This function uses a Gibbs sampler within a mixture model to estimate the optimal number of behavioral states, the state-dependent distributions, and to assign behavioral states to each observation. This model does not assume an underlying mechanistic process.

cluster_obs(dat, alpha, ngibbs, nmaxclust, nburn)

Arguments

dat

A data frame that **only** contains columns for the discretized movement variables.

alpha

numeric. A single value used to specify the hyperparameter for the prior distribution.

ngibbs

numeric. The total number of iterations of the MCMC chain.

nmaxclust

numeric. A single number indicating the maximum number of clusters to test.

nburn

numeric. The length of the burn-in phase.

Value

A list of model results is returned where elements include the phi matrix for each data stream, theta matrix, log likelihood estimates for each iteration of the MCMC chain loglikel, a list of the MAP estimates of the latent states for each observation z.MAP, a matrix of the whole posterior of state assignments per observation z.posterior, and a vector gamma1 of estimates for the gamma hyperparameter.

Details

The mixture model analyzes all animal IDs pooled together, thus providing a population-level estimate of behavioral states.

Examples

# \donttest{ data(tracks.list) #convert from list to data frame tracks.list<- dplyr::bind_rows(tracks.list) #only retain id and discretized step length (SL) and turning angle (TA) columns tracks<- subset(tracks.list, select = c(SL, TA)) set.seed(1) # Define model params alpha=0.1 ngibbs=1000 nburn=ngibbs/2 nmaxclust=7 dat.res<- cluster_obs(dat = tracks, alpha = alpha, ngibbs = ngibbs, nmaxclust = nmaxclust, nburn = nburn) # }