| A | A matrix |
| array2matrix | Convert an array into a matrix |
| bayes.factors | Calculate Bayes factors and posterior model probabilities |
| block.boot | Generate block bootstrap replicates of sampled power... |
| C | 29 3D landmarks from the skulls of 19 carnivoran specimens... |
| calibrations | Calibration densities |
| carnivores | Carnivores dataset |
| carnivores19x29.raw | 29 3D landmarks from the skulls of 19 carnivoran specimens |
| C.arr.unal | 29 3D landmarks from the skulls of 19 carnivoran specimens... |
| C.mat.unal | 29 3D landmarks from the skulls of 19 carnivoran specimens... |
| C.PS | Object of class procSym output by Morpho after PA |
| ctlMCMCtree | Generating the control file to run MCMCtree when using... |
| dBD | Birth-death process with species sampling |
| gauss.quad | Estimate marginal likelihood by thermodynamic integration |
| hominids | A BPP A00 MCMC sample for an hominid phylogeny |
| lmk_imp | Import various landmark files for different specimens at once |
| logL.boot | Estimate marginal likelihood from bootstrap replicates |
| make.beta | Make beta values for marginal likelihood calculation |
| make.bfctlf | Prepare mcmctree or bpp control files for marginal likelihood... |
| matrix2array | Convert a matrix into an array |
| mcmc2anc | Ancestral character reconstruction from an MCMC sample |
| mcmc2densitree | Plot a densi-tree from an MCMC sample |
| mcmc2multiphylo | Convert an MCMC sample from MCMCTree or BPP to a list of... |
| mcmc.sum | Calculate summaries from an MCMC run |
| microcebus | A BPP A00 MCMC sample for a mouse lemur phylogeny |
| proc2MCMCtree | Procrustes alignment output in MCMCtree format for Bayesian... |
| R.sh | Estimated shrinkage correlation matrix |
| sim.morpho | Simulate a continuous morphological alignment |
| sim.pop | Simulate a population matrix |
| sim.R | Correlation matrix for simulations |
| sim.tree | Simulated 8-species tree |
| stepping.stones | Estimate marginal likelihood by stepping stones |
| treeMCMCtree | Generating a tree file in MCMCtree format when using... |
| V | 29 3D landmarks from the skulls of 19 carnivoran specimens... |
| var.foxes | Vector with the population variance of Vulpes vulpes |
| V.arr.unal | 29 3D landmarks from the skulls of 21 Vulpes vulpes specimens... |
| V.mat.unal | 29 3D landmarks from the skulls of 19 carnivoran specimens... |
| V.PS.nov1 | Object of class array output by Morpho after PA |
| vulpes21x29.raw | 29 3D landmarks from the skulls of 21 Vulpes vulpes specimens |
| write.morpho | Generate a file with a morphological alignment for MCMCtree |
