OUwie.fixed: Generalized Hansen model likelihood calculator

In OUwie: Analysis of Evolutionary Rates in an OU Framework

Generalized Hansen model likelihood calculator

Description

Allows the user to calculate the likelihood given a specified set of parameter values

Usage

OUwie.fixed(phy, data, model=c("BM1","BMS","OU1","OUM","OUMV","OUMA","OUMVA"), 
simmap.tree=FALSE, root.age=NULL, scaleHeight=FALSE, root.station=FALSE, 
get.root.theta=FALSE, shift.point=0.5, alpha=NULL, sigma.sq=NULL, theta=NULL, 
clade=NULL, mserr="none", check.identify=TRUE, algorithm=c("invert", "three.point"), 
tip.paths=NULL, quiet=FALSE)

Arguments

phy	a phylogenetic tree, in ape “phylo” format and with internal nodes labeled denoting the ancestral selective regimes
data	a dataframe containing species information (see Details)
model	models to fit to comparative data (see Details).
simmap.tree	a logical indicating whether the input tree is in SIMMAP format. The default is FALSE.
root.age	indicates the age of the tree. This is to be used in cases where the "tips" are not contemporary, such as in cases for fossil trees. Default is NULL meaning latest tip is modern day.
scaleHeight	a logical indicating whether the total tree height should be scaled to 1 (see Details). The default is FALSE.
root.station	a logical indicating whether the starting state, theta_0, should be estimated.
get.root.theta	a logical indicating whether the starting state, theta_0, should be estimated (see Details).
shift.point	the point along a branch where a regime change is assumed to have occurred (if SIMMAP=FALSE. The default is set to 0.5, or halfway along a branch.
alpha	a numeric vector giving the values of alpha for each selective regime
sigma.sq	a numeric vector giving the values of sigma^2 for each selective regime
theta	a numeric vector giving the values of theta for each selective regime
clade	a list containing a pair of taxa whose MRCA is the clade of interest.
mserr	designates whether a fourth column in the data matrix contains measurement error for each species value ("known"). The measurement error is assumed to be the standard error of the species mean. The default is "none".
check.identify	a logical indicating whether to check that the user-supplied regime paintings will produce identifiable theta estimates. The default is TRUE.
algorithm	designates whether the standard matrix inversion ('invert') or the faster 'three-point' algorithm of Ho and Ane (2013) should be used.
tip.paths	an optional list that can be provided by the user where each element from 1:nTips is the path from tip to root by labeled node number. The default is NULL and this option is used for internal speedups.
quiet	a logical indicating whether or not to print progress to the screen. The default is "FALSE".

Details

The input is a tree and a data file. The tree must be of class “phylo” and must contain the ancestral selective regimes as internal node labels. The data file is a data.frame that must have column entries in the following order: [,1] species names and [,2] their current selective regime. The user specifies the parameter values (i.e. alpha, sigma^2, and theta).

Value

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

$loglik	the maximum log-likelihood.
$AIC	Akaike information criterion.
$AICc	Akaike information criterion corrected for sample-size.
$BIC	Schwartz information criterion.
$model	The model being fit
$param.count	The number of parameters counted in the model.
$solution	a matrix containing the maximum likelihood estimates of alpha and sigma^2.
$theta	a matrix containing the maximum likelihood estimates of theta.
$tot.state	A vector of names for the different regimes
$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 (see Details)
$simmap.tree	A logical indicating whether the input phylogeny is a SIMMAP formatted tree.
$root.age	The user-supplied age at the root of the tree.
$shift.point	The user-specified portion of the branch where a regime shift occurs.
$data	User-supplied dataset
$phy	User-supplied tree
$root.station	A logical indicating whether the starting state, theta_0, was estimated
$scaleHeight	Indicates whether the tree was constrained to a total height of 1.
$get.root.theta	Indicates whether the root.theta was included in the model.
$regime.weights	A table containing parameter estimates and the weights for time spent in each regime for each tip.
$algorithm	The algorithm used to estimate parameters.

Author(s)

Jeremy M. Beaulieu

Examples

data(tworegime)

#Calculate the likelihood based on known values of
#alpha, sigma^2, and theta:
alpha=c(0.5632459,0.1726052)
sigma.sq=c(0.1064417,0.3461386)
theta=c(1.678196,0.4185894)

OUwie.fixed(tree,trait,model=c("OUMVA"), simmap.tree=FALSE, scaleHeight=FALSE,
clade=NULL, alpha=alpha,sigma.sq=sigma.sq,theta=theta, algorithm="three.point")

OUwie documentation built on June 15, 2022, 5:15 p.m.