plant: A package for modelling forest trait ecology and evolution

The plant package for R is an extensible framework for modelling size- and trait-structured demography, ecology and evolution in simulated forests. At its core, plant is an individual-based model where plant physiology and demography are mediated by traits. Individual plants from multiple species can be grown in isolation, in patches of competing plants or in metapopulations under a disturbance regime. These dynamics can be integrated into metapopulation-level estimates of invasion fitness and vegetation structure. Accessed from R, the core routines in plant are written in C++. The package provides for alternative physiologies and for capturing trade-offs among parameters. A detailed test suite is provided to ensure correct behaviour of the code.

Citation

Falster DS, FitzJohn RG, Brännström Å, Dieckmann U, Westoby M (2016) plant: A package for modelling forest trait ecology & evolution. Methods in Ecology and Evolution 7: 136-146. doi: 10.1111/2041-210X.12525

Documentation

For an overview of the plant package see the above publication. Further background on the default FF16 growth model is available in Falster et al 2011 (10.1111/j.1365-2745.2010.01735.x) and Falster et al 2017 (10.1101/083451).

Run library(help=plant) to see the index of functions.

plant comes with a lot of documentation. Initial versions were included as supplementary material with the publication about plant, which can be accessed here. Updated versions can be built from within the package (instructions below) or accessed online:

Details of the modelling approaches:

  • vignette("demography"): Modelling demography of plants, patches and metapopulations online
  • vignette("physiology"): Plant physiological model online

Details of using plant from R:

If you want to build the vignettes locally, see inst/docs/README.md for details. The vignettes are not built as part of the package installation as they take a couple of hours to build.

Details on package structure

Plant is a complex package. It uses C++11 behind the scenes for speed, and R6 classes.

In this blog post, Rich FitzJohn and I describe the key technologies used to build the plant package.

Developer Notes

If you are interested in developing plant you should read the developer notes.

Installation

You must be using R 3.3.0 or newer. At this stage the package is not on CRAN. You’re options for installing are described below.

Installation requires a C++11 compatible C compiler (OSX >= 10.10/Yosemite satisfies this, as do standard linux Ubuntu 12.04 and 14.04). On Windows machines you will need to install Rtools. When I tried this in Rstudio, the program automagically sensed the absence of a compiler and asked if I wanted to install Rtools. Click Yes!

Option 1, using devtools::install_github

(install devtools with install.packages("devtools"))

The plant package can be installed direct from github using the devtools package. plant also requires the packages loggr and RcppR6 packages. Install those with

devtools::install_github("smbache/loggr", dependencies=TRUE)
devtools::install_github("richfitz/RcppR6", dependencies=TRUE)

Then install plant:

devtools::install_github("traitecoevo/plant", dependencies=TRUE)

Option 2, download and install locally

If installing locally you will still need to install the loggr and RcppR6 packages. Install using devtools::install_github as above, or alternatively do as follows.

Additionally install other dependencies from CRAN:

Then download a zip file from github of the dependencies RcppR6 and loggr (if needed), plus plant.

Unzip these archives and then for each package run the command

where path_to_package is the folder for each package, e.g. ~/Downloads/plant-master

Installing different versions

To install a specific (older) release, decide for the version number that you want to install in https://github.com/traitecoevo/plant/releases e.g.

devtools::install_github("traitecoevo/plant", ref = "v1.0.0", dependencies=TRUE)

with "v1.0.0" replaced by the appropriate version number.

Usage

Plant has been used in the following publications:

  • Falster DS, FitzJohn RG, Brännström Å, Dieckmann U, Westoby M (2016) plant: A package for modelling forest trait ecology & evolution. Methods in Ecology and Evolution 7: 136-146. doi: 10.1111/2041-210X.12525  code: github
  • Falster DS, Duursma RA, FitzJohn RG (2016) Trajectories: how functional traits influence plant growth and shade tolerance across the life-cycle. bioRxiv: 083451. doi: 10.1101/083451  code: github