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)... |
covFunPOUMM | A vectorized expected covariance function for a given tree... |
covHPDFunPOUMM | A vectorized function returning HPD intervals of the expected... |
covPOUMM | Expected covariance of two tips at given root-tip time and... |
covVTipsGivenTreePOUMM | Variance covariance matrix of the values at the tips of a... |
dVNodesGivenTreePOUMM | Multivariate density of observed values along a tree given an... |
edgesFrom | Edge indices of the edges in tree starting from n |
fitted.POUMM | Extract maximum likelihood expected genotypic values at the... |
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... |
likPOUMMGivenTreeVTipsC | Fast (parallel) POUMM likelihood calculation using the SPLITT... |
loglik_abc_g0_g0Prior | Processing of the root value and calculation of the maximum... |
logLik.POUMM | Extract maximum likelihood and degrees of freedom from a... |
maxLikPOUMMGivenTreeVTips | Find a maximum likelihood fit of the POUMM model |
mcmcPOUMMGivenPriorTreeVTips | MCMC-sampling from a posterior distribution of a P(OU)MM... |
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,... |
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... |
residuals.POUMM | Extract maximum likelihood environmental contributions... |
rTrajectoryOU | Generation of a random trajectory of an OU process starting... |
rTrajectoryOUDef | Generation of a random trajectory of an OU process starting... |
rVNodesGivenTreePOUMM | Random generation of values along a phylogenetic tree... |
simulatePOUMMLikelihoodMainLoop | Writes verbose messages of the order of tree traversal during... |
simulateTrait | Simulate a trait on a tree under a ML fit of the POUMM model |
specPOUMM | Specifying a POUMM fit |
statistics | Extract statistics from sampled or inferred parameters of a... |
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 |
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