See full documentation here, including tutorials and examples.
CoexistenceHoles is a
R package that originally was made for the project “Coexistence holes characterize the assembly and disassembly of multispecies sytems”. However, the package has the potential for a variety of applications. In short, it provides efficient tools for analyzing the homology of general hypergraphs.
This package is not registered (yet). You can install it via the Julia REPL like this:
julia> using Pkg julia> Pkg.add(PackageSpec(url="https://github.com/SyntheticDynamics/CoexistenceHoles.jl.git", rev="master"))
Or you can install it via the Pkg REPL like this:
(v1.3) pkg> add https://github.com/SyntheticDynamics/CoexistenceHoles.jl.git#master
If you already have
R installed then you’ll need
to download install
julia. You can check if julia is
installed correctly by running the
julia command in a terminal. If this command
is not found, you will need to add it to your path following the proper
instructions for your operating system.
JuliaCall is used to interface between languages. For function summaries see this document.
However studying these functions is not necessary since
shows the proper functions to use from
JuliaCall in the tutorial and examples.
The follwoing are steps to install
R. See the examples
or tutorials for more specific instructions.
install.packages("JuliaCall") library(JuliaCall) julia <- julia_setup() # only need to run this once julia_install_package("https://github.com/SyntheticDynamics/CoexistenceHoles.jl.git#master") # add the library every time you open a new session of R and want to use CoexistenceHoles julia_library("CoexistenceHoles")
Example code for both
If you use CoexistenceHoles for academic research, please cite the following paper:
Angulo, M.T., Kelley, A., Montejano, L. et al. Coexistence holes characterize the assembly and disassembly of multispecies systems. Nat Ecol Evol 5, 1091–1101 (2021). https://doi.org/10.1038/s41559-021-01462-8
- Marco Tulio
- Aaron Kelley