RPANDA (version 2.3)

getMAPS_ClaDS0: Gets the Maximum A Posteriori for each ClaDS0 parameter

Description

Extract the MAPs (Maximum A Posteriori) for the marginal posterior distributions estimated with run_ClaDS0.

Usage

getMAPS_ClaDS0(phylo, 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[1:3] are the estimated hyperparameters, with MAPS[1] the sigma parameter (new rates stochasticity), MAPS[2] the alpha parameter (new rates trend), and MAPS[3] the initial speciation rate lambda_0.

MAPS[-(1:3)] are the estimated branch-specific speciation rates, given in the same order as the phylo$edges.

Arguments

phylo

An object of class 'phylo'.

sampler

The output of a run_ClaDS0 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_ClaDS0, plot_ClaDS0_chains, getMAPS_ClaDS

Examples

set.seed(1)

test = FALSE
if(test){
obj= sim_ClaDS( lambda_0=0.1,    
                mu_0=0.5,      
                sigma_lamb=0.7,         
                alpha_lamb=0.90,     
                condition="taxa",    
                taxa_stop = 20,    
                prune_extinct = TRUE)  

tree = obj$tree
speciation_rates = obj$lamb[obj$rates]
extinction_rates = obj$mu[obj$rates]
data("ClaDS0_example")

# extract the Maximum A Posteriori for each of the parameters
MAPS = getMAPS_ClaDS0(ClaDS0_example$tree, 
                      ClaDS0_example$Cl0_chains, 
                      thin = 10)

# plot the simulated (on the left) and inferred speciation rates (on the right)
# on the same color scale
plot_ClaDS_phylo(ClaDS0_example$tree, 
          ClaDS0_example$speciation_rates, 
          MAPS[-(1:3)])
}