## 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