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README.md

Paper about the plant package

This repository contains code needed to reproduce the article:

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

Instructions

Recreating all the figures from the paper will take around 2 hrs.

Install relevant software

All analyses were done in R. You need to download this repository, and then open an R session with working directory set to the root of the project.

To compile the paper, including figures and supplementary material we use the remake package for R. You can install remake using the devtools package (run install.packages("devtools") to install devtools if needed):

devtools::install_github("richfitz/storr", dependencies=TRUE)
devtools::install_github("richfitz/remake", dependencies=TRUE)

We use the non-CRAN packages plant and sowsear. These can be installed by remake:

remake::install_missing_packages()

Compilation requires also pandoc, or the rmarkdown renderer will fail with a cryptic error (version 0.5.1 at least). Finally, compiling the paper requires a reasonably complete LaTeX installation (e.g. MacTeX for OSX or MikTex for windows). The LaTeX compilation will depend on a few packages from CTAN, make sure to allow automatic package installation by your LaTeX distribution

Re run analyses

To compile everything, run

remake::make()

Compiling just the figures and manuscript can be done with:

remake::make("ms.pdf")

and should only take 20 minutes or so.