Analysis of BAAD (Duursma and Falster, New Phytologist, 2016)
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README.md

Leaf mass per area, not total leaf area, drives differences in above-ground biomass distribution among woody plant functional types

This repository contains code needed to reproduce the article:

Duursma RA, Falster DS, "Leaf mass per area, not total leaf area, drives differences in above-ground biomass distribution among woody plant functional types", New Phytologist (accepted 2016-04-28).

DOI

Instructions

All analyses were done in R. To compile the paper, including figures and supplementary material we use the remake package for R. You can install remake using the devtools package:

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

(run install.packages("devtools") to install devtools if needed.)

The remake package also depends on storr, install it like this:

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

Next you need to download this repository, and then open an R session with working directory set to the root of the project.

We use a number of packages, these can be easily installed by remake:

remake::install_missing_packages()

The above command may not install the baad.data package correctly, for that do:

devtools::install_github("richfitz/datastorr")
devtools::install_github("traitecoevo/baad.data")

Then, to generate all figures, analyses, and manuscript (PDF, using LaTeX), simply do:

remake::make()

The last step of making the pdf 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.

You can also decide to reproduce only the figures, to do this run:

remake::make("figures")

To make only any of the figures, run a command like

remake::make("figures/Figure1.pdf")

The list of targets can be gleaned from the file remake.yml.

If you find remake confusing and prefer to run plain R, you can use remake to build a script build.Rthat produces a given output, e.g.

remake::make_script(filename="build.R")

Many thanks to Rich FitzJohn for helping us develop this work flow.