.filter_extinct         Filter Extinct Species
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
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
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
schneider               Default parameters as in Schneider et al.
                        (2016)
sort_input              Sort custom input
