Package: ATNr 1.1.0

Benoit Gauzens

ATNr: Run Allometric Trophic Networks Models

Implements the differential equations associated to different versions of Allometric Trophic Models (ATN) to estimate the temporal dynamics of species biomasses in food webs. It offers several features to generate synthetic food webs and to parametrise models as well as a wrapper to the ODE solver deSolve.

Authors:Benoit Gauzens [cre, aut], Emilio Berti [aut]

ATNr_1.1.0.tar.gz
ATNr_1.1.0.tar.gz(r-4.5-noble)ATNr_1.1.0.tar.gz(r-4.4-noble)
ATNr_1.1.0.tgz(r-4.4-emscripten)ATNr_1.1.0.tgz(r-4.3-emscripten)
ATNr.pdf |ATNr.html✨
ATNr/json (API)
NEWS

# Install 'ATNr' in R:
install.packages('ATNr', repos = 'https://cloud.r-project.org')
Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • schneider - Default parameters as in Schneider et al.

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblascppopenmp

3.00 score 335 downloads 17 exports 9 dependencies

Last updated 2 years agofrom:6aa6aa06e5. Checks:1 ERROR, 2 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesFAILMar 24 2025
R-4.5-linux-x86_64NOTEMar 24 2025
R-4.4-linux-x86_64NOTEMar 24 2025

Exports:create_Lmatrixcreate_matrix_parametercreate_model_Scaledcreate_model_Unscaledcreate_model_Unscaled_nutscreate_niche_modelinitialise_default_Scaledinitialise_default_Unscaledinitialise_default_Unscaled_nutsis_connectedjacobianlsoda_wrapperplot_odewebremove_speciesrun_checkssort_inputTroLev

Dependencies:deSolvedigestR.cacheR.methodsS3R.ooR.rspR.utilsRcppRcppArmadillo

ATNr

Rendered fromATNr.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2023-09-04
Started: 2022-02-01

model descriptions

Rendered frommodel_descriptions.ltxusingR.rsp::texon Mar 24 2025.

Last update: 2023-09-04
Started: 2022-02-07

Citation

To cite package ‘ATNr’ in publications use:

Gauzens B, Berti E (2023). ATNr: Run Allometric Trophic Networks Models. R package version 1.1.0, https://CRAN.R-project.org/package=ATNr.

Corresponding BibTeX entry: 

  @Manual{,
    title = {ATNr: Run Allometric Trophic Networks Models},
    author = {Benoit Gauzens and Emilio Berti},
    year = {2023},
    note = {R package version 1.1.0},
    url = {https://CRAN.R-project.org/package=ATNr},
  }

Readme and manuals

Beta version of the ATNr package that propose solutions to estimate populations dynamics in food webs with Allometric Trophic Networks

To do

There might be some opportunities to optimise execution time of the armadillo models, especially regarding bracketing of expressions based on matrix algebra. Not important to investigate, but could be nice to have a look at some point. Need a good knowledge of the approach though

Some parameters now use the same values for all nodes it refers to. Maybe we should change that to vectors to make them node specific and having something more general:

  • In Schneider: D (turnover rate of the nutrients) is a single value common to all nutrient pools.
  • In all models, interspecific competition is a scalar.

Help Manual

Help pageTopics
Filter Extinct Species.filter_extinct
Make L matrixcreate_Lmatrix
Make parameter matrixcreate_matrix_parameter
Initialize an ATN model, following Delmas et al. 2017, Methods in Ecology and Evolutioncreate_model_Scaled
Initialize an ATN model, following Binzer et al. 2016, Global Change Biologycreate_model_Unscaled
Initialize an ATN model, following Schneider et al. 2016, Nature Communicationcreate_model_Unscaled_nuts
Create a food web based on the niche modelcreate_niche_model
Default parameters for the scaled version of ATN as in Delmas et al. 2016initialise_default_Scaled
Default parameters for the scaled version of ATN as in Binzer et al. 2016, with updates from Gauzens et al. 2020initialise_default_Unscaled
Default model parameters as in Schneider et al. 2016initialise_default_Unscaled_nuts
Detect whether a food web is composed of several disconnected sub-networksis_connected
Estimate the Jacobian matrix of a ODE systemjacobian
Wrapper for lsodalsoda_wrapper
Plot food web dynamicsplot_odeweb
Function to remove species from a model classremove_species
Run checks on model parametersrun_checks
Store parameters and functions associated to the scaled version of ATNScaled
Store parameters and functions associated to the scaled version of ATNScaled_loops
Default parameters as in Schneider et al. (2016)schneider
Sort custom inputsort_input
Calculate trophic level of speciesTroLev
Store parameters and functions associated to the unscaled version of ATNUnscaled
Store parameters and functions associated to the unscaled version of ATNUnscaled_loops
Store parameters and functions associated to the unscaled version of ATN including nutrient dynamicsUnscaled_nuts
Store parameters and functions associated to the unscaled version of ATNUnscaled_nuts_loops