Run Allometric Trophic Networks Models


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Documentation for package ‘ATNr’ version 1.0.1

Help Pages

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. 201, 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
Joacobian 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