Index

A

acc_external_input_vector() (CompartmentalSystems.discrete_model_run_with_gross_fluxes.DiscreteModelRunWithGrossFluxes method) acc_external_output_vector() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) acc_gross_external_input_vector() (CompartmentalSystems.discrete_model_run_with_gross_fluxes.DiscreteModelRunWithGrossFluxes method) (CompartmentalSystems.model_run.ModelRun method) (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) acc_gross_external_input_vector_Delta_14C() (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method) acc_gross_external_output_vector() (CompartmentalSystems.discrete_model_run_with_gross_fluxes.DiscreteModelRunWithGrossFluxes method) (CompartmentalSystems.model_run.ModelRun method) (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method) acc_gross_external_output_vector_Delta_14C() (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method) acc_gross_internal_flux_matrix() (CompartmentalSystems.discrete_model_run_with_gross_fluxes.DiscreteModelRunWithGrossFluxes method) (CompartmentalSystems.model_run.ModelRun method) (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) acc_gross_internal_flux_matrix_Delta_14C() (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method) acc_internal_flux_matrix() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) acc_net_external_input_vector() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) (CompartmentalSystems.model_run.ModelRun method) (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) acc_net_external_input_vector_Delta_14C() (CompartmentalSystems.discrete_model_run_14C.DiscreteModelRun_14C method) (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method) acc_net_external_output_vector() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) (CompartmentalSystems.discrete_model_run_14C.DiscreteModelRun_14C method) (CompartmentalSystems.model_run.ModelRun method) (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method)

acc_net_external_output_vector_Delta_14C() (CompartmentalSystems.discrete_model_run_14C.DiscreteModelRun_14C method) (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method) acc_net_internal_flux_matrix() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) (CompartmentalSystems.model_run.ModelRun method) (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) acc_net_internal_flux_matrix_Delta_14C() (CompartmentalSystems.discrete_model_run_14C.DiscreteModelRun_14C method) (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method) add_constant_age_distribution_surface_plotly() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) add_line_to_density_plot_plotly() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) add_xhist_data_to_scatter() (in module CompartmentalSystems.bins.plot_helpers) advanced() (CompartmentalSystems.bins.CompatibleTsTpMassFieldsPerPool.CompatibleTsTpMassFieldsPerPool method) age_densities() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) age_densities_1_single_value_func() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) age_densities_2_single_value_func() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) age_densities_single_value_func() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) age_moment_system() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method) age_moment_vector() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) age_moment_vector_from_densities() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) age_moment_vector_semi_explicit() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) age_quantiles_at_time() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) all_fluxes() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method) apply_to_forward_transit_time_simulation() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) apply_to_forward_transit_time_simulation_its() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) arrange_subplots() (in module CompartmentalSystems.helpers_reservoir) array_integration_by_ode() (in module CompartmentalSystems.helpers_reservoir) array_integration_by_values() (in module CompartmentalSystems.helpers_reservoir) array_quad_result() (in module CompartmentalSystems.helpers_reservoir)

B

B_func() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) B_pwc() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method) backward_transit_time_density() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) backward_transit_time_density_single_value_func() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) backward_transit_time_moment() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method)

backward_transit_time_moment_from_density() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) block_solve() (CompartmentalSystems.BlockIvp.BlockIvp method) block_solve_functions() (CompartmentalSystems.BlockIvp.BlockIvp method) BlockIvp (class in CompartmentalSystems.BlockIvp) blockIvp() (CompartmentalSystems.BlockOde.BlockOde method) BlockOde (class in CompartmentalSystems.BlockOde) boundaries() (CompartmentalSystems.pwc_model_run.PWCModelRun property) build_rhss() (CompartmentalSystems.BlockIvp.BlockIvp class method)

C

Cache (class in CompartmentalSystems.Cache) cc() (in module CompartmentalSystems.bins.plot_helpers) check_block_exists() (CompartmentalSystems.BlockIvp.BlockIvp method) (CompartmentalSystems.BlockOde.BlockOde method) check_parameter_dict_complete() (in module CompartmentalSystems.helpers_reservoir) combine_pools_and_system_values() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) compartmental_matrix() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) CompartmentalSystems module CompartmentalSystems.bins module CompartmentalSystems.bins.CompatibleTsTpMassFieldsPerPool module CompartmentalSystems.bins.density_algorithm module CompartmentalSystems.bins.FieldsPerTimeStep module CompartmentalSystems.bins.getsizeof module CompartmentalSystems.bins.gv module CompartmentalSystems.bins.plot_helpers module CompartmentalSystems.bins.TimeBin module CompartmentalSystems.bins.TimeField module CompartmentalSystems.bins.TimeMassField module CompartmentalSystems.bins.TimeStep module CompartmentalSystems.bins.TimeStepIterator module CompartmentalSystems.bins.TimeStepPlotter module CompartmentalSystems.bins.TsMassField module CompartmentalSystems.bins.TsMassFieldsPerTimeStep module CompartmentalSystems.bins.TstBin module CompartmentalSystems.bins.TsTpBin module CompartmentalSystems.bins.TsTpDeathRateField module CompartmentalSystems.bins.TsTpField module CompartmentalSystems.bins.TsTpMassField module CompartmentalSystems.bins.TsTpMassFields module CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep module CompartmentalSystems.bins.TsTpMassFieldsPerTimeStep module CompartmentalSystems.BlockIvp module

CompartmentalSystems.BlockOde module CompartmentalSystems.Cache module CompartmentalSystems.cs_plotter module CompartmentalSystems.discrete_model_run module CompartmentalSystems.discrete_model_run_14C module CompartmentalSystems.discrete_model_run_with_gross_fluxes module CompartmentalSystems.example_smooth_model_runs module CompartmentalSystems.example_smooth_reservoir_models module CompartmentalSystems.helpers_reservoir module CompartmentalSystems.model_run module CompartmentalSystems.myOdeResult module CompartmentalSystems.picklegzip module CompartmentalSystems.pwc_model_run module CompartmentalSystems.pwc_model_run_14C module CompartmentalSystems.pwc_model_run_fd module CompartmentalSystems.smooth_model_run module, [1] CompartmentalSystems.smooth_model_run_14C module CompartmentalSystems.smooth_reservoir_model module, [1] CompartmentalSystems.smooth_reservoir_model_14C module CompartmentalSystems.start_distributions module, [1] CompatibleTsTpMassFieldsPerPool (class in CompartmentalSystems.bins.CompatibleTsTpMassFieldsPerPool) compute_fixedpoint_numerically() (in module CompartmentalSystems.start_distributions) compute_start_age_moments() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) compute_start_m_factorial_moment() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) const_of_t_maker() (in module CompartmentalSystems.helpers_reservoir) create_B_generic() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method) create_srm_generic() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method) create_u_generic() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method) critics() (in module CompartmentalSystems.example_smooth_model_runs) (in module CompartmentalSystems.example_smooth_reservoir_models) CSPlotter (class in CompartmentalSystems.cs_plotter) cumulative_backward_transit_time_distribution_single_value() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) cumulative_forward_transit_time_distribution_single_value_func() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) cumulative_pool_age_distributions_single_value() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) cumulative_system_age_distribution_single_value() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) custom_lru_cache_wrapper() (in module CompartmentalSystems.helpers_reservoir)

D

decay_symbol (CompartmentalSystems.smooth_reservoir_model_14C.SmoothReservoirModel_14C attribute) default_data_type() (in module CompartmentalSystems.bins.gv) default_plot_args() (CompartmentalSystems.bins.TsMassField.TsMassField method) (CompartmentalSystems.bins.TsTpField.TsTpField method) density_values() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) density_values_for_pools() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) deprecation_warning() (in module CompartmentalSystems.helpers_reservoir) DiscreteModelRun (class in CompartmentalSystems.discrete_model_run) DiscreteModelRun_14C (class in CompartmentalSystems.discrete_model_run_14C) DiscreteModelRunWithGrossFluxes (class in CompartmentalSystems.discrete_model_run_with_gross_fluxes)

distribution_quantile() (CompartmentalSystems.smooth_model_run.SmoothModelRun static method) distribution_quantiles() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) DMRError, [1] draw_rv() (in module CompartmentalSystems.helpers_reservoir) dts() (CompartmentalSystems.discrete_model_run.DiscreteModelRun property) (CompartmentalSystems.model_run.ModelRun property) (CompartmentalSystems.pwc_model_run.PWCModelRun property) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD property) (CompartmentalSystems.smooth_model_run.SmoothModelRun property) dump() (in module CompartmentalSystems.picklegzip)

E

emanuel() (in module CompartmentalSystems.example_smooth_reservoir_models) emanuel_1() (in module CompartmentalSystems.example_smooth_model_runs) end_time_from_phi_ind() (CompartmentalSystems.Cache.Cache method) Error, [1], [2], [3], [4], [5], [6] external_death_rate_maker() (in module CompartmentalSystems.bins.TimeStepIterator) external_input_flux_funcs() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) external_input_flux_funcss() (CompartmentalSystems.pwc_model_run.PWCModelRun method) external_input_maker() (in module CompartmentalSystems.bins.TimeStepIterator) external_input_vector() (CompartmentalSystems.smooth_model_run.SmoothModelRun property) external_input_vector_func() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method)

external_inputs() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) external_losses() (CompartmentalSystems.bins.TsTpMassFields.TsTpMassFieldsPerPool method) external_output_flux_funcs() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method) external_output_flux_funcss() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) external_output_vector() (CompartmentalSystems.discrete_model_run_14C.DiscreteModelRun_14C property) (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C property) (CompartmentalSystems.smooth_model_run.SmoothModelRun property) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C property) external_outputs() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property)

F

F() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) F_Delta_14C() (in module CompartmentalSystems.helpers_reservoir) f_of_t_maker() (in module CompartmentalSystems.helpers_reservoir) factor_out_from_matrix() (in module CompartmentalSystems.helpers_reservoir) fake_discretized_Bs() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) fake_gross_discretized_output() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) fake_net_discretized_output() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) FieldsPerTimeStep (class in CompartmentalSystems.bins.FieldsPerTimeStep) figure() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method) flux_dict_string() (in module CompartmentalSystems.helpers_reservoir) forward_transit_time_density_func() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) forward_transit_time_density_single_value_func() (CompartmentalSystems.smooth_model_run.SmoothModelRun method)

free_symbols() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) from_B_u() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel class method) from_Bs_and_net_Us() (CompartmentalSystems.discrete_model_run.DiscreteModelRun class method) from_Bs_and_us() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method) from_file() (CompartmentalSystems.Cache.Cache class method) from_fluxes() (CompartmentalSystems.discrete_model_run.DiscreteModelRun class method) from_gross_fluxes() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method) from_ode_reservoir_model_run() (CompartmentalSystems.bins.TimeStepIterator.TimeStepIterator class method) from_SmoothModelRun() (CompartmentalSystems.discrete_model_run.DiscreteModelRun class method) (CompartmentalSystems.discrete_model_run_with_gross_fluxes.DiscreteModelRunWithGrossFluxes class method) from_state_variable_indexed_fluxes() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel class method) from_time_step_iterator() (CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep.TsTpMassFieldsPerPoolPerTimeStep class method) func_set (CompartmentalSystems.smooth_model_run.SmoothModelRun attribute) func_subs() (in module CompartmentalSystems.helpers_reservoir) function_expressions() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property)

G

gains() (CompartmentalSystems.bins.TsTpMassFields.TsTpMassFieldsPerPipe property) (in module CompartmentalSystems.bins.density_algorithm)

generalized_inverse_CDF() (in module CompartmentalSystems.helpers_reservoir) get_sub_t_spans() (in module CompartmentalSystems.myOdeResult)

H

has_pw() (in module CompartmentalSystems.helpers_reservoir)

I

indexed_color() (in module CompartmentalSystems.bins.gv) indexed_filled_marker() (in module CompartmentalSystems.bins.gv) initialize_state_transition_operator_cache() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) input_fluxes (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel attribute) integrate_array_func_for_nested_boundaries() (in module CompartmentalSystems.helpers_reservoir) internal_death_rate_maker() (in module CompartmentalSystems.bins.TimeStepIterator) internal_flux_funcs() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) internal_flux_funcss() (CompartmentalSystems.pwc_model_run.PWCModelRun method)

internal_fluxes (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel attribute) internal_inputs() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) internal_losses() (CompartmentalSystems.bins.TsTpMassFields.TsTpMassFieldsPerPool method) internal_outputs() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) is_compartmental() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) (in module CompartmentalSystems.helpers_reservoir) is_DiracDelta() (in module CompartmentalSystems.helpers_reservoir) is_linear() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) is_state_dependent() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method)

J

jacobian() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) (in module CompartmentalSystems.helpers_reservoir)

join_flux_funcss_rc() (CompartmentalSystems.pwc_model_run.PWCModelRun method) join_functions_rc() (CompartmentalSystems.pwc_model_run.PWCModelRun method)

L

lapm_for_steady_state() (in module CompartmentalSystems.start_distributions) legend() (CompartmentalSystems.cs_plotter.CSPlotter method) linearize() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) linearize_old() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) load() (in module CompartmentalSystems.picklegzip) load_csv() (in module CompartmentalSystems.helpers_reservoir) load_density_csv() (CompartmentalSystems.smooth_model_run.SmoothModelRun method)

load_from_file() (CompartmentalSystems.discrete_model_run.DiscreteModelRun class method) load_pools_and_system_densities_csv() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) load_pools_and_system_value_csv() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) load_state_transition_operator_cache() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) load_value_csv() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) loss() (CompartmentalSystems.bins.TsTpMassField.TsTpMassField method) losses() (in module CompartmentalSystems.bins.density_algorithm)

M

make_cut_func_set() (in module CompartmentalSystems.helpers_reservoir) matrix_plot() (CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep.TsTpMassFieldsPerPoolPerTimeStep method) matrix_plot3d() (CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep.TsTpMassFieldsPerPoolPerTimeStep method) max_number_of_Ts_entries() (CompartmentalSystems.bins.TsMassFieldsPerTimeStep.TsMassFieldsPerTimeStep property) max_Tp() (CompartmentalSystems.bins.TsTpField.TsTpField property) max_Ts() (CompartmentalSystems.bins.TimeField.TimeField property) (CompartmentalSystems.bins.TsMassFieldsPerTimeStep.TsMassFieldsPerTimeStep property) melt() (in module CompartmentalSystems.helpers_reservoir) MH_sampling() (in module CompartmentalSystems.helpers_reservoir) minimal() (in module CompartmentalSystems.example_smooth_reservoir_models) model (CompartmentalSystems.smooth_model_run.SmoothModelRun attribute) model() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD property) ModelRun (class in CompartmentalSystems.model_run) module CompartmentalSystems CompartmentalSystems.bins CompartmentalSystems.bins.CompatibleTsTpMassFieldsPerPool CompartmentalSystems.bins.density_algorithm CompartmentalSystems.bins.FieldsPerTimeStep CompartmentalSystems.bins.getsizeof CompartmentalSystems.bins.gv CompartmentalSystems.bins.plot_helpers CompartmentalSystems.bins.TimeBin CompartmentalSystems.bins.TimeField CompartmentalSystems.bins.TimeMassField CompartmentalSystems.bins.TimeStep CompartmentalSystems.bins.TimeStepIterator CompartmentalSystems.bins.TimeStepPlotter CompartmentalSystems.bins.TsMassField CompartmentalSystems.bins.TsMassFieldsPerTimeStep CompartmentalSystems.bins.TstBin CompartmentalSystems.bins.TsTpBin CompartmentalSystems.bins.TsTpDeathRateField CompartmentalSystems.bins.TsTpField CompartmentalSystems.bins.TsTpMassField CompartmentalSystems.bins.TsTpMassFields CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep CompartmentalSystems.bins.TsTpMassFieldsPerTimeStep CompartmentalSystems.BlockIvp CompartmentalSystems.BlockOde CompartmentalSystems.Cache CompartmentalSystems.cs_plotter CompartmentalSystems.discrete_model_run CompartmentalSystems.discrete_model_run_14C CompartmentalSystems.discrete_model_run_with_gross_fluxes CompartmentalSystems.example_smooth_model_runs CompartmentalSystems.example_smooth_reservoir_models CompartmentalSystems.helpers_reservoir CompartmentalSystems.model_run CompartmentalSystems.myOdeResult CompartmentalSystems.picklegzip CompartmentalSystems.pwc_model_run CompartmentalSystems.pwc_model_run_14C CompartmentalSystems.pwc_model_run_fd CompartmentalSystems.smooth_model_run, [1] CompartmentalSystems.smooth_model_run_14C CompartmentalSystems.smooth_reservoir_model, [1] CompartmentalSystems.smooth_reservoir_model_14C CompartmentalSystems.start_distributions, [1]

moments_from_densities() (CompartmentalSystems.smooth_model_run.SmoothModelRun static method) myhash() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) myOdeResult (class in CompartmentalSystems.myOdeResult)

N

net_Fs_from_discrete_Bs_and_xs() (in module CompartmentalSystems.helpers_reservoir) net_Rs_from_discrete_Bs_and_xs() (in module CompartmentalSystems.helpers_reservoir) net_Us() (CompartmentalSystems.discrete_model_run.DiscreteModelRun property) net_Us_from_discrete_Bs_and_xs() (in module CompartmentalSystems.helpers_reservoir) no_input_model() (CompartmentalSystems.smooth_model_run.SmoothModelRun property) (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) nonlinear_two_pool() (in module CompartmentalSystems.example_smooth_model_runs) (in module CompartmentalSystems.example_smooth_reservoir_models) nr_intervals() (CompartmentalSystems.pwc_model_run.PWCModelRun property) nr_pools() (CompartmentalSystems.discrete_model_run.DiscreteModelRun property) (CompartmentalSystems.model_run.ModelRun property) (CompartmentalSystems.pwc_model_run.PWCModelRun property) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD property) (CompartmentalSystems.smooth_model_run.SmoothModelRun property) (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property)

number_of_pools() (CompartmentalSystems.bins.CompatibleTsTpMassFieldsPerPool.CompatibleTsTpMassFieldsPerPool property) (CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep.TsTpMassFieldsPerPoolPerTimeStep property) number_of_Tp_entries() (CompartmentalSystems.bins.TsTpField.TsTpField property) number_of_Ts_entries() (CompartmentalSystems.bins.TimeField.TimeField property) numerical_function_from_expression() (in module CompartmentalSystems.helpers_reservoir) numerical_rhs() (in module CompartmentalSystems.helpers_reservoir) numerical_rhs_old() (in module CompartmentalSystems.helpers_reservoir) numsol_symbolic_system_old() (in module CompartmentalSystems.helpers_reservoir) numsol_symbolical_system() (in module CompartmentalSystems.helpers_reservoir)

O

output_fluxes (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel attribute) output_fluxes_corrected_for_decay() (CompartmentalSystems.smooth_reservoir_model_14C.SmoothReservoirModel_14C property)

output_rate_vector() (CompartmentalSystems.smooth_model_run.SmoothModelRun property) output_rate_vector_at_t() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) output_vector_func() (CompartmentalSystems.smooth_model_run.SmoothModelRun method)

P

parameter_dict (CompartmentalSystems.smooth_model_run.SmoothModelRun attribute) parse_input_function() (in module CompartmentalSystems.helpers_reservoir) pfile_C14Atm_NH() (in module CompartmentalSystems.pwc_model_run_14C) (in module CompartmentalSystems.smooth_model_run_14C) Phi() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) Phi_func() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) phi_ind() (CompartmentalSystems.Cache.Cache method) phi_tmax() (in module CompartmentalSystems.helpers_reservoir) plot() (CompartmentalSystems.bins.TimeBin.TimeBin method) (CompartmentalSystems.bins.TstBin.TstBin method) (CompartmentalSystems.bins.TsTpBin.TsTpBin method) (CompartmentalSystems.cs_plotter.Pool method) plot_3d_density_plotly() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_attributes() (in module CompartmentalSystems.model_run) plot_bins() (CompartmentalSystems.bins.TsMassField.TsMassField method) (CompartmentalSystems.bins.TsMassFieldsPerTimeStep.TsMassFieldsPerTimeStep method) (CompartmentalSystems.bins.TsTpField.TsTpField method) plot_contents_and_gains() (in module CompartmentalSystems.bins.TimeStepPlotter) plot_contents_and_losses() (in module CompartmentalSystems.bins.TimeStepPlotter) plot_external_gains() (in module CompartmentalSystems.bins.TimeStepPlotter) plot_external_input_fluxes() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_external_output_fluxes() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_figure_per_pipe() (in module CompartmentalSystems.bins.TimeStepPlotter) plot_figure_per_pool() (in module CompartmentalSystems.bins.TimeStepPlotter) plot_input_flux() (CompartmentalSystems.cs_plotter.Pool method) plot_internal_flux_to() (CompartmentalSystems.cs_plotter.Pool method) plot_internal_fluxes() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_internal_gains() (in module CompartmentalSystems.bins.TimeStepPlotter)

plot_mean_ages() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_mean_backward_transit_time() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_name() (CompartmentalSystems.cs_plotter.Pool method) plot_output_flux() (CompartmentalSystems.cs_plotter.Pool method) plot_pdfs() (CompartmentalSystems.bins.TimeStepPlotter.TimeStepPlotter method) plot_phase_plane() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_phase_planes() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_pools_and_fluxes() (CompartmentalSystems.cs_plotter.CSPlotter method) (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method) plot_solutions() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) plot_stocks_and_fluxes() (in module CompartmentalSystems.model_run) plot_surface() (CompartmentalSystems.bins.TsMassFieldsPerTimeStep.TsMassFieldsPerTimeStep method) (CompartmentalSystems.bins.TsTpField.TsTpField method) plot_system_age_distributions_as_surfaces() (CompartmentalSystems.bins.TsTpMassFieldsPerTimeStep.TsTpMassFieldsPerTimeStep method) plot_system_age_distributions_with_bins() (CompartmentalSystems.bins.TsTpMassFieldsPerTimeStep.TsTpMassFieldsPerTimeStep method) plot_total_contents() (CompartmentalSystems.bins.TsTpMassFieldsPerTimeStep.TsTpMassFieldsPerTimeStep method) Pool (class in CompartmentalSystems.cs_plotter) pool_age_densities_func() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) pool_age_densities_single_value() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) pool_age_distribution_quantiles_pool_by_ode() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) pool_age_distributions_quantiles() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) pool_age_distributions_quantiles_by_ode() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) port_controlled_Hamiltonian_representation() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method) print_quantile_error_statisctics() (in module CompartmentalSystems.helpers_reservoir) PWCModelRun (class in CompartmentalSystems.pwc_model_run) PWCModelRun_14C (class in CompartmentalSystems.pwc_model_run_14C) PWCModelRunFD (class in CompartmentalSystems.pwc_model_run_fd) PWCModelRunFDError

R

receive() (CompartmentalSystems.bins.TsTpMassField.TsTpMassField method) (CompartmentalSystems.bins.TsTpMassFields.TsTpMassFieldsPerPool method) receive_external() (CompartmentalSystems.bins.TsTpMassField.TsTpMassField method) (CompartmentalSystems.bins.TsTpMassFields.TsTpMassFieldsPerPool method) reconstruct_B() (CompartmentalSystems.discrete_model_run.DiscreteModelRun class method) reconstruct_B_surrogate() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method) reconstruct_Bs() (CompartmentalSystems.discrete_model_run.DiscreteModelRun class method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method)

reconstruct_Bs_without_xs() (CompartmentalSystems.discrete_model_run.DiscreteModelRun class method) reconstruct_from_fluxes_and_solution() (CompartmentalSystems.discrete_model_run.DiscreteModelRun class method) (CompartmentalSystems.discrete_model_run_with_gross_fluxes.DiscreteModelRunWithGrossFluxes class method) remove() (CompartmentalSystems.bins.TsTpMassFields.TsTpMassFieldsPerPool method) remove_loss() (CompartmentalSystems.bins.TsTpMassField.TsTpMassField method) reset() (CompartmentalSystems.bins.TimeStepIterator.TimeStepIterator method) resize() (CompartmentalSystems.bins.TsTpMassField.TsTpMassField method) rotated_access() (in module CompartmentalSystems.bins.gv)

S

save() (CompartmentalSystems.Cache.Cache method) save_csv() (in module CompartmentalSystems.helpers_reservoir) save_density_csv() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) save_pools_and_system_density_csv() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) save_pools_and_system_value_csv() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) save_state_transition_operator_cache() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) save_to_file() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) save_value_csv() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) set_limits() (CompartmentalSystems.bins.TsTpField.TsTpField method) set_ticks_and_labels() (CompartmentalSystems.bins.TsTpField.TsTpField method) shape() (CompartmentalSystems.bins.TimeField.TimeField property) shift() (CompartmentalSystems.bins.TsTpMassField.TsTpMassField method) (CompartmentalSystems.bins.TsTpMassFields.TimeMassFields method) (CompartmentalSystems.bins.TsTpMassFields.TsTpMassFieldsPerPool method) shifted() (CompartmentalSystems.bins.TsMassField.TsMassField method) single_pool_cartoon() (CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep.TsTpMassFieldsPerPoolPerTimeStep method) SinglePlotFigureHandler (class in CompartmentalSystems.bins.plot_helpers) singlePoolPyramid() (CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep.TsTpMassFieldsPerPoolPerTimeStep method) SmoothModelRun (class in CompartmentalSystems.smooth_model_run) SmoothModelRun_14C (class in CompartmentalSystems.smooth_model_run_14C) SmoothReservoirModel (class in CompartmentalSystems.smooth_reservoir_model) SmoothReservoirModel_14C (class in CompartmentalSystems.smooth_reservoir_model_14C) sol_funcs() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) sol_funcs_dict_by_name() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) sol_funcs_dict_by_symbol() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) sol_funcs_old() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) solve() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) (CompartmentalSystems.model_run.ModelRun method) (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) solve_Delta_14C() (CompartmentalSystems.discrete_model_run_14C.DiscreteModelRun_14C method) (CompartmentalSystems.pwc_model_run_14C.PWCModelRun_14C method) (CompartmentalSystems.smooth_model_run_14C.SmoothModelRun_14C method)

solve_func() (CompartmentalSystems.pwc_model_run.PWCModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method) solve_ivp_pwc() (in module CompartmentalSystems.myOdeResult) solve_old() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) solve_single_value_old() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) start_age_densities_func() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) start_age_distributions_from_empty_spinup() (in module CompartmentalSystems.start_distributions) start_age_distributions_from_steady_state() (in module CompartmentalSystems.start_distributions) start_age_distributions_from_zero_age_initial_content() (in module CompartmentalSystems.start_distributions) start_age_distributions_from_zero_initial_content() (in module CompartmentalSystems.start_distributions) start_age_moments_from_empty_spinup() (in module CompartmentalSystems.start_distributions) start_age_moments_from_steady_state() (in module CompartmentalSystems.start_distributions) start_age_moments_from_zero_initial_content() (in module CompartmentalSystems.start_distributions) start_time_from_phi_ind() (CompartmentalSystems.Cache.Cache method) start_values (CompartmentalSystems.smooth_model_run.SmoothModelRun attribute) start_values() (CompartmentalSystems.discrete_model_run.DiscreteModelRun property) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD property) state_variable_set() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel property) state_variables (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel attribute) state_vector (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel attribute) steady_states() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method) stochastic_collocation_transform() (in module CompartmentalSystems.helpers_reservoir) stride() (in module CompartmentalSystems.helpers_reservoir) subs() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method) sum_over_all_pool_ages() (CompartmentalSystems.bins.TsTpMassField.TsTpMassField method) system_age_density() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) system_age_density_single_value() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) system_age_distribution_quantiles() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) system_age_distribution_quantiles_by_ode() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) system_age_distributions() (CompartmentalSystems.bins.TsTpMassFieldsPerTimeStep.TsTpMassFieldsPerTimeStep method) system_age_moment() (CompartmentalSystems.discrete_model_run.DiscreteModelRun method) (CompartmentalSystems.smooth_model_run.SmoothModelRun method)

T

t_max() (CompartmentalSystems.bins.FieldsPerTimeStep.FieldsPerTimeStep property) t_min() (CompartmentalSystems.bins.FieldsPerTimeStep.FieldsPerTimeStep property) time_symbol (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel attribute) TimeBin (class in CompartmentalSystems.bins.TimeBin) TimeField (class in CompartmentalSystems.bins.TimeField) TimeMassField (class in CompartmentalSystems.bins.TimeMassField) TimeMassFields (class in CompartmentalSystems.bins.TsTpMassFields) times (CompartmentalSystems.smooth_model_run.SmoothModelRun attribute) times() (CompartmentalSystems.bins.FieldsPerTimeStep.FieldsPerTimeStep property) (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD property) TimeStep (class in CompartmentalSystems.bins.TimeStep) TimeStepIterator (class in CompartmentalSystems.bins.TimeStepIterator) TimeStepPlotter (class in CompartmentalSystems.bins.TimeStepPlotter) to_14C_explicit() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) total_content() (CompartmentalSystems.bins.TsTpMassField.TsTpMassField property) total_contents() (CompartmentalSystems.bins.TsTpMassFieldsPerTimeStep.TsTpMassFieldsPerTimeStep property)

total_size() (in module CompartmentalSystems.bins.getsizeof) TsMassField (class in CompartmentalSystems.bins.TsMassField) TsMassFieldsPerPool (class in CompartmentalSystems.bins.TsTpMassFields) TsMassFieldsPerTimeStep (class in CompartmentalSystems.bins.TsMassFieldsPerTimeStep) tss() (CompartmentalSystems.bins.FieldsPerTimeStep.FieldsPerTimeStep property) (CompartmentalSystems.bins.TimeStepIterator.TimeStepIterator property) (CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep.TsTpMassFieldsPerPoolPerTimeStep property) TstBin (class in CompartmentalSystems.bins.TstBin) TsTpBin (class in CompartmentalSystems.bins.TsTpBin) TsTpDeathRateField (class in CompartmentalSystems.bins.TsTpDeathRateField) TsTpField (class in CompartmentalSystems.bins.TsTpField) TsTpMassField (class in CompartmentalSystems.bins.TsTpMassField) TsTpMassFieldsPerPipe (class in CompartmentalSystems.bins.TsTpMassFields) TsTpMassFieldsPerPool (class in CompartmentalSystems.bins.TsTpMassFields) TsTpMassFieldsPerPoolPerTimeStep (class in CompartmentalSystems.bins.TsTpMassFieldsPerPoolPerTimeStep) TsTpMassFieldsPerTimeStep (class in CompartmentalSystems.bins.TsTpMassFieldsPerTimeStep) tup2str() (in module CompartmentalSystems.helpers_reservoir)

U

u_pwc() (CompartmentalSystems.pwc_model_run_fd.PWCModelRunFD class method)

updated_content() (CompartmentalSystems.bins.TimeStep.TimeStep property)

V

verts() (CompartmentalSystems.bins.TimeBin.TimeBin method)

W

warning() (in module CompartmentalSystems.helpers_reservoir)

X

x_phi_ode() (in module CompartmentalSystems.helpers_reservoir) x_phi_tmax() (in module CompartmentalSystems.helpers_reservoir)

x_solve_func_skew() (CompartmentalSystems.smooth_model_run.SmoothModelRun method) x_tmax() (in module CompartmentalSystems.helpers_reservoir) xi_T_N_u_representation() (CompartmentalSystems.smooth_reservoir_model.SmoothReservoirModel method)