updateGCMM {activityGCMM}R Documentation

Extend GCMM analysis

Description

Extend GCMM analysis using extend.jags from package runjags

Usage

updateGCMM(
  model,
  burnin = 0,
  sample = 10000,
  saveclustIDs = FALSE,
  saveREs = FALSE,
  saveResids = FALSE,
  autorun = TRUE,
  minESS = 5000,
  maxrep = 5,
  drop.chain = 0
)

Arguments

model

Object of class GCMM that is produced by the GCMM function

burnin

Number of iterations per MCMC chain to be discarded as a burn-in

sample

Number of iterations per MCMC chain

saveclustIDs

Whether to save component cluster identification for the data points; default=FALSE

saveREs

Whether random intercepts are saved in output; recommended to save only one of saveREs, saveResids or saveYExp at one time due to memory limitations; default=FALSE

saveResids

Whether model residuals are saved in output; recommended to save only one of saveREs, saveResids or saveYExp at one time due to memory limitations

autorun

Whether to automatically extend the analysis until MCMC chain convergence and minimum effective sample size (ESS) is achieved; default is TRUE

minESS

Desired minimum effective sample size (MCMC) when automatically extending the analysis using autorun=TRUE; default is 5000

maxrep

Maximum number of times to automatically extend the analysis if MCMC chains have not converged or the minimum effective sample size is not reached; default=5

drop.chain

A number indicating which MCMC chain to drop from the updated analysis. This may be useful if one chain happens to converge on opposite clusters than the others.

Value

Returns an object of class GCMM with a list of analysis details and output; see GCMM. A mixture plot of the estimated activity curve is also printed.

See Also

GCMM extend.jags

Examples

 FoxActivityGCMM<-GCMM(data=redfoxsample$Radians, 
              RE1=redfoxsample$SamplingPeriod, family="vonmises", autorun=FALSE,
              adapt=0, sample=300, burnin=300, thin=1, n.chains=2)
           updateFoxGCMM<-updateGCMM(FoxActivityGCMM, sample=300, autorun=FALSE) 


[Package activityGCMM version 1.1.1 Index]