Caprimulgidae_ClaDS2 | R Documentation |
An example of the run on the inference of ClaDS2 on the Caprimulgidae phylogeny, thinned every 10 iterations.
data("Caprimulgidae_ClaDS2")
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.
The Caprimulgidae phylogeny was obtained from Jetz et al. (2012)
O. Maliet
Jetz, W., G. Thomas, J. Joy, K. Hartmann, and A. Mooers. 2012. The global diversity of birds in space and time. Nature 491:444.
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
fit_ClaDS
, plot_ClaDS_chains
, getMAPS_ClaDS0
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)])
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