Package: ATNr 1.1.2

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_1.1.2.tar.gz
ATNr_1.1.2.tar.gz(r-4.7-arm64)ATNr_1.1.2.tar.gz(r-4.7-x86_64)ATNr_1.1.2.tar.gz(r-4.6-arm64)ATNr_1.1.2.tar.gz(r-4.6-x86_64)
ATNr_1.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ATNr/json (API)

# Install 'ATNr' in R:
install.packages('ATNr', repos = c('https://cran.r-universe.dev', '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

3.40 score 25 scripts 461 downloads 17 exports 9 dependencies

Last updated from:5d8065d2ae. Checks:4 NOTE, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE177
linux-devel-x86_64NOTE156
source / vignettesERROR262
linux-release-arm64NOTE193
linux-release-x86_64NOTE175
wasm-releaseOK145

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

model descriptions
Unscaled version | Scaled version | Unscaled version with nutrient dynamic
Rendered frommodel_descriptions.ltxusingR.rsp::tex

Last update: 2025-11-15
Started: 2022-02-07

ATNr
A quick go through | Creating a model | Generating synthetic food webs (if needed) | Creating a specific ATN model | Running the population dynamics | The food web generative functions | Examples | effect of temperature on species persistence | Effect of predator-prey body mass ratio and temperature on species persistence | Paradox of enrichment | Common mistakes, things to not do | Not updating model parameters properly in the model object | Updating key parameters without creating a new model object | Changing the dimensions of vectors and matrix fields in a model object without doing it consistently. | Shallow copying models | Modifying a model object in a *apply function
Rendered fromATNr.Rmdusingknitr::rmarkdown

Last update: 2025-04-28
Started: 2022-02-01

Readme and manuals

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