| alpha | 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 | 
| dOU | Distribution of an Ornstein-Uhlenbeck Process at Time t, Given Initial State at Time 0 | 
| dVNodesGivenTreePOUMM | Multivariate density of observed values along a tree given an OU process of evolution and root-value | 
| dVTipsGivenTreePOUMM | Density of observed tip-values given a tree, assuming Ornstein-Uhlenbeck process for the genetic contributions along the tree and normally distributed environmental deviations. | 
| 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 | 
| H2 | Phylogenetic heritability estimated at time t | 
| H2e | Phylogenetic Heritability | 
| 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 | 
| mcmc.poumm | MCMC-sampling from a posterior distribution of a P(OU)MM model given tree, values at the tips and a prior distribution | 
| mcmcPOUMMGivenPriorTreeVTips | MCMC-sampling from a posterior distribution of a P(OU)MM model given tree, values at the tips and a prior distribution | 
| meanOU | Distribution of an Ornstein-Uhlenbeck Process at Time t, Given Initial State at Time 0 | 
| 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 | 
| OU | Distribution of an Ornstein-Uhlenbeck Process at Time t, Given Initial State at Time 0 | 
| PhylogeneticH2 | Phylogenetic Heritability | 
| plot.POUMM | Plots of a POUMM-fit | 
| plot.summary.POUMM | Plot a summary of a POUMM fit | 
| POUMM | The Phylogenetic (Ornstein-Uhlenbeck) Mixed Model | 
| POUMMIsADevRelease | Check if the POUMM version correpsonds to a dev release | 
| pruneTree | Extract information for fast likelihood calculation using the breadth-first pruning algorithm. | 
| residuals.POUMM | Extract maximum likelihood environmental contributions (residuals) at the tips of a tree, to which a POUMM model has been fitted. | 
| rOU | Distribution of an Ornstein-Uhlenbeck Process at Time t, Given Initial State at Time 0 | 
| 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 | 
| sdOU | Distribution of an Ornstein-Uhlenbeck Process at Time t, Given Initial State at Time 0 | 
| sigmae | Phylogenetic Heritability | 
| sigmaOU | Phylogenetic Heritability | 
| 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 | 
| specifyPMM | Specifying a POUMM fit | 
| specifyPMM_H2tMeanSe | Specifying a POUMM fit | 
| specifyPMM_H2tMeanSeG0 | Specifying a POUMM fit | 
| specifyPMM_SSeG0 | Specifying a POUMM fit | 
| specifyPOUMM | Specifying a POUMM fit | 
| specifyPOUMM_ATH2tMeanSe | Specifying a POUMM fit | 
| specifyPOUMM_ATH2tMeanSeG0 | Specifying a POUMM fit | 
| specifyPOUMM_ATS | Specifying a POUMM fit | 
| specifyPOUMM_ATSG0 | Specifying a POUMM fit | 
| specifyPOUMM_ATSSeG0 | Specifying a POUMM fit | 
| specPOUMM | Specifying a POUMM fit | 
| statistics | Extract statistics from sampled or inferred parameters of a POUMM fit | 
| statistics.POUMM | 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 | 
| varOU | Distribution of an Ornstein-Uhlenbeck Process at Time t, Given Initial State at Time 0 | 
| vignetteCachedResults | Cached objects for the POUMM vignettes and examples |