Individual-level analyses as published in:

Barneche DR, Kulbicki M, Floeter SR, Friedlander AM, Maina J, Allen AP. Scaling metabolism from individuals to reef-fish communities at broad spatial scales. Ecology Letters 10.1111/ele.12309

One can click here for the article URL

Overview

This repository contains all analyses, figures and tables presented at the above-mentioned paper. It deals only with the individual-level metabolic rates analyses, both in the main text and the SI.

• first I advise that you open your R GUI (R, RStudio, or starting on terminal) from the ELEbarneche2014.RData file...
• ...this is an empty file that sets the absolute path to your project so everything will work independently on any machine;
• pay attention to the required packages at the beginning of each file;
• in the project root folder, some summary statistics are provided in the file analyses-00-all.R;
• a file called figures.R also reproduces all the figures 2, S1-S5 exactly as they are shown in the paper and online SI;
• the figures will be automatically placed in a folder called output (it is going to be automatically created for you);
• I have also provided a tables.R file that creates Tables 1, S1-S3 as presented in the paper and online SI;
• analyses are broken down into individual files and are located in the re-run folder; they should all run independently;
• files that start with analyses-* followed by a number relate to analyses presented on the main text;
• analyses presented at the SI are found within files that follow the pattern analyses-a*;
• I have provided .RData files in re-run to facilitate visualization of summary statistics, but feel free to re-run all;
• notice, though, that some of these analyses may take up to 2 days to run on a regular computer;
• finally, I created a file with hypothetical data demonstrating how one propagates model uncertainties from JAGS to the community level. The file is called hardwire-example.R.

Important remarks: these analyses require specific versions of:

• R: version 2.15.3 (for lme4 analyses) or R version 3.0.2 (for R2jags analyses);
• package lme4: version 0.999999-0;
• package R2jags: version 0.04-01;
• JAGS 3.3.0 (for R2jags analyses)

Please report if you run into problems or spot a bug on the code:

d13g0 DOT b4rn3ch3 AT mq DOT 3du DOT 4u (replace the 0 for o, 1 for i, 3 for e, 4 for a)

How to download this project for people not familiar with GitHub:

• on the project main page on GitHub, click on the right-bottom corner where it says Download ZIP;