dbarneche / vo2Inverts

Relative tolerance of native and invasive species to low oxygen conditions

Do low oxygen environments facilitate marine invasions? Relative tolerance of native and invasive species to low oxygen conditions

This repository contains code and data needed to reproduce the article:

Lagos ME, Barneche DR, White CR, Marshall DJ, Do low oxygen environments facilitate marine invasions? Relative tolerance of native and invasive species to low oxygen conditions. Global Change Biology. doi:10.1111/gcb.13668 (accepted 2017-02-08)

Instructions

All analyses were done in R. To compile the paper, including figures and tables 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)

You also need to install the software JAGS, as per these instructions here.

Next you need to open an R session with working directory set to the root of the project.

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

remake::install_missing_packages()

To generate all figures, analyses, and tables, simply do:

remake::make()

All output will be automatically placed in a directory called output (it is going to be automatically created for you).

Also notice that the Bayesian analysis in this paper will take many hours to run on a regular computer.

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

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

The paper can be reproduced using the following software and associated packages:

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] R2jags_0.5-7      rjags_4-6         coda_0.18-1       plyr_1.8.4        LoLinR_0.0.0.9000

loaded via a namespace (and not attached):
[1] zoo_1.7-13       parallel_3.3.2   abind_1.4-5      Rcpp_0.12.9      grid_3.3.2       lmtest_0.9-34    boot_1.3-18      lattice_0.20-34  R2WinBUGS_2.1-21

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

d13g0 DOT b4rn3ch3 AT m0n4sh DOT 3du (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 green button clone or download and then click on Download ZIP