# The Phylogenetic Ornstein-Uhlenbeck Mixed Model

## Documentation for package ‘POUMM’ version 2.1.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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