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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

694

Version

1.1.0

License

GPL (>= 2)

Maintainer

Benoit Gauzens

Last Published

September 4th, 2023

Functions in ATNr (1.1.0)

remove_species

Function to remove species from a model class
lsoda_wrapper

Wrapper for lsoda
jacobian

Estimate the Jacobian matrix of a ODE system
schneider

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

Sort custom input
is_connected

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

Plot food web dynamics
run_checks

Run checks on model parameters
initialise_default_Scaled

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

Make parameter matrix
Scaled

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

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

Calculate trophic level of species
Unscaled_loops

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

Make L matrix
Scaled_loops

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

Store parameters and functions associated to the unscaled 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
.remove_Scaled

Internal function to remove species from a Scaled model
initialise_default_Unscaled

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

Default model parameters as in Schneider et al. 2016
create_model_Unscaled

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

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

Internal function to remove species from a Unscaled model
.remove_Unscaled_nuts

Internal function to remove species from a Unscaled_nuts model
create_niche_model

Create a food web based on the niche model
.filter_extinct

Filter Extinct Species