circuitscaper

circuitscaper provides a streamlined R interface for Circuitscape.jl and Omniscape.jl. It allows you to run these high-performance landscape connectivity models entirely from R, while Julia handles the heavy lifting under the hood.

• Native R Workflow: Input and output terra raster objects directly.
• Automated Setup: One-line installation of Julia and all required dependencies.
• High Performance: Leverages Julia’s state-of-the-art solvers for large landscapes.

Note: circuitscaper is an independent R package and is not affiliated with the Circuitscape development team. It is a lightweight wrapper to the excellent Julia tools developed by Brad McRae, Viral Shah, Tanmay Mohapatra, Ranjan Anantharaman, and collaborators.

Installation

# 1. Install the R package
remotes::install_github("matthewkling/circuitscaper")

# 2. Let the package install Julia and the necessary Julia libraries
library(circuitscaper)
cs_install_julia()

Example

library(circuitscaper)
library(terra)

# Load an example resistance raster
resistance <- rast(system.file("extdata/resistance.tif", package = "circuitscaper"))

# Pairwise Circuitscape
# (result is a list containing the pairwise resistance matrix and current maps)
focal_sites <- matrix(c(10, 40, 40, 40, 25, 10), ncol = 2, byrow = TRUE)
result <- cs_pairwise(resistance, focal_sites)
plot(result$current_map)

# Omniscape -- wall-to-wall moving-window connectivity
# (result is a multi-layer raster of current flow variables)
result <- os_run(resistance, radius = 10)
plot(result$normalized_current)

Functions

Function	Description	Julia backend
cs_pairwise()	Pairwise effective resistance and current flow	Circuitscape.compute()
cs_one_to_all()	One-to-all connectivity analysis	Circuitscape.compute()
cs_all_to_one()	All-to-one connectivity analysis	Circuitscape.compute()
cs_advanced()	Advanced mode with custom sources and grounds	Circuitscape.compute()
os_run()	Omniscape moving-window connectivity	Omniscape.run_omniscape()
cs_setup()	Initialize Julia session (called automatically)	JuliaCall::julia_library()
cs_install_julia()	Install Julia and required packages	JuliaCall::install_julia(), JuliaCall::julia_install_package()

Requirements

• R >= 4.0
• Julia >= 1.9 (installed automatically via cs_install_julia())
• R packages: terra, JuliaCall

Learn More

• Getting started vignette
• Circuitscape user guide
• Omniscape documentation
• McRae, B.H. (2006). Isolation by resistance. Evolution, 60(8), 1551-1561.
• McRae, B.H. & Beier, P. (2007). Circuit theory predicts gene flow in plant and animal populations. PNAS, 104(50), 19885-19890.
• McRae, B.H., Dickson, B.G., Keitt, T.H. & Shah, V.B. (2008). Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology, 89(10), 2712-2724.