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 onDownload ZIP
Bug reporting
- Please report any issues or bugs.