View source: R/plot_ClaDS_chains.R
plot_ClaDS_chains | R Documentation |
Plot the MCMC chains obtained with fit_ClaDS.
plot_ClaDS_chains(sampler, burn = 1/2, thin = 1,
param = c("sigma", "alpha", "mu", "LP"))
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. |
Plot representing parameter MCMC chains
O. Maliet
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
, getMAPS_ClaDS
, plot_ClaDS0_chains
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))
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