amt: od – R documentation

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od

Occurrence Distribution

Description

od is a wrapper around ctmm::occurrence. See help(ctmm::occurrence) for more details. rolling_od estimates occurrence distributions for a subset of a track.

Usage

rolling_od(x, ...)

## S3 method for class 'track_xyt'
rolling_od(
  x,
  trast,
  model = fit_ctmm(x, "bm"),
  res.space = 10,
  res.time = 10,
  n.points = 5,
  show.progress = TRUE,
  ...
)

od(x, ...)

## S3 method for class 'track_xyt'
od(x, trast, model = fit_ctmm(x, "bm"), res.space = 10, res.time = 10, ...)

Arguments

`x`	`[track_xyt]` A track created with `make_track` that includes time.
`...`	Further arguments, none implemented.
`trast`	`[RasterLayer]` A template raster for the extent and resolution of the result.
`model`	`[An output of fit_ctmm]` The autocorrelation model that should be fit to the data. `bm` corresponds to Brownian motion, `ou` to an Ornstein-Uhlenbeck process, `ouf` to an Ornstein-Uhlenbeck forage process.
`res.space`	`[numeric(1)=10]` Number of grid point along each axis, relative to the average diffusion (per median timestep) from a stationary point. See also `help(ctmm::occurrence)`.
`res.time`	`[numeric(1)=10]` Number of temporal grid points per median timestep.
`n.points`	`[numeric(1)=5]` This argument is only relevant for `rolling_od` and specifies the window size for the od estimation.
`show.progress`	`[logical(1)=TRUE]` Indicates if a progress bar is used.

References

Fleming, C. H., Fagan, W. F., Mueller, T., Olson, K. A., Leimgruber, P., & Calabrese, J. M. (2016). Estimating where and how animals travel: an optimal framework for path reconstruction from autocorrelated tracking data. Ecology.

Examples

## Not run: 
data(deer)
mini_deer <- deer[1:100, ]
trast <- make_trast(mini_deer)
md <- od(mini_deer, trast = trast)
raster::plot(md)

# rolling ud
xx <- rolling_od(mini_deer, trast)

## End(Not run)

amt

Animal Movement Tools

v0.1.4

GPL-3

Authors

Johannes Signer [aut, cre], Brian Smith [ctb], Bjoern Reineking [ctb], Ulrike Schlaegel [ctb], John Fieberg [ctb], Scott LaPoint [dtc]

Initial release

od

Description

Usage

Arguments

References

Examples

amt

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