RPANDA (version 1.9)

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)

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.

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.

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

# NOT RUN {
data("Caprimulgidae_ClaDS2")

# }
# NOT RUN {
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)])
# }