species

Creates a species, characterized by one or more behavioral states, to be simulated with function <code><a href="/link/simulate?package=SiMRiv&version=1.0.7" data-mini-rdoc="SiMRiv::simulate">simulate</a></code>.

Provides functions to generate and analyze spatially-explicit individual-based multistate movements in rivers,
heterogeneous and homogeneous spaces. This is done by incorporating landscape bias on local behaviour, based on
resistance rasters. Although originally conceived and designed to simulate trajectories of species constrained to
linear habitats/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 on 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 (Potts & Lewis 2014, <DOI:10.1098/rspb.2014.0231>) to test a variety of 'Movement Ecology'
hypotheses (Nathan et al. 2008, <DOI:10.1073/pnas.0800375105>), including landscape effects (e.g. resources,
infrastructures) on animal movement and species site fidelity, or for predictive purposes (e.g. road mortality risk,
dispersal/connectivity). The package should be relevant to explore a broad spectrum of ecological phenomena, such as
those at the interface of animal behaviour, management, landscape and movement ecology, disease and invasive species
spread, and population dynamics.

Miguel Porto

SiMRiv

Simulating Multistate Movements in River/Heterogeneous
Landscapes

Lorenzo Quaglietta

Erida Gjini

species function

<dl> <dt>states</dt>
<dd>a list of <code>state</code>s characterizing the behavior of the species, or a single <code>state</code>, for simple movements</dd> <dt>trans</dt>
<dd>a square state transition matrix, defining the probability of changing between states. For convenience, use the function <code>transitionMatrix</code>. Can be omitted if this species has a single-state movement.</dd> <dt>name</dt>
<dd>the name of the species</dd> <dt>resistanceMap</dt>
<dd>not used. Will be implemented in future versions.</dd></dl>

Arguments

Creates a species, characterized by one or more behavioral states, to be simulated with function <code><a href='https://rdrr.io/r/stats/simulate.html'>simulate</a></code>.

Create a species — species

<dl>

 <dt>states</dt>
<dd>a list of <code>state</code>s characterizing the behavior of the species, or a single <code>state</code>, for simple movements</dd>

 <dt>trans</dt>
<dd>a square state transition matrix, defining the probability of changing between states. For convenience, use the function <code>transitionMatrix</code>. Can be omitted if this species has a single-state movement.</dd>

 <dt>name</dt>
<dd>the name of the species</dd>

 <dt>resistanceMap</dt>
<dd>not used. Will be implemented in future versions.</dd>

</dl>

species: Create a species

Description

Usage

Value

Arguments

Details

See Also

Examples