dbarneche / fishFecundity

Fish reproductive-energy output increases disproportionately with body size

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

Barneche DR, Robertson DR, White CR, Marshall DJ (accepted) Fish reproductive-energy output increases disproportionately with body size. Science. doi: 10.1126/science.aao6868

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()

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 all the combined Bayesian models in this paper will take a several days (up to a month) 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')

This paper was produced 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     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] png_0.1-7         Hmisc_4.1-1       Formula_1.2-2     survival_2.41-3   lattice_0.20-35   HDInterval_0.1.3  LoLinR_0.0.0.9000 brms_2.1.0        ggplot2_2.2.1     Rcpp_0.12.15     
[11] rfishbase_2.1.2.4 ape_5.0           rotl_3.0.3        plyr_1.8.4       

loaded via a namespace (and not attached):
 [1] Brobdingnag_1.2-4    httr_1.3.1           tidyr_0.8.0          jsonlite_1.5         splines_3.4.3        gtools_3.5.0         StanHeaders_2.17.2   threejs_0.3.1        shiny_1.0.5         
[10] assertthat_0.2.0     stats4_3.4.3         latticeExtra_0.6-28  progress_1.1.2       backports_1.1.2      pillar_1.1.0         glue_1.2.0           digest_0.6.15        checkmate_1.8.5     
[19] RColorBrewer_1.1-2   colorspace_1.3-2     htmltools_0.3.6      httpuv_1.3.5         Matrix_1.2-12        dygraphs_1.1.1.4     XML_3.98-1.9         pkgconfig_2.0.1      rncl_0.8.2          
[28] rstan_2.17.3         purrr_0.2.4          xtable_1.8-2         mvtnorm_1.0-7        scales_0.5.0         htmlTable_1.11.2     tibble_1.4.2         bayesplot_1.4.0      DT_0.4              
[37] shinyjs_1.0          nnet_7.3-12          lazyeval_0.2.1       magrittr_1.5         mime_0.5             nlme_3.1-131         foreign_0.8-69       xts_0.10-1           colourpicker_1.0    
[46] data.table_1.10.4-3  rsconnect_0.8.5      loo_1.1.0            prettyunits_1.0.2    matrixStats_0.53.0   stringr_1.2.0        munsell_0.4.3        cluster_2.0.6        bindrcpp_0.2        
[55] compiler_3.4.3       rlang_0.1.6          grid_3.4.3           rstudioapi_0.7       htmlwidgets_1.0      crosstalk_1.0.0      igraph_1.1.2         miniUI_0.1.1         base64enc_0.1-3     
[64] gtable_0.2.0         rentrez_1.1.0        inline_0.3.14        abind_1.4-5          markdown_0.8         reshape2_1.4.3       R6_2.2.2             gridExtra_2.3        rstantools_1.4.0    
[73] zoo_1.8-1            knitr_1.19           bridgesampling_0.4-0 dplyr_0.7.4          bindr_0.1            shinystan_2.4.0      shinythemes_1.1.1    stringi_1.1.6        parallel_3.4.3      
[82] rpart_4.1-11         acepack_1.4.1        coda_0.19-1          lmtest_0.9-35       

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

Bug reporting

• Please report any issues or bugs.