View source: R/getMAPS_ClaDS.R
getMAPS_ClaDS | R Documentation |
Extract the MAPs (Maximum A Posteriori) for the marginal posterior distributions estimated with fit_ClaDS
getMAPS_ClaDS(sampler, burn = 1/2, thin = 1)
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 kept to compute the MAPs. |
A vector MAPS containing the MAPs for the marginal posterior distribution for each of the model's parameters.
MAPS[1:4] are the estimated hyperparameters, with MAPS[1] the sigma parameter (new rates stochasticity), MAPS[2] the alpha parameter (new rates trend), MAPS[3] the turnover rate epsilon, and MAPS[4] the initial speciation rate lambda_0.
MAPS[-(1:4)] are the estimated branch-specific speciation rates, given in the same order as the edges of the phylogeny on which the inference was performed.
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
, plot_ClaDS_chains
, getMAPS_ClaDS0
data("Caprimulgidae_ClaDS2") if(test){ MAPS = getMAPS_ClaDS(Caprimulgidae_ClaDS2$sampler, thin = 1) print(paste0("sigma = ", MAPS[1], " ; alpha = ", MAPS[2], " ; epsilon = ", MAPS[3], " ; l_0 = ", MAPS[4] )) plot_ClaDS_phylo(Caprimulgidae_ClaDS2$tree, MAPS[-(1:4)]) }
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