Model API

The model API combines constructor functions with two wrapper classes: MizerParams for configured models and MizerSim for projection results.

Constructors

  • new_community_params()
  • new_multispecies_params()
  • new_single_species_params()
  • read_params()

Common MizerParams Methods

  • state inspection: initial_n(), initial_n_resource(), biomass(), abundance(), ssb()
  • size-resolved rates: pred_rate(), pred_mort(), feeding_level(), diet(), trophic_level(), pred_kernel()
  • indicators: mean_weight(), mean_max_weight(), proportion_of_large_fish(), community_slope()
  • parameter editing: set_interaction(), set_resource(), set_initial_values(), set_metadata(), set_reproduction(), set_search_volume(), set_max_intake_rate(), set_metabolic_rate(), set_pred_kernel()
  • steady-state workflows: project_to_steady(), steady(), steady_single_species()
  • simulation: project()

Common MizerSim Methods

  • projection summaries: times(), biomass(), abundance(), yield_(), ssb()
  • state and rate diagnostics: initial_n(), initial_n_resource(), pred_rate(), pred_mort(), feeding_level(), f_mort(), f_mort_gear()
  • ecological summaries: diet(), growth_curves(), trophic_level(), trophic_level_by_species()

Editing Workflow

The editing methods mirror the mizer design: they do not mutate the current object in place. Instead they return a new MizerParams wrapper with the updated R object inside it.

Typical usage looks like:

interaction = params.interaction_matrix()
interaction.iloc[0, 1] = 0.0

updated = params.set_interaction(interaction)
sim = updated.project(t_max=2, dt=0.1, t_save=1, effort=0, progress_bar=False)

Steady-State Workflow

The wrapper exposes both lower-level and higher-level steady-state helpers:

  • project_to_steady() searches for convergence under the current dynamics
  • steady() applies the more opinionated mizer::steady() workflow
  • steady_single_species() solves selected species against the current rates

Filtering And Return Types

Many summary methods accept arguments such as species=, min_w=, max_w=, min_l=, and max_l=. In general:

  • time-by-species summaries return pandas.DataFrame
  • spectra and size-resolved arrays return xarray.DataArray
  • one-dimensional indicators return float or pandas.Series

Generated API Pages

For full signatures, docstrings, and class reference pages, see: