restoptr {restoptr}

restoptr: Ecological Restoration Planning

Description

The restoptr package relies on Constraint Programming (CP) to build and solve ecological restoration planning problems. A restoptr problem starts from an existing habitat (raster), where the aim is to identify optimal areas that are suitable for restoration. Several constraints are available to define what is expected for a suitable area for (e.g. it must be connected, compact, must respect a budget, etc). Several optimization objective are also available to define what is a good restoration area (e.g. it must reduce fragmentation, increase ecological connectivity, minimize costs, etc.). restoptr relies on advanced landscape indices such as the effective mesh size (Jaeger, 2000), or the integral index of connectivity (Pascual-Hortal & Saura, 2006) to address complex restoration planning problems.

Details

restoptr relies on Choco-solver (https://choco-solver.org/), an open-source Java CP solver (Prud'homme et al., 2017). The computationally intensive solving part is thus delegated to Java (see restopt, https://github.com/dimitri-justeau/restopt), and the communication between R and Java is handled with the rJava package. Therefore, a Java Runtime Environment (>= 8) is necessary to use restopt.

Note that the methodology used in restoptr was first described in Justeau-Allaire et al. (2021), but restoptr provides much more flexibility, new features (e.g. reliable and consistent data preprocessing), new constraints, new optimization objectives, and an improved computational efficiency. Also note that the API was inspired by the prioritizr package.

This package contains several vignettes to detail its usage and showcase its features. You can explore these vignettes using browseVignettes("restoptr")

References

Hanson JO, Schuster R, Morrell N, Strimas-Mackey M, Edwards BPM, Watts ME, Arcese P, Bennett J, Possingham HP (2022). prioritizr: Systematic Conservation Prioritization in R. R package version 7.1.1. Available at https://CRAN.R-project.org/package=prioritizr.

Jaeger, J. A. G. (2000). Landscape division, splitting index, and effective mesh size: New measures of landscape fragmentation. Landscape Ecology, 15(2), 115‑130.

Justeau-Allaire, D., Vieilledent, G., Rinck, N., Vismara, P., Lorca, X., & Birnbaum, P. (2021). Constrained optimization of landscape indices in conservation planning to support ecological restoration in New Caledonia. Journal of Applied Ecology, 58(4), 744‑754.

Pascual-Hortal, L., & Saura, S. (2006). Comparison and development of new graph-based landscape connectivity indices: Towards the priorization of habitat patches and corridors for conservation. Landscape Ecology, 21(7), 959‑967.

Prud'homme, C., Fages, J.-G., & Lorca, X. (2017). Choco documentation.