Package: EcoDiet 2.0.1

Pierre-Yves Hernvann

EcoDiet: Estimating a Diet Matrix from Biotracer and Stomach Content Data

Biotracers and stomach content analyses are combined in a Bayesian hierarchical model to estimate a probabilistic topology matrix (all trophic link probabilities) and a diet matrix (all diet proportions). The package relies on the JAGS software and the 'jagsUI' package to run a Markov chain Monte Carlo approximation of the different variables.

Authors:Pierre-Yves Hernvann [cre, aut], Didier Gascuel [aut], Dorothee Kopp [aut], Marianne Robert [aut], Jerome Guitton [aut], Etienne Rivot [aut], Heloise Thero [aut]

EcoDiet_2.0.1.tar.gz
EcoDiet_2.0.1.tar.gz(r-4.5-noble)EcoDiet_2.0.1.tar.gz(r-4.4-noble)
EcoDiet_2.0.1.tgz(r-4.4-emscripten)EcoDiet_2.0.1.tgz(r-4.3-emscripten)
EcoDiet.pdf |EcoDiet.html✨
EcoDiet/json (API)
NEWS

# Install 'EcoDiet' in R:
install.packages('EcoDiet', repos = 'https://cloud.r-project.org')

Bug tracker:https://github.com/pyhernvann/ecodiet/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

jagscpp

3.18 score 256 downloads 7 exports 50 dependencies

Last updated 1 years agofrom:ccbbaba659. Checks:3 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKMar 21 2025
R-4.5-linuxOKMar 21 2025
R-4.4-linuxOKMar 21 2025

Exports:diagnose_modelplot_dataplot_priorplot_resultspreprocess_datarun_modelwrite_model

Dependencies:clicodacolorspacecpp11crayondplyrfansifarverforcatsgenericsGGallyggmcmcggplot2ggstatsgluegtablehmsisobandjagsUIlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkpillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcpprjagsrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Introduction - How to use EcoDiet

Heloise Thero, Pierre-Yves Hernvann

Rendered fromintroduction_EcoDiet.Rmdusingknitr::rmarkdownon Mar 21 2025.

Last update: 2024-03-26
Started: 2020-03-05

EcoDiet explored on a realistic example

Heloise Thero, Pierre-Yves Hernvann

Rendered fromrealistic_example.Rmdusingknitr::rmarkdownon Mar 21 2025.

Last update: 2024-03-26
Started: 2020-03-05

How to deal with convergence problems

Heloise Thero, Pierre-Yves Hernvann

Rendered fromconvergence_problems.Rmdusingknitr::rmarkdownon Mar 21 2025.

Last update: 2023-01-06
Started: 2020-03-05

Citation

To cite EcoDiet in publications use:

Pierre-Yves Hernvann, Didier Gascuel, Dorothee Kopp, Marianne Robert, Etienne Rivot (2022). EcoDiet: A hierarchical Bayesian model to combine stomach, biotracer, and literature data into diet matrix estimation.

To know more about the EcoDiet project, go see https://www.researchgate.net/project/EcoDiet-model-Incorporating-multiple-data-types-into-the-estimation-of-diet-matrices

Corresponding BibTeX entry: 

  @Article{,
    title = {EcoDiet: A hierarchical Bayesian model to combine stomach,
      biotracer, and literature data into diet matrix estimation},
    author = {Pierre Yves Hernvann and Didier Gascuel and Dorothee Kopp
      and Marianne Robert and Etienne Rivot},
    journal = {Ecological Applications},
    year = {2022},
    volume = {32},
    number = {2},
    pages = {e2521},
    url = {https://doi.org/10.1002/eap.2521},
  }

Readme and manuals

EcoDiet

Description

The EcoDiet package estimates a probabilistic topology matrix (all trophic link probabilities) and a diet matrix (all diet proportions) for food webs by combining biotracer and stomach content analyses in a Bayesian hierarchical model.

The full model and its application to a real dataset are described in Hernvann et al. (in press). When using EcoDiet, please cite both Hernvann et al. and the package (citation("EcoDiet")):

Hernvann, P. Y., Gascuel, D., Kopp, D., Robert, M., & Rivot, E. (2022). EcoDiet: A hierarchical Bayesian model to combine stomach, biotracer, and literature data into diet matrix estimation. Ecological Applications, 32(2), e2521.

Théro, H., Rivot, E., Robert, M., Guitton, J., Kopp, D., Gascuel, D., et Hernvann, P.Y. (2020) EcoDiet. R package. doi: 10.5281/zenodo.4081537

To access the citation and DOI of the latest development version, check the Zenodo repository

Recent updates: The latest updates of the `EcoDiet` package (> v 2.0.0) include major differences with the original version (v 1.*...*). Please read the **NEWS** file for more details.

Using EcoDiet

R installation

EcoDiet is a R package so, first and foremost, you should download and install/update R.

JAGS installation

EcoDiet relies on the JAGS software, so you also need to download and install/update JAGS. You should install the last version of JAGS so that your model will run at maximal speed.

For Windows users

Download JAGS from here, then follow the indications.

For MacOS and Linux users

Try this command if you are on MacOS:

sudo brew update
sudo brew install jags

or this command if you are on Linux:

sudo apt-get update
sudo apt-get install jags

If you get an error message during installation, check this post from Yu-Sung Su's blog.

EcoDiet installation

To download the EcoDiet package from GitHub, you need to use the install_github function from the devtools package to load it. First, install the devtools package:

install.packages("devtools")

Once devtools has been installed, you can load the EcoDiet package:

devtools::install_github("pyhernvann/EcoDiet", build_vignettes = TRUE, dependencies = TRUE)

Since the 6th of May 2020 EcoDiet is also available on the CRAN. You can directly install it from R and load it:

install.packages("EcoDiet")

library("EcoDiet")
Learn how to use EcoDiet

Several vignettes explain how to use the package. Run the following in R and click on the HTML button next to "1. Introduction - How to use EcoDiet":

browseVignettes("EcoDiet")

Or use this if the former does not work:

vignette("introduction_EcoDiet")