amt: sim_ud – R documentation

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amt

sim_ud

Simulate UD from fitted SSF

Description

Function to obtain a habitat kernel from a fitted (i)SSF.

Usage

habitat_kernel(coef, resources, exp = TRUE)

movement_kernel(scale, shape, template, quant = 0.99)

simulate_ud(movement_kernel, habitat_kernel, start, n = 100000L)

simulate_tud(movement_kernel, habitat_kernel, start, n = 100, n_rep = 5000)

Arguments

`coef`	`[list]` Vector with coeffiecients, not yet implemented.
`resources`	`[RasterLayer, RasterStack]` The resources.
`exp`	A logical scalar, indicating whether or not the resulting habitat kernel should be exponentiated. This is usually `TRUE`.
`scale, shape`	`[numeric](1)` Scale and scale parameter of the gamma distribution of step lengths.
`template`	`[RasterLayer,RasterStack]` A raster serving as template for the simulations.
`quant`	A numeric scalar, quantile of the step-length distribution that is the maximum movement distance.
`movement_kernel`	`[RasterLayer]` The movement kernel.
`habitat_kernel`	`[RasterLayer]` The habitat kernel.
`start`	`[numeric(2)]` Starting point of the simulation.
`n`	`[integer(1)=1e5]` The number of simulation steps.
`n_rep`	`[integer(1)=5e3]{>0}` The number of times the animal walks of the final position. The mean of all replicates is returned.

Details

movement_kernel(): calculates a movement kernel from a fitted (i)SSF. The method is currently only implemented for the gamma distribution.

The habitat kernel is calculated by multiplying resources with their corresponding coefficients from the fitted (i)SSF.

simulate_ud(): simulates a utilization distribution (UD) from a fitted Step-Selection Function.

simulate_tud(): Is a convenience wrapper around simulate_ud to simulate transition UDs (i.e., starting at the same position many times and only simulate for a short time).

Value

The habitat kernel, as RasterLayer.

Note

This functions are still experimental and should be used with care. If in doubt, please contact the author.

Author(s)

Johannes Signer (jmsigner@gmail.com)

References

Avgar T, Potts JR, Lewis MA, Boyce MS (2016). “Integrated step selection analysis: bridging the gap between resource selection and animal movement.” Methods in Ecology and Evolution. Signer J, Fieberg J, Avgar T (2017). “Estimating Utilization Distributions from fitted Step-Selection Functions.” Ecosphere.

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