Description Usage Arguments Details Value Author(s) References Examples
View source: R/utilitiesphylo.R
applying various transformation to the branches of a phylogenetic tree.
1 2 3 
x 
an object of class phylo 
model 
a model used to transform the tree (see Details) 
... 
argument(s) to be passed to the transformation function (see Examples) 
This function takes a tree and returns either a transformed tree if ...
is not empty and gives the parameter value(s) for the tree transformation. If ...
is left empty, a function is returned to the user that can be efficiently iterated over many parameter values for transformation. The available models are meant to correspond with changing the model of phenotypic evolution for discrete or continuous characters.
A transformation function (or rescaled phylogenetic tree of class 'phylo' (ape format) is returned. Possible transforms include the following:
BM 
is the Brownian motion model, which fits a random walk with variance 
OU 
is the OrnsteinUhlenbeck model (Butler and King 2004), which fits a random walk with a central tendency with an attraction strength proportional to the parameter 
EB 
is the Earlyburst model (Harmon et al. 2010) and also called the 
nrate 
is the multiplerates model where time slices have independent rates of evolution. The parameters used for transformation are 
lrate 
is the multiplerates model where local clades have independent rates of evolution. The parameters used for transformation are 
trend 
is a diffusion model with linear trend in rates through time. The parameter used for transformation is 
lambda 
is one of the Pagel (1999) models that fits the extent to which the phylogeny predicts covariance among trait values for species. The model effectively transforms the tree as follows: values of 
kappa 
is a punctuational (speciational) model of trait evolution (Pagel 1999), where character divergence is related to the number of speciation events between two species. Note that if there are missing speciation events in the given phylogeny (due to extinction or incomplete sampling), interpretation under the 
delta 
is a timedependent model of trait evolution (Pagel 1999). The 
white 
is a 
depth 
is simply a transformation of the total depth of the tree; stretching the tree has an effect of increasing rates of evolution under Brownian motion (relative to characters evolved on the unstretched tree), and compressing the tree has the opposite effect. The parameter used for transformation is 
LJ Harmon and JM Eastman
Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877884.
Butler, M.A. and A.A. King, 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683695.
Various papers in prep., L. J. Harmon and J. T. Weir.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30  geo < get(data(geospiza))
## returning a function
ltrns < rescale(geo$phy, "lambda")
plot(ltrns(0))
title("lambda: 0.0")
plot(ltrns(0.5))
title("lambda: 0.5")
plot(ltrns(1))
title("lambda: 1")
## transforming the tree
lphy < rescale(geo$phy, "lambda", 0.5) # transform tree in one fell swoop
plot(lphy)
title("lambda: 0.5")
## multirate tree  time
rtrns < rescale(geo$phy, "nrate")
rphy < rtrns(time=c(0.2, 0.4, 0.6, 0.8), rate=c(2, 4, 8, 16))
plot(rphy)
title("5rate tree: by time")
## multirate tree  lineages
mtrns < rescale(geo$phy, "lrate")
mphy < mtrns(node=c(25, 20), rate=c(4, 8))
plot(mphy)
title("3rate tree: by lineages")

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