.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 |