plot_ClaDS_chains: Plot the MCMC chains obtained when infering ClaDS parameters

In RPANDA: Phylogenetic ANalyses of DiversificAtion

Plot the MCMC chains obtained when infering ClaDS parameters

Description

Plot the MCMC chains obtained with fit_ClaDS.

Usage

plot_ClaDS_chains(sampler, burn = 1/2, thin = 1, 
                  param = c("sigma", "alpha", "mu", "LP"))

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 plotted.
param	Either a vector of "character" elements with the name of the parameter to plot, or a vector of integers indicating what parameters to plot.

Author(s)

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_ClaDS, getMAPS_ClaDS, plot_ClaDS0_chains

Examples

data("Caprimulgidae_ClaDS2")

plot_ClaDS_chains(Caprimulgidae_ClaDS2$sampler)

plot_ClaDS_chains(Caprimulgidae_ClaDS2$sampler, burn = 1/4, 
                  param = c("sigma", "alpha", "l_0", "LP"))

plot_ClaDS_chains(Caprimulgidae_ClaDS2$sampler, burn = 1/5, thin = 5, param = c(1,5,6,15))

RPANDA documentation built on Oct. 24, 2022, 5:06 p.m.