Fish predators control outbreaks of Crown-of-Thorns Starfish

This repository contains code needed to reproduce the output of the project:

Kroon FJ, Barneche DR, Emslie MJ Fish predators control outbreaks of Crown-of-Thorns Starfish. Nature Communications (accepted).

When using the data or code from this project, please cite it as:

Kroon FJ, Barneche DR, Emslie MJ (2021) open-AIMS/cots_fish_trends: Accepted version of paper data and code of manuscript: Fish predators control outbreaks of Crown-of-Thorns Starfish (Nature Communications). Zenodo.

Instructions

Before proceeding with the steps below, please note that this code will only work after saving additional files to the data folder which are currently not publicly available. The data that support the findings of this study are available from the Australian Institute of Marine Science (AIMS) and Queensland Department of Agriculture and Fisheries (QDAF). Restrictions apply to the availability of the QDAF data (all models associated with Figure 1 of the manuscript), which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of QDAF.

All processing was done in R. This routine uses the drake R package to compile the output time table. First install drake:

install.packages("drake")

Next you need to open an R session with working directory set to the root of the project.

This routine loads multiple packages which are found in R/packages.R, so make sure to successfully install and load them before running drake.

Then, to reproduce the data analyses and figures, do:

source("make.R")
drake::loadd()

All output will be automatically placed in a directory called output (it is going to be automatically created for you). Please note that the analyses may take a more than a day to run on a regular computer. They ran in 20 hours in a regular 2015 iMac (16 Gb RAM).

The current output of this project was produced using the following software and associated packages:

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] patchwork_1.1.1    png_0.1-7          RColorBrewer_1.1-2 gridExtra_2.3      Hmisc_4.5-0        Formula_1.2-4      survival_3.2-11    lattice_0.20-44    emmeans_1.6.0      DHARMa_0.4.1       brms_2.15.0        Rcpp_1.0.6        
[13] forcats_0.5.1      stringr_1.4.0      dplyr_1.0.6        purrr_0.3.4        readr_1.4.0        tidyr_1.1.3        tibble_3.1.2       ggplot2_3.3.3      tidyverse_1.3.1    plyr_1.8.6         readxl_1.3.1       drake_7.13.2      

loaded via a namespace (and not attached):
  [1] backports_1.2.1      igraph_1.2.6         splines_4.1.0        storr_1.2.5          crosstalk_1.1.1      TH.data_1.0-10       rstantools_2.1.1     inline_0.3.18        digest_0.6.27        foreach_1.5.1        htmltools_0.5.1.1   
 [12] rsconnect_0.8.18     fansi_0.5.0          checkmate_2.0.0      magrittr_2.0.1       base64url_1.4        cluster_2.1.2        modelr_0.1.8         RcppParallel_5.1.4   matrixStats_0.58.0   xts_0.12.1           sandwich_3.0-1      
 [23] prettyunits_1.1.1    jpeg_0.1-8.1         colorspace_2.0-1     rvest_1.0.0          xfun_0.23            haven_2.4.1          callr_3.7.0          crayon_1.4.1         jsonlite_1.7.2       lme4_1.1-27          zoo_1.8-9           
 [34] iterators_1.0.13     glue_1.4.2           gtable_0.3.0         V8_3.4.2             pkgbuild_1.2.0       rstan_2.21.3         abind_1.4-5          scales_1.1.1         mvtnorm_1.1-1        DBI_1.1.1            miniUI_0.1.1.1      
 [45] htmlTable_2.2.1      xtable_1.8-4         progress_1.2.2       foreign_0.8-81       txtq_0.2.4           stats4_4.1.0         StanHeaders_2.21.0-7 DT_0.18              htmlwidgets_1.5.3    httr_1.4.2           threejs_0.3.3       
 [56] ellipsis_0.3.2       pkgconfig_2.0.3      loo_2.4.1            nnet_7.3-16          dbplyr_2.1.1         utf8_1.2.1           tidyselect_1.1.1     rlang_0.4.11         reshape2_1.4.4       later_1.2.0          munsell_0.5.0       
 [67] cellranger_1.1.0     tools_4.1.0          cli_2.5.0            generics_0.1.0       broom_0.7.6          ggridges_0.5.3       fastmap_1.1.0        knitr_1.33           processx_3.5.2       fs_1.5.0             nlme_3.1-152        
 [78] mime_0.10            projpred_2.0.2       xml2_1.3.2           compiler_4.1.0       bayesplot_1.8.0      shinythemes_1.2.0    rstudioapi_0.13      filelock_1.0.2       gamm4_0.2-6          curl_4.3.1           reprex_2.0.0        
 [89] stringi_1.6.2        ps_1.6.0             Brobdingnag_1.2-6    Matrix_1.3-3         nloptr_1.2.2.2       markdown_1.1         shinyjs_2.0.0        vctrs_0.3.8          pillar_1.6.1         lifecycle_1.0.0      bridgesampling_1.1-2
[100] estimability_1.3     data.table_1.14.0    httpuv_1.6.1         latticeExtra_0.6-29  R6_2.5.0             promises_1.2.0.1     codetools_0.2-18     boot_1.3-28          colourpicker_1.1.0   MASS_7.3-54          gtools_3.8.2        
[111] assertthat_0.2.1     withr_2.4.2          shinystan_2.5.0      multcomp_1.4-17      mgcv_1.8-35          parallel_4.1.0       hms_1.1.0            rpart_4.1-15         coda_0.19-4          minqa_1.2.4          shiny_1.6.0         
[122] lubridate_1.7.10     base64enc_0.1-3      dygraphs_1.1.1.6    

License

This repository is provided by the authors under the MIT License (MIT).

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.