emilio-berti/enerscape

Development version of the enerscape R package: https://cran.r-project.org/web/packages/enerscape/index.html

enerscape

Calculate Energy Landscapes For Terrestrial Animals.

Changelog

1.0.0

This follows the transfer of functionalists of old GIS packages to terra, with rgdal, rgeos scheduled to be retired in 2023: https://r-spatial.org/r/2022/04/12/evolution.html. I removed dependencies on gDistance, raster, sp, rgeos, and rgdal.

Energy landscapes are now calculated using a zonal (kernel) based method, implemented in C++ functions. This is faster that previous versions, but it does not return the transition matrix or the conductance matrix. Because of this, least cost paths functions are not supported any more. Instead, use circuitscape or omniscape; see circuitscape_skeleton() and omniscape_skeleton() to generate the initialization files to run in Julia.

The cyclist model is also not supported any more; custom models must be written in the C++ functions. I plan to add a customizable function soon to do that.

Installation

You can install the released version of enerscape from CRAN with:

install.packages("enerscape")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("emilio-berti/enerscape")

To start with enerscape, check the vignette:

vignette("enerscape")

Releases

All releases are also archived on GitHub at https://github.com/emilio-berti/enerscape/releases.

From release 1.0.0, enerscape is also archived in Zenodo: https://doi.org/10.5281/zenodo.7445654.

enerscape's Issues

Error in x$.self$finalize() : attempt to apply non-function

When running on a server cluster, I often get the error:

Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function

This seems to be an error message due to some Rcpp libraries and that can be ignored: sneumann/xcms#288 and rspatial/terra#30.

Store data

Need to store all data used in the vignettes in an archive.

Resolution check

enerscape/R/enerscape.R

Line 48 in 5a8c97d

stopifnot(res(dem)[1] == res(dem)[2])

This needs a round() or a less strict check, as numerical error will make this often not true.

Update raster names in vignette

Need to change rasters$Work to rasters$EnergyScape in all vignettes: https://emilio-berti.github.io/enerscape.html#landscape-connectivity-for-the-marsican-bear-ursus-arctos-marsicanus-in-the-sirente-velino-regional-park.