Body size, reef area, and temperature predict global reef-fish species richness across spatial scales

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

Barneche DR, Rezende EL, Parravicini V, Maire E, Edgar GJ, Stuart-Smith RD, Arias-González JE, Ferreira CEL, Friedlander AM, Green AL, Luiz OJ, Rodríguez-Zaragoza FA, Vigliola L, Kulbicki M, Floeter SR, Body size, reef area, and temperature predict global reef-fish species richness across spatial scales. Global Ecology and Biogeography. 10.1111/geb.12851

Instructions

All analyses were done in R. To compile the figures, analyses and tables we use the remake package for R. The remake package depends on storr, so install it first like this:

devtools::install_github('richfitz/storr', dependencies=TRUE)

Run install.packages('devtools') to install devtools first if needed. Then you can install remake using the devtools package:

devtools::install_github('richfitz/remake', 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 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 might take up to 2 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 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

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] Hmisc_4.1-1        Formula_1.2-2      survival_2.41-3    mapproj_1.2-5      maps_3.2.0         fontcm_1.1        
 [7] extrafont_0.17     LoLinR_0.0.0.9000  vegan_2.4-6        lattice_0.20-35    permute_0.9-4      ape_5.0           
[13] brms_2.6.0         Rcpp_0.12.19       iNEXT_2.0.12       plyr_1.8.4         rstan_2.18.2       StanHeaders_2.18.0
[19] ggplot2_3.0.0     

loaded via a namespace (and not attached):
 [1] nlme_3.1-131         matrixStats_0.53.0   xts_0.11-1           RColorBrewer_1.1-2   threejs_0.3.1       
 [6] backports_1.1.2      R6_2.3.0             DT_0.4               rpart_4.1-11         lazyeval_0.2.1      
[11] mgcv_1.8-22          colorspace_1.3-2     nnet_7.3-12          withr_2.1.2          tidyselect_0.2.4    
[16] gridExtra_2.3        processx_3.1.0       Brobdingnag_1.2-4    compiler_3.4.3       extrafontdb_1.0     
[21] htmlTable_1.11.2     shinyjs_1.0          colourpicker_1.0     checkmate_1.8.5      scales_1.0.0        
[26] dygraphs_1.1.1.6     lmtest_0.9-36        mvtnorm_1.0-7        ggridges_0.5.1       callr_2.0.4         
[31] stringr_1.3.1        digest_0.6.18        foreign_0.8-69       base64enc_0.1-3      pkgconfig_2.0.2     
[36] htmltools_0.3.6      htmlwidgets_1.3      rlang_0.2.2          rstudioapi_0.8       shiny_1.1.0         
[41] bindr_0.1.1          zoo_1.8-4            crosstalk_1.0.0      gtools_3.8.1         acepack_1.4.1       
[46] dplyr_0.7.6          inline_0.3.15        magrittr_1.5         loo_2.0.0            bayesplot_1.6.0     
[51] Matrix_1.2-14        munsell_0.5.0        abind_1.4-5          stringi_1.2.4        yaml_2.2.0          
[56] MASS_7.3-47          storr_1.1.3          pkgbuild_1.0.0       grid_3.4.3           promises_1.0.1      
[61] crayon_1.3.4         miniUI_0.1.1         splines_3.4.3        knitr_1.20           pillar_1.1.0        
[66] igraph_1.1.2         markdown_0.8         shinystan_2.5.0      codetools_0.2-15     reshape2_1.4.3      
[71] stats4_3.4.3         rstantools_1.5.1     glue_1.3.0           latticeExtra_0.6-28  data.table_1.10.4-3 
[76] httpuv_1.4.5         Rttf2pt1_1.3.5       gtable_0.2.0         purrr_0.2.5          assertthat_0.2.0    
[81] mime_0.6             xtable_1.8-3         coda_0.19-1          later_0.7.5          rsconnect_0.8.8     
[86] tibble_1.4.2         shinythemes_1.1.1    bindrcpp_0.2.2       cluster_2.0.6        remake_0.3.0        
[91] 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

Bug reporting

• Please report any issues or bugs.