SiMRiv-package {SiMRiv}

Simulating Multistate Movements in River/Heterogeneous Landscapes

Description

Provides functions to generate and analyze individual-based, spatially-explicit simulations of multi-state movements in homogeneous or heterogeneous landscapes, based on "resistance" rasters. Although originally conceived and designed to simulate spatially-explicit trajectories of species constrained to linear habitats or dendritic ecological networks (e.g., river networks), the simulation algorithm is built to be highly flexible and can be applied to any (aquatic, semi-aquatic or terrestrial) organism, independently of the landscape in which it moves. Thus, the user will be able to use the package to simulate movements either in homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving mainly along rivers but also using the matrix), or even in highly contrasted landscapes (e.g. fish in a river network). The algorithm and its input parameters are the same for all cases, so that results are comparable. Simulated trajectories can then be used as mechanistic null models (Moorcroft and Lewis 2006) to test e.g. for species site fidelity (Powell 2000) and other 'Movement Ecology' hypotheses (Nathan et al. 2008), or for other predictive purposes. The package should thus be relevant to explore a broad spectrum of ecological phenomena, such as those at the interface of animal behaviour, landscape, spatial and movement ecology, disease and invasive species spread, and population dynamics.

Details

simulate is the central function. See the examples in ?simulate to quickly get started, or the vignette for a more verbose tutorial.

Index of help topics:

Arith-methods           Shortcuts for defining species movement states
SiMRiv-package          Simulating Multistate Movements in
                        River/Heterogeneous Landscapes
adjustModel             Finds ("estimates") simulation input parameters
                        able to replicate a given (real) trajectory,
                        assuming the given species model
binCounts               Count values in given bins
generationPlot          Plots input parameter optimization results
perceptualRange         Define a perceptual range
resistanceFromShape     Build resistance raster by combining shapefiles
river                   Sample River Network in Raster Format
sampleMovement          Resample a simulated movement and compute
                        step-wise statistics
simulate                Simulate movements in river networks,
                        homogeneous, or heterogeneous landscapes
species                 Create a species
speciesModel            Defines a species model to adjust to a real
                        trajectory
state                   Define a movement state
transitionMatrix        Define a state transition matrix

Further information is available in the following vignettes:

SiMRiv	Usage of the SiMRiv package (source)

References

• Powell, R. A. 2000. Animal home ranges and territories and home range estimators. In: Research techniques in animal ecology: controversies and consequences, 442. Boitani, L., & Fuller, T. (Eds.). Columbia university press, New York: pp.65-110.

• Moorcroft, P. R. & Lewis, M. A. 2006. Mechanistic Home Range Analysis. Monographs in Population Biology 43. Eds. Levin S.A. and H.S. Horn. Princeton University Press. pp 172.

• Nathan, R., Getz, W. M., Revilla, E., Holyoak, M., Kadmon, R., Saltz, D., & Smouse, P. E. 2008. A movement ecology paradigm for unifying organismal movement research. Proceedings of the National Academy of Sciences,105(49), 19052-19059.

Examples

## a simple Levy-like movement in homogeneous space
## see ?simulate for more complex examples

LevyWalker <- species(
    state.RW() + state.CRW(0.99),
    transitionMatrix(0.005, 0.02))

sim <- simulate(LevyWalker, 20000)
plot(sim, type="l", asp=1)