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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.

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Version

Install

install.packages('ATNr')

Monthly Downloads

368

Version

1.1.2

License

GPL (>= 2)

Maintainer

Benoit Gauzens

Last Published

November 15th, 2025

Functions in ATNr (1.1.2)

lsoda_wrapper

Wrapper for lsoda
initialise_default_Unscaled

Default parameters for the scaled version of ATN as in Binzer et al. 2016, with updates from Gauzens et al. 2020
schneider

Default parameters as in Schneider et al. (2016)
sort_input

Sort custom input
.filter_extinct

Filter Extinct Species
run_checks

Run checks on model parameters
is_connected

Detect whether a food web is composed of several disconnected sub-networks
remove_species

Function to remove species from a model class
create_niche_model

Create a food web based on the niche model
jacobian

Estimate the Jacobian matrix of a ODE system
create_model_Unscaled_nuts

Initialize an ATN model, following Schneider et al. 2016, Nature Communication
Scaled

Store parameters and functions associated to the scaled version of ATN
Unscaled_nuts_loops

Store parameters and functions associated to the unscaled version of ATN
Unscaled_nuts

Store parameters and functions associated to the unscaled version of ATN including nutrient dynamics
create_Lmatrix

Make L matrix
create_model_Scaled

Initialize an ATN model, following Delmas et al. 2017, Methods in Ecology and Evolution
create_matrix_parameter

Make parameter matrix
Scaled_loops

Store parameters and functions associated to the scaled version of ATN
TroLev

Calculate trophic level of species
Unscaled

Store parameters and functions associated to the unscaled version of ATN
initialise_default_Unscaled_nuts

Default model parameters as in Schneider et al. 2016
.remove_Scaled

Internal function to remove species from a Scaled model
Unscaled_loops

Store parameters and functions associated to the unscaled version of ATN
create_model_Unscaled

Initialize an ATN model, following Binzer et al. 2016, Global Change Biology
.remove_Unscaled

Internal function to remove species from a Unscaled model
.remove_Unscaled_nuts

Internal function to remove species from a Unscaled_nuts model
plot_odeweb

Plot food web dynamics
initialise_default_Scaled

Default parameters for the scaled version of ATN as in Delmas et al. 2016