Nutrient limitation, bioenergetics, and stoichiometry: a new model to predict elemental fluxes mediated by fishes
This repository contains code and data needed to reproduce the figures and tables of the manuscript:
Schiettekatte, N. M. D., Barneche, D. R., Villéger, S., Allgeier, J, Burkepile, D.; Brandl, S.J., Casey, J. M.; Mercière, A; Munsterman, K; Morat, F; Parravicini, V (2020) (in press.) Nutrient limitation, bioenergetics, and stoichiometry: a new model to predict elemental fluxes mediated by fishes. Functional ecology
All analyses were done in R. To compile the paper, including figures and tables we use the remake package for R. You can install remake using the devtools package:
devtools::install_github("richfitz/remake", dependencies = TRUE)(run install.packages("devtools") to install devtools if needed.)
The remake package also depends on storr, install it like this:
devtools::install_github("richfitz/storr", 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()To replicate the analyses, it is nescessary to install fishflux through GitHub. To do so, follow instructions in this link.
Then, to generate all figures and tables, simply run:
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 all the combined Bayesian models in this paper will take a several hours (up to a day) 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')R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] egg_0.4.5 gridExtra_2.3 tidybayes_2.0.1 knitr_1.28 rmarkdown_2.1 plyr_1.8.5 png_0.1-7 fishualize_0.2.0
[9] dplyr_0.8.5 purrr_0.3.3 ggplot2_3.3.0 fishflux_0.0.0.9001 Rcpp_1.0.4.6
loaded via a namespace (and not attached):
[1] lattice_0.20-40 tidyr_1.0.2 prettyunits_1.1.1 ps_1.3.2 assertthat_0.2.1 digest_0.6.25 R6_2.4.1
[8] stats4_3.6.2 coda_0.19-3 evaluate_0.14 httr_1.4.1 pillar_1.4.3 rlang_0.4.5 rstudioapi_0.11
[15] callr_3.4.3 labeling_0.3 stringr_1.4.0 loo_2.2.0 munsell_0.5.0 xfun_0.12 compiler_3.6.2
[22] rstan_2.19.3 pkgconfig_2.0.3 pkgbuild_1.0.6 htmltools_0.4.0 rstantools_2.0.0.9000 tidyselect_1.0.0 tibble_3.0.0
[29] arrayhelpers_1.1-0 codetools_0.2-16 matrixStats_0.55.0 fansi_0.4.1 remake_0.3.0 crayon_1.3.4 withr_2.1.2
[36] gtable_0.3.0 lifecycle_0.2.0 magrittr_1.5 storr_1.2.1 StanHeaders_2.19.2 scales_1.1.0 cli_2.0.2
[43] stringi_1.4.6 farver_2.0.3 ellipsis_0.3.0 vctrs_0.2.4 cowplot_1.0.0 tools_3.6.2 forcats_0.4.0
[50] svUnit_0.7-12 glue_1.4.0 processx_3.4.2 parallel_3.6.2 yaml_2.2.1 inline_0.3.15 colorspace_1.4-1
- on the project main page on GitHub, click on the green button
clone or downloadand then click onDownload ZIP
- Please report any issues or bugs.