The Phylogenetic Ornstein-Uhlenbeck Mixed Model

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Documentation for package ‘POUMM’ version 2.1.7

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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