fishflux: A tool to model elemental fluxes in fishes
Overview
The fishflux package provides a tool to model fluxes of C (carbon), N
(nitrogen) and P (phosphorus) in fishes. It combines basic principles
from elemental stoichiometry and metabolic theory. The package offers a
user-friendly interface to apply the model. fishflux is ideal for fish
ecologists wishing to predict ingestion, egestion and excretion to study
fluxes of elements.
Main assets:
- Provides function to model fluxes of carbon, nitrogen and phosphorus for fishes
- Allows for the estimation of uncertainty, depending on the uncertainty of the input parameters
- Provides some functions to help find parameters as inputs for the model
- Provides functions to extract and illustrate results
Theoretical framework
For more information on the theoretical framework behind
cnp_model_mcmc(), check out the
paper.
Installing and loading fishflux
First, make sure your R version is 3.4 or higher and you have rtools installed.
CRAN
fishflux is now available on CRAN:
install.packages("fishflux")
library(fishflux)Note that if you are using a linux operating system, you still need a c++ compiler to install the package from CRAN. If you are using Windows or Mac, you can install a pre-compiled binary version and thus don’t need a compiler.
GitHub
Please follow these steps to install the development version of the
package from Github. fishflux uses Markov Chain Monte Carlo
simulations provided by
stan.
Therefore, the first step is to install
rstan.
It’s important to closely follow all the steps described on the page
depending on your operating system, because rstan requires a functioning
C++ compiler. Furthermore, fishflux depends on the package
rstantools version 2.0.0 or higher. This means that if you already
have an older version of rstantools installed, you will have to
reinstall it, prior to the installation of fishflux.
Once you have your c++ compiler set up correctly, you are ready to install it from GitHub.
install.packages("devtools")
devtools::install_github("nschiett/fishflux", dependencies=TRUE)
library(fishflux)Downloaded package file
Another option is to download the source file available on github here.
install.packages(path_to_fishflux_file, repos = NULL, type = "source")
library(fishflux)Documentation
See package vignette for an introduction and help pages. For more information on the theoretical model see here.
License
This R package is provided for use under the MIT License (MIT) by the author.
Citation
When using the bioenergetic model featured in this package, please cite:
Schiettekatte, NMD, Barneche, DR, Villéger, S, et al. Nutrient limitation, bioenergetics and stoichiometry: A new model to predict elemental fluxes mediated by fishes. Funct Ecol. 2020; 34: 1857– 1869. https://doi.org/10.1111/1365-2435.13618