phylosig: Compute phylogenetic signal with two methods

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Compute phylogenetic signal with two methods

Description

Calculate phylogenetic signal using two different methods (Pagel, 1999; Blomberg et al., 2003).

Usage

phylosig(tree, x, method="K", test=FALSE, nsim=1000, se=NULL, start=NULL,
   control=list(), niter=10)
## S3 method for class 'phylosig'
plot(x, ...)

Arguments

tree	a phylogenetic tree in "phylo" format.
x	vector containing values for a single continuously distributed trait. In the case of the plot method, x is an object of class "phylosig".
method	method to compute signal: can be "K" or "lambda".
test	logical indicating whether or not to conduct a hypothesis test of "K" or "lambda".
nsim	for method="K", number of simulations in randomization test.
se	named vector containing the standard errors for each species.
start	vector of starting values for optimization of (respectively) \sigma^2 and \lambda. Only used in method="lambda" and se!=NULL.
control	list of control parameters for multidimensional optimization, implemented in optim. Only used in method="lambda" and se!=NULL.
niter	number of iterations for likelihood optimization of \lambda (if se!=NULL), or the number of intervals between 0 and the maximum possible value of \lambda for univariate optimization of \lambda (if se==NULL).
...	optional arguments for plot method.

Details

This function computes phylogenetic signal using two different methods. It can also conduct the hypothesis tests for significant phylogenetic signal, and estimate phylogenetic signal incorporating sampling error following Ives et al. (2007).

\lambda optimization is performed using optimize with the range of \lambda set between 0 and the theoretical upper limit of \lambda (determined by the relative height of the most recent internal node on the tree).

plot.phylosig creates either a plot of the null distribution of K or a likelihood surface, depending on the value of method.

Value

The function returns an object of class "phylosig". With default arguments (method="K", test=FALSE, and se=NULL), this will be a single numeric value. Otherwise, if (method="K"), it will consist of a list with up to the following elements:

K	value of the K-statistic.
sig2	rate of evolution, \sigma^2, for estimation with sampling error.
logL	log-likelihood, for estimation with sampling error.
P	optionally, the P-value from the randomization test.

If (method="lambda"), it will be a list with up to the following elements:

lambda	fitted value of \lambda.
sig2	rate of evolution, \sigma^2, for estimation with sampling error.
logL	log-likelihood.
logL0	log-likelihood for \lambda=0.
P	P-value of the likelihood ratio test.
convergence	value for convergence, for estimation with sampling error only. (See optim).
message	message from optim, for estimation with sampling error only.

Author(s)

Liam Revell [e-mail]

References

Blomberg, S. P., T. Garland Jr., and A. R. Ives (2003) Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution, 57, 717-745.

Ives, A. R., P. E. Midford, and T. Garland Jr. (2007) Within-species variation and measurement error in phylogenetic comparative biology. Systematic Biology, 56, 252-270.

Pagel, M. (1999) Inferring the historical patterns of biological evolution. Nature, 401, 877-884.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

Examples

## load data from Garland et al. (1992)
data(mammal.tree)
data(mammal.data)
## extract characters of interest
ln.bodyMass<-log(setNames(mammal.data$bodyMass,
    rownames(mammal.data)))
ln.homeRange<-log(setNames(mammal.data$homeRange,
    rownames(mammal.data)))
## compute phylogenetic signal K
K.bodyMass<-phylosig(mammal.tree,ln.bodyMass,
    test=TRUE)
print(K.bodyMass)
plot(K.bodyMass)
K.homeRange<-phylosig(mammal.tree,ln.homeRange,
    test=TRUE)
print(K.homeRange)
plot(K.homeRange)
## compute phylogenetic signal lambda
lambda.bodyMass<-phylosig(mammal.tree,ln.bodyMass,
    method="lambda",test=TRUE)
print(lambda.bodyMass)
plot(lambda.bodyMass)
lambda.homeRange<-phylosig(mammal.tree,ln.homeRange,
    method="lambda",test=TRUE)
print(lambda.homeRange)
plot(lambda.homeRange)

phytools documentation built on June 22, 2024, 10:39 a.m.