updateGCMM: Extend GCMM analysis

In activityGCMM: Circular Mixed Effect Mixture Models of Animal Activity Patterns

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) 

activityGCMM documentation built on June 15, 2021, 1:06 a.m.