OUwie.fixed: Generalized Hansen model likelihood calculator
In thej022214/OUwie: Analysis of Evolutionary Rates in an OU Framework

OUwie.fixed

R Documentation

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, tip.fog="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.
`tip.fog`	designates whether a fourth column in the data matrix contains tip fog for each species value ("known"). The tip fog is assumed to be the standard error of the species mean. If a single numeric value is supplied it will be applied to all species uniformly. The default is "none", meaning no tip fog is used.
`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")

thej022214/OUwie documentation built on April 13, 2025, 9:36 a.m.