cs_setup: Set Up Julia and Load Circuitscape/Omniscape

In circuitscaper: 'Circuitscape' and 'Omniscape' Connectivity Analysis via 'Julia'

Set Up Julia and Load Circuitscape/Omniscape

Description

Initialize the Julia session and load the Circuitscape and Omniscape Julia packages. This is called automatically on first use of any ⁠cs_*⁠ or ⁠os_*⁠ function. Call explicitly to control the Julia path, number of threads, or pre-warm the session.

Usage

cs_setup(julia_home = NULL, threads = 1L, quiet = TRUE, ...)

Arguments

julia_home	Character. Path to the Julia ⁠bin/⁠ directory. If NULL (default), the system PATH and common locations are searched.
threads	Integer. Number of Julia threads to start. Default 1L. Must be set before Julia initializes — once Julia is running, the thread count cannot be changed without restarting R. This setting controls parallelism for os_run() only; Circuitscape functions (⁠cs_*⁠) run single-threaded regardless of this value.
quiet	Logical. Suppress Julia startup messages. Default TRUE.
...	Additional arguments passed to JuliaCall::julia_setup().

Details

cs_setup() does not install Julia or Julia packages. If Julia is not found or the required packages are missing, it throws an informative error directing you to cs_install_julia().

cs_setup() will:

• Verify that Julia is installed and accessible.

• Verify that the Circuitscape and Omniscape Julia packages are installed.

• Load both packages and warm up the JIT compiler.

Once Julia is initialized, it stays warm for the R session. Subsequent calls to cs_setup() return immediately.

Threading

Julia's thread count is fixed at startup and cannot be changed mid-session. Multi-threading is used by os_run() when parallelize = TRUE. Circuitscape functions (cs_pairwise, cs_one_to_all, etc.) do not benefit from multiple threads.

cs_setup(threads = 4)
os_run(resistance, radius = 50, parallelize = TRUE)

Value

Invisibly returns TRUE on success.

References

McRae, B.H. (2006). Isolation by resistance. Evolution, 60(8), 1551–1561. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.0014-3820.2006.tb00500.x")}

Landau, V.A., Shah, V.B., Anantharaman, R. & Hall, K.R. (2021). Omniscape.jl: Software to compute omnidirectional landscape connectivity. Journal of Open Source Software, 6(57), 2829. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.21105/joss.02829")}

Circuitscape.jl: https://docs.circuitscape.org/Circuitscape.jl/latest/

Omniscape.jl: https://docs.circuitscape.org/Omniscape.jl/latest/

See Also

cs_install_julia(), cs_pairwise(), os_run()

Examples

cs_setup()
cs_setup(threads = 4)
cs_setup(julia_home = "/usr/local/julia/bin")

circuitscaper documentation built on April 9, 2026, 5:09 p.m.