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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.