Man pages for POUMM
The Phylogenetic Ornstein-Uhlenbeck Mixed Model
| 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 |
