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
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')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
- on the project main page on GitHub, click on the green button
clone or downloadand then click onDownload ZIP
- Please report any issues or bugs.