RPANDA (version 2.3)

getMAPS_ClaDS: Gets the Maximum A Posteriori for each ClaDS parameter

Description

Extract the MAPs (Maximum A Posteriori) for the marginal posterior distributions estimated with fit_ClaDS

Usage

getMAPS_ClaDS(sampler, burn = 1/2, thin = 1)

Value

A vector MAPS containing the MAPs for the marginal posterior distribution for each of the model's parameters.

MAPS[1:4] are the estimated hyperparameters, with MAPS[1] the sigma parameter (new rates stochasticity), MAPS[2] the alpha parameter (new rates trend), MAPS[3] the turnover rate epsilon, and MAPS[4] the initial speciation rate lambda_0.

MAPS[-(1:4)] are the estimated branch-specific speciation rates, given in the same order as the edges of the phylogeny on which the inference was performed.

Arguments

sampler

The output of a fit_ClaDS run.

burn

Number of iterations to drop in the beginning of the chains.

thin

Thinning parameter, one iteration out of "thin" is kept to compute the MAPs.

Author

O. Maliet

References

Maliet O., Hartig F. and Morlon H. 2019, A model with many small shifts for estimating species-specific diversificaton rates, Nature Ecology and Evolution, doi 10.1038/s41559-019-0908-0

See Also

fit_ClaDS, plot_ClaDS_chains, getMAPS_ClaDS0

Examples

data("Caprimulgidae_ClaDS2")

test = FALSE
if(test){
MAPS = getMAPS_ClaDS(Caprimulgidae_ClaDS2$sampler, thin = 1)

print(paste0("sigma = ", MAPS[1], " ; alpha = ", 
  MAPS[2], " ; epsilon = ", MAPS[3], " ; l_0 = ", MAPS[4] ))
plot_ClaDS_phylo(Caprimulgidae_ClaDS2$tree, MAPS[-(1:4)])
}