Description Usage Arguments Details Value

MCMC-sampling from a posterior distribution of a P(OU)MM model given tree, values at the tips and a prior distribution

1 2 3 4 | ```
mcmcPOUMMGivenPriorTreeVTips(loglik, fitML = NULL, parMapping,
parInitMCMC, parPriorMCMC, parScaleMCMC, nSamplesMCMC, nAdaptMCMC,
thinMCMC, accRateMCMC, gammaMCMC, nChainsMCMC, samplePriorMCMC,
pruneInfo, ..., verbose = FALSE, parallelMCMC = FALSE)
``` |

`loglik` |
a log-likelihood function. |

`fitML` |
an object returned by the maxLikPOUMMGivenTreeVTips |

`parMapping` |
a function(numeric-vector) transforming a sampled vector on the scale of the parameters alpha, theta, sigma, sigmae and g0. |

`parInitMCMC` |
a function(chainNumber) returning the starting point of the MCMC as a vector. |

`parPriorMCMC` |
a function(numeric-vector) returning the log-prior of the supplied vector |

`parScaleMCMC` |
numeric matrix indicating the initial jump-distribution matrix |

`nSamplesMCMC` |
integer indicating how many iterations should the mcmc-chain contain |

`nAdaptMCMC` |
integer indicating how many initial iterations should be used for adaptation of the jump-distribution matrix |

`thinMCMC` |
integer indicating the thinning interval of the mcmc-chain |

`accRateMCMC` |
(MCMC) numeric between 0 and 1 indicating the target acceptance rate Passed on to adaptMCMC::MCMC. |

`gammaMCMC` |
(MCMC) controls the speed of adaption. Should be in the interval (0.5,1]. A lower gammaMCMC leads to faster adaption. Passed on to adaptMCMC::MCMC. |

`nChainsMCMC` |
integer indicating the number of chains to run. Defaults to 1. |

`samplePriorMCMC` |
logical indicating if only the prior distribution should be sampled. This can be useful to compare with mcmc-runs for an overlap between prior and posterior distributions. |

`pruneInfo` |
a list-object returned from the pruneTree(tree, z) function. |

`...` |
Additional arguments. Currently not used except for the following: If ... includes debug = TRUE, some debug messages will be written also outside of the call to loglik. |

`verbose` |
Logical indicating if some informal messages should be written during run. This parameter is passed to loglik. |

`parallelMCMC` |
Logical indicating if chains should be run in parallel. |

Currently, this function calls the MCMC function from the adaptMCMC package.

a list of coda objects

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