Function reference • POUMM

All functions
`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
`H2()`	Phylogenetic heritability estimated at time t
`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
`dOU()` `rOU()` `meanOU()` `varOU()` `sdOU()`	Distribution of an Ornstein-Uhlenbeck Process at Time \(t\), Given Initial State at Time \(0\)
`alpha()` `sigmaOU()` `sigmae()` `H2e()`	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.
`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
`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
`specifyPOUMM()` `specifyPOUMM_ATS()` `specifyPOUMM_ATSG0()` `specifyPOUMM_ATSSeG0()` `specifyPMM()` `specifyPMM_SSeG0()` `specifyPOUMM_ATH2tMeanSe()` `specifyPOUMM_ATH2tMeanSeG0()` `specifyPMM_H2tMeanSe()` `specifyPMM_H2tMeanSeG0()`	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

Reference

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