Caprimulgidae_ClaDS2: An example run of ClaDS2.

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

An example run of ClaDS2.

Description

An example of the run on the inference of ClaDS2 on the Caprimulgidae phylogeny, thinned every 10 iterations.

Usage

data("Caprimulgidae_ClaDS2")

Format

A list object with fields :

tree

The Caprimulgidae phylogeny on which we ran the model.

sample_fraction

The sample fraction for the clade.

sampler

The chains obtained by running ClaDS2 on the Caprimulgidae phylogeny.

Details

The Caprimulgidae phylogeny was obtained from Jetz et al. (2012)

Author(s)

O. Maliet

Source

Jetz, W., G. Thomas, J. Joy, K. Hartmann, and A. Mooers. 2012. The global diversity of birds in space and time. Nature 491:444.

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")

# plot the mcmc chains
plot_ClaDS_chains(Caprimulgidae_ClaDS2$sampler)


# extract the Maxima A Posteriori for each parameter
maps = getMAPS_ClaDS(Caprimulgidae_ClaDS2$sampler, thin = 1)
print(paste0("sigma = ", maps[1], " ; alpha = ", 
  maps[2], " ; epsilon = ", maps[3], " ; l_0 = ", maps[4] ))
  
# plot the infered branch specific speciation rates
plot_ClaDS_phylo(Caprimulgidae_ClaDS2$tree, maps[-(1:4)])

hmorlon/PANDA documentation built on April 24, 2024, 3:27 a.m.