[Table of Contents]
Package JuliaCall is an R interface to
Julia, which is a high-level, high-performance dynamic
programming language for numerical computing, see https://julialang.org/ for
more information. Below is an image for Mandelbrot set.
JuliaCall brings more than 100 times speedup of the
calculation! See https://github.com/Non-Contradiction/JuliaCall/tree/master/example/mandelbrot
for more information.
You can install JuliaCall just like any other R packages
by
install.packages("JuliaCall")To use JuliaCall you must have a working installation of
Julia. This can be easily done via:
library(JuliaCall)
install_julia()which will automatically install and setup a version of Julia specifically for use with JuliaCall. Or you can do
library(JuliaCall)
julia_setup(installJulia = TRUE)which will invoke install_julia automatically if Julia
is not found and also do initialization of JuliaCall.
You can also setup Julia manually by downloading a generic binary
from https://julialang.org/downloads/ and add it to your
path. Currently Julia v0.6.x and the
Julia v1.x releases are all supported by
JuliaCall.
You can get the development version of JuliaCall by
devtools::install_github("Non-Contradiction/JuliaCall")Before using JuliaCall, you need to do initial setup by
function julia_setup() for automatic type conversion, Julia
display systems, etc. It is necessary for every new R session to use the
package. If not carried out manually, it will be invoked automatically
before other julia_xxx functions. Solutions to some common
error in julia_setup() are documented in the troubleshooting
section.
library(JuliaCall)
julia <- julia_setup()
#> Julia version 1.7.2 at location /Applications/Julia-1.7.app/Contents/Resources/julia/bin will be used.
#> Loading setup script for JuliaCall...
#> Finish loading setup script for JuliaCall.
## If you want to use `Julia` at a specific location, you could do the following:
## julia_setup(JULIA_HOME = "the folder that contains Julia binary").
## You can also set JULIA_HOME in command line environment or use `options(...)`.
## Different ways of using Julia to calculate sqrt(2)
# julia$command("a = sqrt(2);"); julia$eval("a")
julia_command("a = sqrt(2);"); julia_eval("a")
#> [1] 1.414214
julia_eval("sqrt(2)")
#> [1] 1.414214
julia_call("sqrt", 2)
#> [1] 1.414214
julia_eval("sqrt")(2)
#> [1] 1.414214
julia_assign("x", sqrt(2)); julia_eval("x")
#> [1] 1.414214
julia_assign("rsqrt", sqrt); julia_call("rsqrt", 2)
#> [1] 1.414214
2 %>J% sqrt
#> [1] 1.414214
## You can use `julia$exists` as `exists` in R to test
## whether a function or name exists in Julia or not
julia_exists("sqrt")
#> [1] TRUE
julia_exists("c")
#> [1] FALSE
## Functions related to installing and using Julia packages
julia_install_package_if_needed("Optim")
julia_installed_package("Optim")
#> [1] "1.6.1"
julia_library("Optim")Make sure the Julia installation is correct.
JuliaCall can find Julia on PATH, and there
are three ways for JuliaCall to find Julia not
on PATH.
julia_setup(JULIA_HOME = "the folder that contains julia binary")options(JULIA_HOME = "the folder that contains julia binary")JULIA_HOME in command line environment.Such problems are usually on Linux machines. The cause for the
problem is that R cannot find the libstdc++ version needed by
Julia. To deal with the problem, users can export
“TheFolderContainsJulia/lib/julia” to R_LD_LIBRARY_PATH.
The issue is usually caused by updates in R, and it can be typically
solved by setting rebuild argument to TRUE in
julia_setup() as follows.
JuliaCall::julia_setup(rebuild = TRUE)ERROR: could not load library "/usr/lib/x86_64-linux-gnu/../bin/../lib/x86_64-linux-gnu/julia/sys.so"This error happens when Julia is built/installed with
MULTIARCH_INSTALL=1, as it is on e.g. Debian. It is caused
by the
bindir-locating code in jl_init not being multiarch-aware. To work
around it, try setting JULIA_BINDIR=/usr/bin in .Renviron.
julia$help as the following example:julia_help("sqrt")
#> ```
#> sqrt(x)
#> ```
#>
#> Return $\sqrt{x}$. Throws [`DomainError`](@ref) for negative [`Real`](@ref) arguments. Use complex negative arguments instead. The prefix operator `√` is equivalent to `sqrt`.
#>
#> See also: [`hypot`](@ref).
#>
#> # Examples
#>
#> ```jldoctest; filter = r"Stacktrace:(\n \[[0-9]+\].*)*"
#> julia> sqrt(big(81))
#> 9.0
#>
#> julia> sqrt(big(-81))
#> ERROR: DomainError with -81.0:
#> NaN result for non-NaN input.
#> Stacktrace:
#> [1] sqrt(::BigFloat) at ./mpfr.jl:501
#> [...]
#>
#> julia> sqrt(big(complex(-81)))
#> 0.0 + 9.0im
#>
#> julia> .√(1:4)
#> 4-element Vector{Float64}:
#> 1.0
#> 1.4142135623730951
#> 1.7320508075688772
#> 2.0
#> ```
#>
#> ```
#> sqrt(A::AbstractMatrix)
#> ```
#>
#> If `A` has no negative real eigenvalues, compute the principal matrix square root of `A`, that is the unique matrix $X$ with eigenvalues having positive real part such that $X^2 = A$. Otherwise, a nonprincipal square root is returned.
#>
#> If `A` is real-symmetric or Hermitian, its eigendecomposition ([`eigen`](@ref)) is used to compute the square root. For such matrices, eigenvalues λ that appear to be slightly negative due to roundoff errors are treated as if they were zero More precisely, matrices with all eigenvalues `≥ -rtol*(max |λ|)` are treated as semidefinite (yielding a Hermitian square root), with negative eigenvalues taken to be zero. `rtol` is a keyword argument to `sqrt` (in the Hermitian/real-symmetric case only) that defaults to machine precision scaled by `size(A,1)`.
#>
#> Otherwise, the square root is determined by means of the Björck-Hammarling method [^BH83], which computes the complex Schur form ([`schur`](@ref)) and then the complex square root of the triangular factor. If a real square root exists, then an extension of this method [^H87] that computes the real Schur form and then the real square root of the quasi-triangular factor is instead used.
#>
#> [^BH83]: Åke Björck and Sven Hammarling, "A Schur method for the square root of a matrix", Linear Algebra and its Applications, 52-53, 1983, 127-140. [doi:10.1016/0024-3795(83)80010-X](https://doi.org/10.1016/0024-3795(83)80010-X)
#>
#> [^H87]: Nicholas J. Higham, "Computing real square roots of a real matrix", Linear Algebra and its Applications, 88-89, 1987, 405-430. [doi:10.1016/0024-3795(87)90118-2](https://doi.org/10.1016/0024-3795(87)90118-2)
#>
#> # Examples
#>
#> ```jldoctest
#> julia> A = [4 0; 0 4]
#> 2×2 Matrix{Int64}:
#> 4 0
#> 0 4
#>
#> julia> sqrt(A)
#> 2×2 Matrix{Float64}:
#> 2.0 0.0
#> 0.0 2.0
#> ```The GitHub Pages for this repository host the documentation for
the development version of JuliaCall: https://non-contradiction.github.io/JuliaCall/.
Also, you are more than welcome to contact me about
JuliaCall at
lch34677@gmail.com
or
cxl508@psu.edu.
If you are interested in developing an R package which
is an interface for a Julia package, JuliaCall
is an ideal choice. You only need to find the Julia
function or Julia module you want to have in
R, using the module, and
julia_call the function. There are some examples:
diffeqr
is a package for solving differential equations in R. It
utilizes DifferentialEquations.jl for
its core routines to give high performance solving of ordinary
differential equations (ODEs), stochastic differential equations (SDEs),
delay differential equations (DDEs), and differential-algebraic
equations (DAEs) directly in R.convexjlr
is an R package for Disciplined Convex Programming (DCP) by
providing a high level wrapper for Julia package Convex.jl.
convexjlr can solve linear programs, second order cone
programs, semidefinite programs, exponential cone programs,
mixed-integer linear programs, and some other DCP-compliant convex
programs through Convex.jl.ipoptjlr
provides an R interface to the Ipopt nonlinear
optimization solver. It provides a simple high-level wrapper for
Julia package [Ipopt.jl] (https://github.com/jump-dev/Ipopt.jl).FixedEffectjlr
uses the Julia package FixedEffectModels.jl
to estimate large fixed effects models in R.JuliaCall and
Julia package MixedModels.jl
to build mixed models in R.autodiffr
provides automatic differentiation to native R functions by
wrapping Julia packages ForwardDiff.jl
and ReverseDiff.jl
through JuliaCall, which is a work in progress.If you have any issues in developing an R package using
JuliaCall, you may report it using the link: https://github.com/Non-Contradiction/JuliaCall/issues/new,
or email me at
lch34677@gmail.com
or
cxl508@psu.edu.
JuliaCall is under active development now. Any
suggestion or issue reporting is welcome! You may report it using the
link: https://github.com/Non-Contradiction/JuliaCall/issues/new,
or email me at
lch34677@gmail.com
or
cxl508@psu.edu.
You are welcome to use the issue
template and the pull
request template. The contributing
guide provides some guidance for making contributions.
JuliaCall
PackageTo check and test the JuliaCall package, you need to
have the source package. You can
JuliaCall from Github,JuliaCall.Rproj in your RStudio or open
R from the downloaded directory,devtools::test() to see the result of the test
suite.devtools::check() or click the Check
button in the RStudio Build panel in the upper right to see the result
of R CMD check.RCall.jl
is a Julia package which embeds R in
Julia. JuliaCall is inspired by
RCall.jl and depends on RCall.jl for many
functionalities like type conversion between R and
Julia.XRJulia
is an R package based on John Chambers’ XR
package and allows for structured integration of R with
Julia. It connects to Julia and uses JSON to
transfer data between Julia and R. A simple
performance comparison between XRJulia and
Julia can be found in JuliaCall JOSS
paper.RJulia
is an R package which embeds Julia in
R as well as JuliaCall. It is not on CRAN yet,
and I haven’t tested it.JuliaCall is licensed under MIT.
Please note that the JuliaCall project is released with
a Contributor
Code of Conduct. By contributing to this project, you agree to abide
by its terms.
If you use JuliaCall in research that resulted in
publications, then please cite the JuliaCall paper using
the following BibTeX entry:
@Article{JuliaCall,
author = {Changcheng Li},
title = {{JuliaCall}: an {R} package for seamless integration between {R} and {Julia}},
journal = {The Journal of Open Source Software},
publisher = {The Open Journal},
year = {2019},
volume = {4},
number = {35},
pages = {1284},
doi = {10.21105/joss.01284},
}