The Phylogenetic Ornstein-Uhlenbeck Mixed Model


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Documentation for package ‘POUMM’ version 1.2.2

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alpha Phylogenetic Heritability
chld Node indices of the direct descendants of n in the phylogeny tree.
coef.POUMM Extract maximum likelihood fitted parameters (coefficients) from 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 POUMM likelihood calculation based on the breadth-first pruning algorithm and Armadillo-library vector operations.
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 (Adaptive) Metropolis Sampler
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
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
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
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