getGibbsSummary: Summarize Output of the CDM Model

Description Usage Arguments Examples

View source: R/getGibbsSumamry.R

Description

This function return a summary of the output from the Gibbs-Sampling of the CDM model.

Usage

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getGibbsSummary(ssOut, burnin = NULL, colNames = NULL,
  sigmaPerSeason = TRUE)

Arguments

ssOut

CDM output list.

burnin

Number of burnin itterations .

colNames

vector of charachters includes names of each variable in the output.

sigmaPerSeason

logical value indicating whether each site/season has a separate process error

Examples

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#Summarize CDM Model Ouput

ssSim <- phenoSim(nSites = 2, #number of sites
                  nTSet = 30, #number of Time steps
                  beta = c(1, 2), #beta coefficients
                  sig = .01, #process error
                  tau = .1, #observation error
                  plotFlag = TRUE, #whether plot the data or not
                  miss = 0.05, #fraction of missing data
                  ymax = c(6, 3) #maximum of saturation trajectory
)

ssOut <- fitCDM(x = ssSim$x, #predictors
                nGibbs = 200,
                nBurnin = 100,
                z = ssSim$z,#response
                connect = ssSim$connect, #connectivity of time data
                quiet=TRUE)

summ <- getGibbsSummary(ssOut, burnin = 100, sigmaPerSeason = FALSE)

colMeans(summ$ymax)
colMeans(summ$betas)
colMeans(summ$tau)
colMeans(summ$sigma)

phenoCDM documentation built on May 2, 2018, 5:04 p.m.