Run Allometric Trophic Networks Models

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Documentation for package ‘ATNr’ version 1.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.filter_extinct	Filter Extinct Species
create_Lmatrix	Make L matrix
create_matrix_parameter	Make parameter matrix
create_model_Scaled	Initialize an ATN model, following Delmas et al. 2017, Methods in Ecology and Evolution
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
create_niche_model	Create a food web based on the niche model
initialise_default_Scaled	Default parameters for the scaled version of ATN as in Delmas et al. 2016
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
is_connected	Detect whether a food web is composed of several disconnected sub-networks
jacobian	Estimate the Jacobian matrix of a ODE system
lsoda_wrapper	Wrapper for lsoda
plot_odeweb	Plot food web dynamics
remove_species	Function to remove species from a model class
run_checks	Run checks on model parameters
Scaled	Store parameters and functions associated to the scaled version of ATN
Scaled_loops	Store parameters and functions associated to the scaled version of ATN
schneider	Default parameters as in Schneider et al. (2016)
sort_input	Sort custom input
TroLev	Calculate trophic level of species
Unscaled	Store parameters and functions associated to the unscaled version of ATN
Unscaled_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
Unscaled_nuts_loops	Store parameters and functions associated to the unscaled version of ATN