ClaDS0_example {RPANDA}

An example run of ClaDS0.

Description

An example of the run on the inference of ClaDS0 on a simulated phylogeny, thinned every 10 iterations.

Usage

data("ClaDS0_example")

Format

A list object with fields :

tree

The simulated phylogeny on which we ran the model.

speciation_rates

The simulated speciation rates.

Cl0_chains

The output of the run_ClaDS0 run.

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

Examples

data(ClaDS0_example)

# plot the resulting chains for the first 4 parameters
plot_ClaDS0_chains(ClaDS0_example$Cl0_chains, param = 1:4)

# 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)])