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Minor tweaks to New Zealand scripts
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'How are competitive interactions influenced by traits? A global analysis based on tree radial growth',

Workshop at Macquarie University September 2013

This repository contains material for an analysis based on following paper, for forest inventory data from around the world.

Kunstler et al. (2012) "Competitive interactions between forest trees are driven by species’ trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly". Ecology Letters, 15, 831–840. DOI: 10.1111/j.1461-0248.2012.01803.x PDF.

Folder structure

The repository has the following basic directories:

  • data: contains raw data and meta data. Treat this as read-only, i.e. do not save output from R scripts here, these go in outputs.
  • R: where all R code used in analysis is saved. The only exception is *.Rmd files used in creating some of the documents, which are stored in docs directory.
  • output: a temporary directory that is used to hold all process data. Material in this directory is not tracked because it can be recreated from scripts.
  • docs: contains documents developed for the project.

Some specific folders of likely interest:

  • docs/meeting.agenda: agenda for workshop
  • docs/analysis.outline: theoretical description of analysis
  • docs/analysis.pipeline: outline of work flow (code, data etc).
  • data/raw: Directory containing all the raw data from different sites. By default, this directory is not available.
  • docs/metadata: Contains information about the dataset from each site
  • ms: eventual home for manuscript materials

Tools

We are making use of the following tools:

  • R stats program, for all analyses
  • A number R libraries. We have embedded a function in the code to load missing packages where possible (see R/packages.R)
  • markdown
  • The knitr package in R, for generating documents with R and markdown. For a n intro see here
  • version control via git (see next section)

Git

Documents are kept under version control using git, and stored on github. To access:

  1. Sign up to github and send your username to Georges so he can add you to the repository for this workshop, called trait.competition.workshop
  2. Download repository via github software
  3. You also view the material online here

For an intro to git, see http://nicercode.github.io/git/

Once downloaded, you can interact with the material via your github software, the shell, or Rstudio - an R editor with built in git capabilities.

Key points for intro

  • Internet access
  • Library access
  • Dropbox folder for temporary terms.
  • Intro to git and github
    • version control
      • problems with dropbox: multiple versions, see what changed, conflicts, instant (feature branches)
    • text files
    • set up:
      • install github, rstudio
  • R project
    • Ideal: run on anyone's computer, never use setwd()
    • break into parts
    • knitr
    • makefiles
  • data
    • what are we willing to share