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Individual-based simulation of multistate movements in rivers, heterogeneous and homogeneous spaces incorporating local landscape bias in R

License: GNU General Public License v3.0

R 73.74% C 26.26%

river-networks movement-ecology simulation heterogeneous-landscapes r-package animal-movement

simriv's Introduction

SiMRiv (R package)

Individual-based simulation of multistate movements in rivers, heterogeneous and homogeneous spaces incorporating local landscape bias in R.

Available on CRAN, can be directly installed from within R.

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) to test a variety of 'Movement Ecology' hypotheses (Nathan et al. 2008), including landscape effects (e.g. resources, infrastructures) on animal movement and species site fidelity (Powell 2000), 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.

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nikapepita bastazini oliviergimenez manalytics

simriv's Issues

Please remove dependencies on rgdal, rgeos, and/or maptools

This package depends on (depends, imports or suggests) raster and one or more of the retiring packages rgdal, rgeos or maptools (https://r-spatial.org/r/2022/04/12/evolution.html, https://r-spatial.org/r/2022/12/14/evolution2.html). Since raster 3.6.3, all use of external FOSS library functionality has been transferred to terra, making the retiring packages very likely redundant. It would help greatly if you could remove dependencies on the retiring packages as soon as possible.

Using state to specify animal step length

The documentation for the designation of a movement state for a species suggests that the steplen passed to state() will generate a distribution of step lengths that are truncated at the value passed to the function (values less than that steplen will be used). However, upon plotting the results of the simulation, it appears that the value passed to state for steplen is used as a lower bound, and step lengths equal to or greater than the value passed to the function are generated.

This is for a simulation with a resistance layer that has the same, low level of resistance across all bodies of water.

Allow specifying multiple rasters, e.g. habitat suitability and physical resistance

Currently, habitat suitability and physical resistance are mixed in a thing called "resistance raster". However, habitat suitability and physical resistance are likely to influence different things in the simulation (i.e., animal behaviour), and thus should be allowed to be specified separately.

Fix last coordinates

Hi,
I am wondering if it is possible to fix not only the initial coordinates in a simulation, but also fix the last coordinates. This could be of high interest for simulating the movement of central place foragers, that return to their origin. Similar functionability is found in other packages like crawl or availability (e.g. https://australianantarcticdatacentre.github.io/availability/articles/availability.html).

Mapping from landscape to resistance values should be a property of the species

...because each species may see landscape differently. It should not be a global parameter of the simulation, but each species should have a mapping from landscape land use classes to resistance values.

Function to conduct null model testing

Automate simulation and analysis of simulated patterns.

Some bug in simulate.c with OMP fails in i386 architecture

This only happens with OMP enabled and in i386 arch: package compiles, but simulations stop with error. Probably some misuse of the OMP pragmas.

Functions for comparing trajectories

Functions to compute kernel density and linear KD, and their overlap/distance

Prepare for multicore

Use OMP better! Current implementation is disabled cause it doesn't make much difference.

Error in documentation of adjustModel

The example in adjustModel help seems broken.
The line
sol <- adjustModel(real.data, species.model, resol = 20, nbins.hist = c(3, 3), step.hist.log = TRUE)
is not working and give the following error :

Error in if (nbins.hist[3] > 0) { : missing value where TRUE/FALSE needed

It works if we add a third value to nbins.hist arguments as follows:
sol <- adjustModel(real.data, species.model, resol = 20, nbins.hist = c(3, 3, 3), step.hist.log = TRUE)

Unable to use this for true spatial data, as geographic coordinates are rounded to the nearest integer.

I'm using true latlong data in order to run simulation models, in which individuals were collected at a specific location. However, running this simulation rounds the latlong coordinates to the nearest whole integer, causing the entire run to be hundred of miles off of the true start location.