The goal of this R project is to reproduce all analyses, figures, and tables of a global analyses on reef fish function. The project uses a drake workflow, which binds all elements of the analyses together with a plan.
The directory contains:
- 📁 R: Folder containing all functions, packages
and drake plan.
- plan.R: File containing the drake plan.
- packages.R: File to load all needed packages.
- functions_wrangling.R: Contains functions to prepare the data for analyses.
- functions_analysis.R: Contains functions to reproduce analysis.
- functions_plots.R: Contains functions to create figures presenting the results. - 📁 data: Folder containing all data.
- 📁 output: All output including results and figures for publication.
- make.R File: Script to run the whole project.
sessionInfo()
#> R version 3.6.3 (2020-02-29)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 18.04.5 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
#>
#> locale:
#> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
#> [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=en_US.utf8
#> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] officer_0.3.14 flextable_0.5.11 broom_0.7.2
#> [4] readr_1.3.1 ggrepel_0.8.1 forcats_0.4.0
#> [7] ggtree_2.0.1 tidytree_0.3.0 ggnewscale_0.4.0
#> [10] fishualize_0.2.0 patchwork_1.0.0 brms_2.14.4
#> [13] Rcpp_1.0.5 e1071_1.7-2 drake_7.12.5
#> [16] tidyr_1.0.0 dplyr_1.0.2 Rphylopars_0.2.11
#> [19] ape_5.3 fishflux_0.0.1.1 ggplot2_3.3.2
#> [22] tidybayes_1.1.0 purrr_0.3.3
#>
#> loaded via a namespace (and not attached):
#> [1] uuid_0.1-4 backports_1.1.5
#> [3] fastmatch_1.1-0 systemfonts_0.1.1
#> [5] plyr_1.8.4 igraph_1.2.4.1
#> [7] lazyeval_0.2.2 splines_3.6.3
#> [9] svUnit_0.7-12 storr_1.2.1
#> [11] crosstalk_1.0.0 listenv_0.7.0
#> [13] rstantools_2.1.1 inline_0.3.15
#> [15] digest_0.6.22 htmltools_0.4.0
#> [17] rsconnect_0.8.15 magrittr_1.5
#> [19] phytools_0.6-99 memoise_1.1.0
#> [21] base64url_1.4 globals_0.12.4
#> [23] RcppParallel_5.0.2 matrixStats_0.55.0
#> [25] xts_0.11-2 prettyunits_1.0.2
#> [27] colorspace_1.4-1 xfun_0.10
#> [29] callr_3.4.4 crayon_1.3.4
#> [31] jsonlite_1.6 lme4_1.1-23
#> [33] zoo_1.8-6 phangorn_2.5.5
#> [35] glue_1.4.2 gtable_0.3.0
#> [37] geiger_2.0.6.2 V8_3.2.0
#> [39] pkgbuild_1.0.6 rstan_2.21.2
#> [41] future.apply_1.3.0 maps_3.3.0
#> [43] abind_1.4-5 scales_1.1.0
#> [45] mvtnorm_1.0-11 miniUI_0.1.1.1
#> [47] plotrix_3.7-6 xtable_1.8-4
#> [49] progress_1.2.2 ggstance_0.3.3
#> [51] subplex_1.5-4 txtq_0.2.3
#> [53] deSolve_1.24 DT_0.9
#> [55] stats4_3.6.3 StanHeaders_2.21.0-6
#> [57] animation_2.6 htmlwidgets_1.5.1
#> [59] httr_1.4.1 threejs_0.3.1
#> [61] arrayhelpers_1.0-20160527 ellipsis_0.3.0
#> [63] pkgconfig_2.0.3 loo_2.3.1
#> [65] reshape2_1.4.3 tidyselect_1.1.0
#> [67] rlang_0.4.7 later_1.0.0
#> [69] munsell_0.5.0 tools_3.6.3
#> [71] cli_1.1.0 generics_0.0.2
#> [73] ggridges_0.5.1 evaluate_0.14
#> [75] stringr_1.4.0 fastmap_1.0.1
#> [77] yaml_2.2.0 processx_3.4.1
#> [79] knitr_1.25 zip_2.1.1
#> [81] gh_1.0.1 future_1.14.0
#> [83] nlme_3.1-149 mime_0.7
#> [85] projpred_2.0.2 xml2_1.2.2
#> [87] doBy_4.6-2 shinythemes_1.1.2
#> [89] rfishbase_3.0.4 compiler_3.6.3
#> [91] bayesplot_1.7.0 filelock_1.0.2
#> [93] curl_4.2 gamm4_0.2-6
#> [95] png_0.1-7 treeio_1.10.0
#> [97] clusterGeneration_1.3.4 tibble_3.0.4
#> [99] statmod_1.4.34 stringi_1.4.3
#> [101] ps_1.3.0 Brobdingnag_1.2-6
#> [103] gdtools_0.2.1 lattice_0.20-41
#> [105] Matrix_1.2-18 markdown_1.1
#> [107] nloptr_1.2.2.2 shinyjs_1.0
#> [109] vctrs_0.3.4 pillar_1.4.6
#> [111] lifecycle_0.2.0 BiocManager_1.30.8
#> [113] combinat_0.0-8 bridgesampling_0.7-2
#> [115] data.table_1.12.8 httpuv_1.5.2
#> [117] R6_2.4.0 promises_1.1.0
#> [119] gridExtra_2.3 mvnmle_0.1-11.1
#> [121] codetools_0.2-16 colourpicker_1.0
#> [123] boot_1.3-25 MASS_7.3-53
#> [125] gtools_3.8.1 assertthat_0.2.1
#> [127] withr_2.1.2 phylolm_2.6
#> [129] shinystan_2.5.0 mnormt_1.5-5
#> [131] mgcv_1.8-33 expm_0.999-4
#> [133] parallel_3.6.3 hms_0.5.1
#> [135] quadprog_1.5-7 grid_3.6.3
#> [137] coda_0.19-3 class_7.3-17
#> [139] minqa_1.2.4 rvcheck_0.1.5
#> [141] rmarkdown_2.1 base64enc_0.1-3
#> [143] numDeriv_2016.8-1.1 scatterplot3d_0.3-41
#> [145] shiny_1.4.0 dygraphs_1.1.1.6