{plant.assembly}: A package for modelling community assembly using the {plant} model trait ecology and evolution
The {plant} package for R is an extensible framework for modelling size-, patch- and trait-structured demography. The {plant.assembly} package extends the capabilities of {plant} to model community assembly using various algorithms.
Current capabilities include
- stochastic assembly.
- fitmax assembly for 1 traits
- Solve 1-species attractor fir 1 trait
Envisioned future capabilities:
- use emulators to approximate fitness landscapes
- More tools for 1D analysis, e.g. PIPs
to do
- community functions for mutant fitness explorer
- community functions for selection gradient function to pass to optimiser
- wire up gp from mlr3mbo
- root solving for first species 2D, 3D examples
Requirements
- You must be using R 4.1.0 or newer. At this stage the package is not on CRAN. Your options for installing are described below.
Option 1, using remotes::install_github
The {plant.assembly] package can be installed direct from GitHub using the remotes package:
remotes::install_github("traitecoevo/plant.assembly", dependencies=TRUE)To install a specific (older) release, decide for the version number that you want to install in https://github.com/traitecoevo/plant.assembly/releases e.g.
remotes::install_github("traitecoevo/[email protected]", dependencies=TRUE)with "v1.0.0" replaced by the appropriate version number.
Option 2, building from source
If familiar with git you might find it easiest to build plant directly from the source code. This is most useful if developing new models or strategies, or to contribute new features.
First, clone the plant repository
git clone https://github.com/traitecoevo/plant
Open an R session in the folder, then to install dependencies run
devtools::install_deps()
Then to compile the project
devtools::install()
or
devtools::load_all()