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plantecophys - an R package for analysing and modelling leaf gas exchange data

DOI

This repository contains the code to generate the figures and manuscript for this paper:

Duursma, R.A., 2015. Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data. PLoS ONE 10, e0143346. doi:10.1371/journal.pone.0143346. (Open Access)

Instructions

  • To compile the entire manuscript, including references, and figures (not embedded but written to the subdirectory output), run:
rmarkdown::render("manuscript.Rmd", "word_document", "manuscript.docx")

This assumes you have the rmarkdown package installed, as well as Pandoc (but not needed if you run this from Rstudio). It also requires an internet connection, needed by Pandoc for formatting the references.

  • To compile the figures only (as PDF), run the following commands.
source("load.R")
source("R/analysis.R")
source("R/make_figures.R")

The load.R script will attempt to install missing packages from CRAN automatically.

  • An example script that shows how to extract additional statistics from fitted A-Ci curves is given in the file R/more_stats_acicurvefit.R.