# Run Allometric Trophic Networks Models

## Documentation for package ‘ATNr’ version 1.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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