Description Usage Arguments Details Value Examples

View source: R/mixmod_gibbs_sampler.R

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.

1 | ```
cluster_obs(dat, alpha, ngibbs, nmaxclust, nburn)
``` |

`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. |

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

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
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)
``` |

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