This repository holds all the code and data needed to reproduce the manuscript:
Ghilardi, M., Schiettekatte, N. M. D., Casey, J. M., Brandl, S. J., Degregori, S., Mercière, A., Morat, F., Letourneur, Y., Bejarano, S., Parravicini, V. (2021) Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes. Ecology and Evolution.
When using code or data from this project, please cite it as:
Ghilardi, M., Schiettekatte, N. M. D., Casey, J. M., Brandl, S. J., Degregori, S., Mercière, A., Morat, F., Letourneur, Y., Bejarano, S., Parravicini, V. (2021) Data and code of accepted version of manuscript: Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes (Ecology and Evolution). Zenodo.
All modelling and plots were produced in R using Stan through the brms package.
If you would like to replicate our analysis, run the code in the folder R/Analysis in this order:
- 0_set_up_project.R
- 1_FishBase_traits.R
- 2_isotope_analysis.R
- 3_intestine_analysis.R
- 4_sensitivity_analysis.R
- 5_figures.R
This will reproduce the entire analysis from start to finish.
The output will be saved in four separate folders:
📁 Models: for the Bayesian models
📁 Trees: for the phylogenetic trees
📁 Figures: for all the figures in the manuscript and supporting information
📁 Tables: for all supplementary tables
Note that running the script 1_FishBase_traits.R may generate slightly different values for the traits from those used in the paper due to updates in FishBase. Also, taxonomic names are continuously revised in FishBase and this may lead to errors when running the script. The complete dataset used in the paper, including traits' values, is included in Data (intestine_fish_Moorea_FB.traits.csv).
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.1252 LC_CTYPE=English_Germany.1252
[3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=English_Germany.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggimage_0.2.8 ggrepel_0.8.2 fishualize_0.2.0 cowplot_1.0.0
[5] ggnewscale_0.4.3 RColorBrewer_1.1-2 ggridges_0.5.2 ggtext_0.1.0
[9] ggtree_2.2.4 ggpubr_0.4.0 ggplot2_3.3.2 extrafont_0.17
[13] bayesplot_1.7.2 tidybayes_2.1.1 brms_2.14.4 Rcpp_1.0.7
[17] fishtree_0.3.2 MCMCglmm_2.29 ape_5.4-1 coda_0.19-3
[21] Matrix_1.2-18 rfishbase_3.0.4 forcats_0.5.0 tidyr_1.1.2
[25] dplyr_1.0.2
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.1.9 plyr_1.8.6
[4] igraph_1.2.5 lazyeval_0.2.2 splines_4.0.2
[7] svUnit_1.0.3 crosstalk_1.1.0.1 rstantools_2.1.1
[10] inline_0.3.15 digest_0.6.25 htmltools_0.5.1.1
[13] magick_2.4.0 rsconnect_0.8.16 fansi_0.4.1
[16] magrittr_1.5 memoise_1.1.0 openxlsx_4.1.5
[19] readr_1.3.1 RcppParallel_5.0.2 matrixStats_0.56.0
[22] xts_0.12-0 extrafontdb_1.0 prettyunits_1.1.1
[25] colorspace_1.4-1 ggdist_2.2.0 haven_2.3.1
[28] xfun_0.16 callr_3.5.1 crayon_1.3.4
[31] jsonlite_1.7.1 lme4_1.1-23 zoo_1.8-8
[34] glue_1.4.2 gtable_0.3.0 V8_3.2.0
[37] distributional_0.2.0 car_3.0-9 pkgbuild_1.1.0
[40] Rttf2pt1_1.3.8 rstan_2.21.2 abind_1.4-5
[43] scales_1.1.1 mvtnorm_1.1-1 rstatix_0.6.0
[46] miniUI_0.1.1.1 gridtext_0.1.1 xtable_1.8-4
[49] gridGraphics_0.5-0 tidytree_0.3.3 foreign_0.8-80
[52] stats4_4.0.2 StanHeaders_2.21.0-6 DT_0.15
[55] htmlwidgets_1.5.1 httr_1.4.2 threejs_0.3.3
[58] arrayhelpers_1.1-0 ellipsis_0.3.1 pkgconfig_2.0.3
[61] loo_2.3.1 farver_2.0.3 ggplotify_0.0.5
[64] tidyselect_1.1.0 rlang_0.4.11 reshape2_1.4.4
[67] later_1.1.0.1 munsell_0.5.0 cellranger_1.1.0
[70] tools_4.0.2 cli_2.0.2 generics_0.1.0
[73] broom_0.7.0 stringr_1.4.0 fastmap_1.0.1
[76] processx_3.4.5 zip_2.1.1 purrr_0.3.4
[79] gh_1.1.0 nlme_3.1-148 mime_0.9
[82] projpred_2.0.2 aplot_0.0.5 xml2_1.3.2
[85] compiler_4.0.2 shinythemes_1.1.2 rstudioapi_0.11
[88] png_0.1-7 curl_4.3 gamm4_0.2-6
[91] ggsignif_0.6.0 treeio_1.12.0 tibble_3.0.3
[94] statmod_1.4.34 stringi_1.4.6 ps_1.3.4
[97] Brobdingnag_1.2-6 cubature_2.0.4.1 lattice_0.20-41
[100] nloptr_1.2.2.2 markdown_1.1 shinyjs_1.1
[103] tensorA_0.36.1 vctrs_0.3.3 pillar_1.4.6
[106] lifecycle_0.2.0 BiocManager_1.30.10 bridgesampling_1.0-0
[109] data.table_1.13.0 corpcor_1.6.9 patchwork_1.0.1
[112] httpuv_1.5.4 R6_2.4.1 promises_1.1.1
[115] gridExtra_2.3 rio_0.5.16 codetools_0.2-16
[118] boot_1.3-25 colourpicker_1.0 MASS_7.3-51.6
[121] gtools_3.8.2 assertthat_0.2.1 withr_2.2.0
[124] shinystan_2.5.0 mgcv_1.8-31 hms_0.5.3
[127] grid_4.0.2 minqa_1.2.4 rvcheck_0.1.8
[130] carData_3.0-4 shiny_1.5.0 base64enc_0.1-3
[133] dygraphs_1.1.1.6 tinytex_0.25
Click on the green button clone or download in the project's main page on GitHub and then click on Download ZIP.
Thanks to Clause Wilke for the function align_legend() that helped adjusting legends' alignment in Fig. 2.
Please report any bug and issue