Predicting the effects of body size, temperature and diet on animal feeding rates

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

Nunes LT^†, Barneche DR^†, Lastrucci NS, Fraga AA, Nunes JACC, Ferreira CEL, Floeter SR (2021) Predicting the effects of body size, temperature and diet on animal feeding rates. Functional Ecology (accepted).

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

Nunes LT^†, Barneche DR^†, Lastrucci NS, Fraga AA, Nunes JACC, Ferreira CEL, Floeter SR (2021) dbarneche/redlip_bites: Accepted version of paper data and code of manuscript: Predicting the effects of body size, temperature and diet on animal feeding rates (Functional Ecology). Zenodo.

^† Equal authorship

Instructions

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).

Also notice that all the combined Bayesian models in this paper may take 20--30 minutes to run on a regular computer.

This paper 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] LoLinR_0.0.0.9000       png_0.1-7               gridExtra_2.3           bayesplot_1.8.0         rerddap_0.7.4          
 [6] rnaturalearthdata_0.1.0 rnaturalearth_0.1.0     sf_0.9-8                rgeos_0.5-5             sp_1.4-5               
[11] patchwork_1.1.1         forcats_0.5.1           stringr_1.4.0           dplyr_1.0.6             purrr_0.3.4            
[16] readr_1.4.0             tidyr_1.1.3             tibble_3.1.2            ggplot2_3.3.3           tidyverse_1.3.1        
[21] plyr_1.8.6              drake_7.13.2            brms_2.15.0             Rcpp_1.0.6             

loaded via a namespace (and not attached):
  [1] readxl_1.3.1         backports_1.2.1      igraph_1.2.6         splines_4.1.0        storr_1.2.5          crosstalk_1.1.1     
  [7] TH.data_1.0-10       rstantools_2.1.1     inline_0.3.18        digest_0.6.27        htmltools_0.5.1.1    rsconnect_0.8.18    
 [13] fansi_0.5.0          magrittr_2.0.1       base64url_1.4        modelr_0.1.8         RcppParallel_5.1.4   matrixStats_0.58.0  
 [19] xts_0.12.1           sandwich_3.0-1       prettyunits_1.1.1    colorspace_2.0-1     rappdirs_0.3.3       rvest_1.0.0         
 [25] hoardr_0.5.2         haven_2.4.1          callr_3.7.0          crayon_1.4.1         jsonlite_1.7.2       lme4_1.1-27         
 [31] survival_3.2-11      zoo_1.8-9            glue_1.4.2           gtable_0.3.0         emmeans_1.6.0        V8_3.4.2            
 [37] pkgbuild_1.2.0       rstan_2.21.3         abind_1.4-5          scales_1.1.1         mvtnorm_1.1-1        DBI_1.1.1           
 [43] miniUI_0.1.1.1       xtable_1.8-4         progress_1.2.2       units_0.7-1          proxy_0.4-25         txtq_0.2.4          
 [49] stats4_4.1.0         StanHeaders_2.21.0-7 DT_0.18              htmlwidgets_1.5.3    httr_1.4.2           threejs_0.3.3       
 [55] ellipsis_0.3.2       pkgconfig_2.0.3      loo_2.4.1            dbplyr_2.1.1         crul_1.1.0           utf8_1.2.1          
 [61] tidyselect_1.1.1     rlang_0.4.11         reshape2_1.4.4       later_1.2.0          munsell_0.5.0        cellranger_1.1.0    
 [67] tools_4.1.0          cli_2.5.0            generics_0.1.0       broom_0.7.6          ggridges_0.5.3       fastmap_1.1.0       
 [73] processx_3.5.2       fs_1.5.0             ncdf4_1.17           nlme_3.1-152         mime_0.10            projpred_2.0.2      
 [79] xml2_1.3.2           compiler_4.1.0       shinythemes_1.2.0    rstudioapi_0.13      filelock_1.0.2       curl_4.3.1          
 [85] gamm4_0.2-6          e1071_1.7-7          reprex_2.0.0         stringi_1.6.2        ps_1.6.0             Brobdingnag_1.2-6   
 [91] lattice_0.20-44      Matrix_1.3-3         classInt_0.4-3       nloptr_1.2.2.2       markdown_1.1         shinyjs_2.0.0       
 [97] vctrs_0.3.8          pillar_1.6.1         lifecycle_1.0.0      lmtest_0.9-38        bridgesampling_1.1-2 estimability_1.3    
[103] data.table_1.14.0    httpuv_1.6.1         R6_2.5.0             promises_1.2.0.1     KernSmooth_2.23-20   codetools_0.2-18    
[109] boot_1.3-28          colourpicker_1.1.0   MASS_7.3-54          gtools_3.8.2         assertthat_0.2.1     httpcode_0.3.0      
[115] withr_2.4.2          shinystan_2.5.0      multcomp_1.4-17      mgcv_1.8-35          parallel_4.1.0       hms_1.1.0           
[121] class_7.3-19         coda_0.19-4          minqa_1.2.4          shiny_1.6.0          lubridate_1.7.10     base64enc_0.1-3     
[127] 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.