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Global environmental drivers of marine fish egg size

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

Barneche DR, Burgess SC, Marshall DJ Global environmental drivers of marine fish egg size. Global Ecology and Biogeography. doi: 10.1111/geb.12748

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)

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 tables, simply run:

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 whole project compilation, including environmental data download from the NOAA database and the Bayesian analyses, may take up to a week 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 all outputs, e.g.

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

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

R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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] tools     parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rmarkdown_1.8         knitr_1.19            envPred_0.0.0.1000    raster_2.6-7          sp_1.2-7              zoo_1.8-1             plyr_1.8.4           
 [8] ncdf4_1.16            noaaErddap_0.0.0.9000 fontcm_1.1            extrafont_0.17        LoLinR_0.0.0.9000     Hmisc_4.1-1           Formula_1.2-2        
[15] survival_2.41-3       lattice_0.20-35       brms_2.1.0            ggplot2_2.2.1         Rcpp_0.12.15          rfishbase_2.1.2.4     ape_5.0              
[22] rotl_3.0.3           

loaded via a namespace (and not attached):
 [1] nlme_3.1-131         matrixStats_0.53.0   xts_0.10-1           RColorBrewer_1.1-2   progress_1.1.2       threejs_0.3.1        httr_1.3.1          
 [8] rprojroot_1.3-2      rstan_2.17.3         backports_1.1.2      R6_2.2.2             DT_0.4               rpart_4.1-11         lazyeval_0.2.1      
[15] colorspace_1.3-2     nnet_7.3-12          gridExtra_2.3        prettyunits_1.0.2    Brobdingnag_1.2-4    compiler_3.4.3       extrafontdb_1.0     
[22] htmlTable_1.11.2     shinyjs_1.0          colourpicker_1.0     scales_0.5.0         dygraphs_1.1.1.4     checkmate_1.8.5      lmtest_0.9-35       
[29] mvtnorm_1.0-7        stringr_1.2.0        digest_0.6.15        StanHeaders_2.17.2   foreign_0.8-69       rentrez_1.1.0        base64enc_0.1-3     
[36] pkgconfig_2.0.1      htmltools_0.3.6      htmlwidgets_1.0      rlang_0.1.6          rstudioapi_0.7       shiny_1.0.5          bindr_0.1           
[43] jsonlite_1.5         crosstalk_1.0.0      gtools_3.5.0         acepack_1.4.1        dplyr_0.7.4          inline_0.3.14        magrittr_1.5        
[50] loo_1.1.0            bayesplot_1.4.0      Matrix_1.2-12        munsell_0.4.3        abind_1.4-5          stringi_1.1.6        yaml_2.1.16         
[57] storr_1.1.3          grid_3.4.3           crayon_1.3.4         miniUI_0.1.1         rncl_0.8.2           splines_3.4.3        pillar_1.1.0        
[64] igraph_1.1.2         markdown_0.8         shinystan_2.4.0      reshape2_1.4.3       stats4_3.4.3         rstantools_1.4.0     XML_3.98-1.9        
[71] glue_1.2.0           evaluate_0.10.1      latticeExtra_0.6-28  data.table_1.10.4-3  httpuv_1.3.5         Rttf2pt1_1.3.5       gtable_0.2.0        
[78] purrr_0.2.4          tidyr_0.8.0          assertthat_0.2.0     mime_0.5             xtable_1.8-2         coda_0.19-1          rsconnect_0.8.5     
[85] tibble_1.4.2         shinythemes_1.1.1    bindrcpp_0.2         cluster_2.0.6        remake_0.3.0         bridgesampling_0.4-0

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

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