corDISC: Correlated evolution binary traits

In corHMM: Hidden Markov Models of Character Evolution

Correlated evolution binary traits

Description

Fits a model of correlated evolution between two or three binary traits

Usage

corDISC(phy,data, ntraits=2, rate.mat=NULL, model=c("ER","SYM","ARD"), 
node.states=c("joint", "marginal", "scaled", "none"), lewis.asc.bias=FALSE, p=NULL, 
root.p=NULL, ip=NULL, lb=0, ub=100, diagn=FALSE)

Arguments

phy	a phylogenetic tree, in ape “phylo” format.
data	a data matrix containing species information (see Details).
ntraits	specifies the number of traits to be included in the analysis.
rate.mat	a user-supplied rate matrix index of parameters to be optimized.
model	specifies the underlying model.
node.states	method used to calculate ancestral states at internal nodes (see Details).
lewis.asc.bias	a logical indicating whether the ascertainment bias correction of Lewis et al. 2001 should be used. The default is FALSE.
p	a vector of transition rates. Allows the user to calculate the likelihood given a specified set of parameter values to specified as fixed and calculate the likelihood.
root.p	a vector used to fix the probabilities at the root, but “yang” and “maddfitz” can also be supplied to use the method of Yang (2006) and FitzJohn et al (2009) respectively (see details).
ip	initial values used for the likelihood search. Can be a single value or a vector of unique values for each parameter. The default is ip=1.
lb	lower bound for the likelihood search. The default is lb=0.
ub	upper bound for the likelihood search. The default is ub=100.
diagn	logical indicating whether diagnostic tests should be performed. The default is FALSE.

Details

__THIS FUNCTION IS NO LONGER NECESSARY AS IT IS NOW ENTIRELY SUBSUMED WITHIN__ corHMM (see _Generalized corHMM_ vignette). But we still provide it for those that are more comfortable using it than exploring the new corHMM function. As before, corDISC takes a tree and a trait file and estimates transition rates and ancestral states for two or three binary characters (see Pagel 1994). Note, however, that rayDISC can be used to evaluate the same models as in corDISC, with the major difference being that, with rayDISC, the rate matrix would have to be manipulated using rate.mat.maker in order to remove parameters associated with dual transitions. With corDISC, the input phylogeny need not be bifurcating as the algorithm is implemented to handle multifucations. Polytomies are allowed by generalizing Felsenstein's (1981) pruning algorithm to be the product of the probability of observing the tip states of n descendant nodes, rather than two, as in the completely bifurcating case. For the trait file, the first column of the trait file must contain the species labels to match to the tree, with the second column onwards corresponding to the binary traits of interest.

The user can fix the root state probabilities by supplying a vector to root.p. For example, in the two trait case, if the hypothesis is that the root is 00, then the root vector would be root.p=c(1,0,0,0) for state combinations 00, 01, 10, and 11, respectively. If the user supplies the flag root.p=“yang”, then the estimated transition rates are used to set the weights at the root (see pg. 124 Yang 2006), whereas specifying root.p=“maddfitz” employs the same procedure described by Maddison et al. (2007) and FitzJohn et al. (2009). Note that the default root.p=NULL assumes equal weighting among all possible states.

We also note that scoring information that is missing for a species can be incorporated in the analysis by including an NA for that particular trait. corDISC will then set the trait vector so that the tip vector will reflect the probabilities that are compatible with our observations. For example, if the scoring for trait 1 is missing, but trait 2 is scored as 0, then the tip vector would be (1,0,1,0), for state combinations 00, 01, 10, and 11 respectively, given our observation that trait 2 is scored 0 (for a good discussion see Felsenstein 2004, pg. 255).

Value

corDISC returns an object of class corDISC. This is a list with elements:

$loglik	the maximum negative log-likelihood.
$AIC	Akaike information criterion.
$AICc	Akaike information criterion corrected for sample size.
$ntraits	The number of traits specified.
$solution	a matrix containing the maximum likelihood estimates of the transition rates.
$solution.se	a matrix containing the approximate standard errors of the transition rates. The standard error is calculated as the square root of the diagonal of the inverse of the Hessian matrix.
$index.mat	The indices of the parameters being estimated are returned. The numbers correspond to the row in the eigvect and can useful for identifying the parameters that are causing the objective function to be at a saddlepoint.
$lewis.asc.bias	The setting describing whether or not the Lewis ascertainment bias correction was used.
$opts	Internal settings of the likelihood search
$data	User-supplied dataset.
$phy	User-supplied tree.
$states	The likeliest states at each internal node.
$tip.states	NULL
$iterations	The number of iterations used by the optimization routine.
$eigval	The eigenvalues from the decomposition of the Hessian of the likelihood function. If any eigval<0 then one or more parameters were not optimized during the likelihood search
$eigvect	The eigenvectors from the decomposition of the Hessian of the likelihood function is returned

Author(s)

Jeremy M. Beaulieu

References

Beaulieu J.M., and M.J. Donoghue 2013. Fruit evolution and diversification in campanulid angiosperms. Evolution, 67:3132-3144.

Felsenstein, J. 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biological Journal of the Linnean Society 16: 183-196.

Felsenstein J. 2004. Inferring phylogenies. Sunderland MA: Sinauer Associates.

FitzJohn, R.G., W.P. Maddison, and S.P. Otto. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Systematic Biology 58:595-611.

Lewis, P.O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50:913-925.

Maddison, W.P., P.E. Midford, and S.P. Otto. 2007. Estimating a binary characters effect on speciation and extinction. Systematic Biology 56:701-710.

Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society, B. 255:37-45.

corHMM documentation built on June 14, 2022, 1:05 a.m.