Temperature effects on mass-scaling exponents in colonial animals: a manipulative test

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

Barneche DR, White CR, Marshall DJ (2017). Temperature effects on mass-scaling exponents in colonial animals: a manipulative test. Ecology, 98:103–111, doi:10.1002/ecy.1624

Code DOI:

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()

And then install the package fontcm, via extrafont. This installs the font CM Roman we use in our figures (for more information on see these instructions:

extrafont::font_install('fontcm')

Then, to generate all figures, analyses, and manuscript (.docx, using Rmarkdown), 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 20–30 min 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 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

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] fontcm_1.1         extrafont_0.17     RColorBrewer_1.1-2 MASS_7.3-45        png_0.1-7          LoLinR_0.0.0.9000  rmarkdown_0.9.6    knitr_1.13         R2jags_0.5-7       rjags_4-6         
[11] coda_0.18-1        plyr_1.8.4         lme4_1.1-12        Matrix_1.2-6      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5      formatR_1.4      nloptr_1.0.4     tools_3.3.1      boot_1.3-18      digest_0.6.10    remake_0.2.0     evaluate_0.9     nlme_3.1-128     lattice_0.20-33  yaml_2.1.13     
[12] parallel_3.3.1   Rttf2pt1_1.3.4   storr_1.0.1      stringr_1.0.0    lmtest_0.9-34    grid_3.3.1       R6_2.2.0         minqa_1.2.4      extrafontdb_1.0  magrittr_1.5     codetools_0.2-14
[23] R2WinBUGS_2.1-21 htmltools_0.3.5  splines_3.3.1    abind_1.4-3      stringi_1.1.1    crayon_1.3.2     zoo_1.7-13

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

Acknowledgements:

Many thanks to Rich FitzJohn, Remko Duursma, and Daniel Falster for providing suggestions and excellent examples on how to implement this work flow using remake.

dbarneche / MTRBrEs