plot_ClaDS0_chains: Plot the MCMC chains obtained when infering ClaDS0 parameters

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Plot the MCMC chains obtained when infering ClaDS0 parameters

Description

Plot the MCMC chains obtained with run_ClaDS0.

Usage

plot_ClaDS0_chains(sampler, burn = 1/2, thin = 1, 
                  param = c("sigma", "alpha", "l_0", "LP"))

Arguments

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 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.

Value

Plot representing parameter MCMC chains

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_ClaDS0, getMAPS_ClaDS0, plot_ClaDS_chains

Examples

data("ClaDS0_example")

plot_ClaDS0_chains(ClaDS0_example$Cl0_chains)
plot_ClaDS0_chains(ClaDS0_example$Cl0_chains, param = paste0("lambda_", c(1,10,5)))

hmorlon/PANDA documentation built on Jan. 13, 2025, 5:35 a.m.