mcmc.fmove {ctmcmove} | R Documentation |

Fits a functional movement model to telemetry data following Buderman et al., 2015.

mcmc.fmove(xy,t,fdabasis,tpred=t,QQ="CAR2",a=1,b=1,r=1,q=1, n.mcmc=100,num.paths.save=10,sigma.fixed=NA)

`xy` |
A two-column matrix with each row corresponding to the x,y locations of a telemetry location. |

`t` |
A numeric vector of length = nrow(xy), with the i-th entry corresponding to the time of the i-th telemetry location in xy. |

`fdabasis` |
A "basisfd" object, typically resulting from a call to "create.bspline.basis" in the fda package. Other basis functions can be used. |

`tpred` |
Numeric vector of times to impute the quasi-continuous path. |

`QQ` |
The precision matrix of the fda basis coefficients. This can either be a string, taking on values of "CAR1" or "CAR2", or can be a user specified matrix (or sparse matrix using the Matrix package) of dimension equal to the number of basis functions in fdabasis. Defaults to "CAR2". "CAR1" will result in less-smooth paths. |

`a` |
The shape parameter of the inverse gamma prior on the observation variance. |

`b` |
The scale parameter of the inverse gamma prior on the observation variance. |

`r` |
The shape parameter of the inverse gamma prior on the partial sill parameter of the spline basis coefficients. |

`q` |
The scale parameter of the inverse gamma prior on the partial sill parameter of the spline basis coefficients. |

`n.mcmc` |
Number of mcmc iterations to run. |

`num.paths.save` |
Number of quasi-continuous path realizations to save. Defaults to 10. |

`sigma.fixed` |
Numeric value (or the default NA). If NA, then the observation variance sigma^2 is estimated using MCMC. If a numeric value, this is the fixed standard deviation of the observation error. |

Fits the functional movement model of Buderman et al., 2015, and outputs quasi-continuous paths that stochastically interpolate between telemetry locations. The model fit is as follows (written out for 1-D):

y_t = observed location at time t

z_t = Sum_k beta_k*phi_k(t) = true location at time t, expressed using a linear combination of spline basis functions phi_k(t).

y_t ~ N( z_t , sigma^2 )

beta ~ N( 0 , tau^2 * QQ^-1 )

sigma^2 ~ IG(a,b)

tau^2 ~ IG(r,q)

`s2.save` |
Numeric vector of the values of sigma^2 at each mcmc iteration |

`tau2.save` |
Numeric vector of the values of tau^2 at each mcmc iteration |

`pathlist` |
A list of length num.paths.save, with each item itself being a list with two entries: xy = a matrix with rows corresponding to x,y locations of the quasi-continuous path imputation t = a vector with entries corresponding to the times at which the quasi-continuous path was imputed |

Ephraim M. Hanks

Buderman, F.E.; Hooten, M. B.; Ivan, J. S. and Shenk, T. M. A functional model for characterizing long-distance movement behavior. Methods in Ecology and Evolution, 2016, 7, 264-273.

## For example code, do ## ## > help(ctmcMove)

[Package *ctmcmove* version 1.2.9 Index]