H2                      Phylogenetic heritability estimated at time t
MCMC                    (Adaptive) Metropolis Sampler
OU                      Distribution of an Ornstein-Uhlenbeck Process
                        at Time t, Given Initial State at Time 0
POUMM                   The Phylogenetic (Ornstein-Uhlenbeck) Mixed
                        Model
PhylogeneticH2          Phylogenetic Heritability
chld                    Node indices of the direct descendants of n in
                        the phylogeny tree.
coef.POUMM              Extract maximum likelihood fitted parameters
                        (coefficients) from a fitted POUMM model.
covPOUMM                Expected covariance of two tips at given
                        root-tip time and phylogenetic distance
covVTipsGivenTreePOUMM
                        Variance covariance matrix of the values at the
                        tips of a tree under an OU process
dVNodesGivenTreePOUMM   Multivariate density of observed values along a
                        tree given an OU process of evolution and
                        root-value
edgesFrom               Edge indices of the edges in tree starting from
                        n
fitted.POUMM            Extract maximum likelihood expected genotypic
                        values at the tips of a tree, to which a POUMM
                        model has been previously fitted
gPOUMM                  Distribution of the genotypic values under a
                        POUMM fit
likPOUMMGivenTreeVTips
                        Density of observed tip-values given a tree,
                        assuming Ornstein-Uhlenbeck process for the
                        genetic contributions along the tree and
                        normally distributed environmental deviations.
likPOUMMGivenTreeVTipsC
                        Fast POUMM likelihood calculation based on the
                        breadth-first pruning algorithm and
                        Armadillo-library vector operations.
logLik.POUMM            Extract maximum likelihood and degrees of
                        freedom from a fitted POUMM model
loglik_abc_g0_g0Prior   Processing of the root value and calculation of
                        the maximum log-likelihood for the given
                        coefficients abc, and parameters theta, g0 and
                        g0Prior. This is an internal function.
maxLikPOUMMGivenTreeVTips
                        Find a maximum likelihood fit of the POUMM
                        model
mcmcPOUMMGivenPriorTreeVTips
                        MCMC-sampling from a posterior distribution of
                        a P(OU)MM model given tree, values at the tips
                        and a prior distribution
nobs.POUMM              Number of tips in a phylogenetic tree, POUMM
                        has been fit on.
nodeTimes               Calculate the time from the root to each node
                        of the tree
plot.POUMM              Plots of a POUMM-fit
plot.summary.POUMM      Plot a summary of a POUMM fit
pruneTree               Extract information for fast likelihood
                        calculation using the breadth-first pruning
                        algorithm.
rTrajectoryOU           Generation of a random trajectory of an OU
                        process starting from a given initial state
rTrajectoryOUDef        Generation of a random trajectory of an OU
                        process starting from a given initial state
                        (only for test purpose)
rVNodesGivenTreePOUMM   Random generation of values along a
                        phylogenetic tree following a branching OU
                        process
residuals.POUMM         Extract maximum likelihood environmental
                        contributions (residuals) at the tips of a
                        tree, to which a POUMM model has been fitted.
simulatePOUMMLikelihoodMainLoop
                        Writes verbose messages of the order of tree
                        traversal during likelihood calculation
specifyPOUMM            Specifying a POUMM fit
statistics              Extract statistics from sampled or inferred
                        parameters of a POUMM fit
summary.POUMM           Summarize the results of a POUMM-fit
validateSpecPOUMM       Validate a POUMM specification
validateZTree           Validate phenotypic values and phylogenetic
                        tree
