StudyingParam {CoDaLoMic} | R Documentation |
Controlling quality of the convergence in BPBM
Description
This function controls that the value of the Rhat is between 0.9 and 1.1. In addition, it controls that the effective sample size is bigger than 100 and that the zero is not at the center of the credible interval (the interval between 2.5 and 97.5). We consider that the zero is in the center of the credible interval when the zero is between the 25 and the 75 quantile of the distribution formed by the limits if the credible interval.
Usage
StudyingParam(Sum, MCMC.CHAINS)
Arguments
Sum |
Matrix with the summary of the "Estimating_BPBM".It is the output of the "Estimating_BPBM" adding "$R2jagsOutput$BUGSoutput$summary". |
MCMC.CHAINS |
Matrix with the values of all the Markov chains for all parameters. It is the output of the "Estimating_BPBM" adding "$SamplesAllChains". |
Value
Returns a list with:
Param.Summary: Matrix. The matrix Sum with a zero in the column
Sum[,"mean"]
when a parameter has the zero in the center of its credible interval.AllChainsJoined: Matrix. The matrix MCMC.CHAINS with a zero in all the iterations of the chain when a parameter has the zero in the center of its credible interval.
Examples
set.seed(314)
especie=t(gtools::rdirichlet(n=6, c(6,6,1,6,6)))
E=5
Tt=6
MatrizPBmodelo=rbind(c(1,1,1,1,1,1),c(-0.3,0.4,0.3,-0.7,-0.4,-0.6),c(0.3,0.5,-0.3,0.1,0.4,0.1))
est=Estimating_BPBM(especie,
Tt,
E,
MatrizPBmodelo,
nn.chain=3,
nn.burnin=1000,
nn.sample=5000,
nn.thin=10)
StudyingParam(est$R2jagsOutput$BUGSoutput$summary,est$SamplesAllChains)