H2                      Phylogenetic heritability estimated at time t
OU                      Distribution of an Ornstein-Uhlenbeck Process
                        at Time t, Given Initial State at Time 0
POUMM                   The Phylogenetic (Ornstein-Uhlenbeck) Mixed
                        Model
POUMMIsADevRelease      Check if the POUMM version correpsonds to a dev
                        release
PhylogeneticH2          Phylogenetic Heritability
analyseMCMCs            Extract data from an MCMC chain This is an
                        internal function.
chld                    Node indices of the direct descendants of n in
                        the phylogeny.
coef.POUMM              Extract maximum likelihood fitted parameters
                        (coefficients) from a fitted POUMM model.
covFunPOUMM             A vectorized expected covariance function for a
                        given tree and a fitted POUMM model
covHPDFunPOUMM          A vectorized function returning HPD intervals
                        of the expected covariance for a given tree and
                        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 (parallel) POUMM likelihood calculation
                        using the SPLITT library
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
simulateTrait           Simulate a trait on a tree under a ML fit of
                        the POUMM model
specPOUMM               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
vignetteCachedResults   Cached objects for the POUMM vignettes and
                        examples
