningwise order. 
check.ultrametric 
if FALSE, the tree is assumed to be
ultrametric and 
D 
vector of ajustments for the external edge lengths, to make the tree ultrametric. Used for the OU transformations only. 
check.names 

Possible phylogenetic models are the Brownian motion model (BM), the
OrnsteinUhlenbeck model (OU), Pagel's lambda model (lambda), Pagel's
kappa model (kappa), Pagel's delta model (delta), the early burst model
(EB), and the Brownian motion with a trend (trend). Edge lengths are
unchanged under BM and the trend model.
Under the kappa model, each branch length l is transformed
to l^kappa.
If the time from the root to a node is t in phy
,
it is transformed to
T * (t/T)^delta
under the delta model, where T is the maximum roottotip
distance. The transformed tree has the same T.
Under EB, t is transformed to
(exp(rate*t)1)/rate,
which is very close to t (i.e. to the BM model)
when rate
is close to 0.
Under the lambda model, the time t from the
root to a node is transformed to
lambda * t for an internal node and
is unchanged for a tip.
Under "OUrandomRoot", t is transformed to
exp(2 alpha (Tt)),
where T is now the mean roottotip distance.
Under "OUfixedRroot", t is transformed to
exp(2 alpha (Tt)) * (1exp(2 alpha t)).
Under the OU models, diagWeight
contains exp(alpha D_i) for tip i, where D_i is the extra
length added to tip i to make the tree ultrametric.
tree 
a rooted tree with a root edge and transformed branch lengths. 
diagWeight 
a vector containing the diagonal elements of the diagonal matrix for the generalized 3point structure. 
The default choice for the parameters are as follows: alpha=0
for
the selection strength in the OU model, lambda=1
, kappa=1
,
delta=1
, rate=0
for the EB model, sigma2_error=0
for the variance of measurement errors. These default choices
correspond to the BM model.
Edges in the output tree are in pruningwise order.
If model="BM"
or model="trend"
, the output tree is the same as the
input tree except that the output tree is in pruningwise order.
Lam Si Tung Ho
Ho, L. S. T. and Ane, C. A lineartime algorithm for Gaussian and nonGaussian trait evolution models. Systematic Biology 63(3):397408.
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