Index

_

__init__() (pypfilt.time.Datetime method) (pypfilt.time.Scalar method)

A

active_particles() (pypfilt.examples.sir.SirCtmc method) adaptive_fit() (in module pypfilt) adaptive_fit_exponents() (pypfilt.pfilter.Results method) add_rows() (pypfilt.examples.sirv.FinalSize method) (pypfilt.summary.BackcastPredictiveCIs method) (pypfilt.summary.EnsembleSnapshot method) (pypfilt.summary.ForecastSnapshot method) (pypfilt.summary.ModelCIs method) (pypfilt.summary.ParamCovar method) (pypfilt.summary.PartitionModelCIs method) (pypfilt.summary.PartitionPredictiveCIs method) (pypfilt.summary.PredictiveCIs method) (pypfilt.summary.SimulatedObs method) (pypfilt.summary.Table method)

add_scalar() (pypfilt.time.Time method) add_to_legend() (pypfilt.plot.Plot method) AfterRegularisation (class in pypfilt.event) AfterResample (class in pypfilt.event) AfterReweight (class in pypfilt.event) AfterTimeStep (class in pypfilt.event) all_observations (pypfilt.build.Context attribute) apply_ground_truth_prior() (in module pypfilt.examples.predation) apply_style() (in module pypfilt.plot) as_list() (in module pypfilt.scenario) avg_var_wt() (in module pypfilt.stats)

B

back_n_steps() (pypfilt.state.Snapshot method) back_n_steps_state_vec() (pypfilt.state.Snapshot method) back_n_units() (pypfilt.state.Snapshot method) back_n_units_state_vec() (pypfilt.state.Snapshot method) backcast (pypfilt.summary.BackcastMonitor attribute) BackcastMonitor (class in pypfilt.summary) BackcastPredictiveCIs (class in pypfilt.summary) Base (class in pypfilt.sampler)

BeforeRegularisation (class in pypfilt.event) BeforeResample (class in pypfilt.event) begin_sim() (pypfilt.summary.BackcastMonitor method) (pypfilt.summary.Monitor method) bisect_cdf() (in module pypfilt.obs) brewer_qual() (in module pypfilt.plot) build() (pypfilt.summary.Metadata method) build_context() (in module pypfilt.build) (pypfilt.scenario.Instance method)

C

call_event_handlers() (pypfilt.build.Context method) can_smooth() (pypfilt.examples.lorenz.Lorenz63 method) (pypfilt.examples.predation.LotkaVolterra method) (pypfilt.examples.sir.SirCtmc method) (pypfilt.examples.sir.SirDtmc method) (pypfilt.examples.sir.SirOdeEuler method) (pypfilt.examples.sir.SirOdeRk method) (pypfilt.examples.sir.SirSde method) (pypfilt.examples.sirv.SirvOde method) (pypfilt.model.Model method) colour_iter() (in module pypfilt.plot) column() (pypfilt.time.Time method) component (pypfilt.build.Context attribute)

Context (class in pypfilt.build) cov_wt() (in module pypfilt.stats) create_backcast() (pypfilt.state.History method) cred_ints() (in module pypfilt.plot) cred_wt() (in module pypfilt.stats) crps_edf_scalar() (in module pypfilt.crps) crps_sample() (in module pypfilt.crps) ctx (pypfilt.event.AfterRegularisation attribute) (pypfilt.event.AfterResample attribute) (pypfilt.event.AfterReweight attribute) (pypfilt.event.AfterTimeStep attribute) (pypfilt.event.BeforeRegularisation attribute) (pypfilt.event.BeforeResample attribute) custom_format_strings() (pypfilt.time.Datetime method)

D

d_dt() (pypfilt.examples.lorenz.Lorenz63 method) (pypfilt.examples.predation.LotkaVolterra method) (pypfilt.examples.sir.SirOdeRk method) (pypfilt.model.OdeModel method) data (pypfilt.build.Context attribute) date_column() (in module pypfilt.io) Datetime (class in pypfilt.time) datetime_column() (in module pypfilt.io) default() (in module pypfilt.cache) default_priors() (in module pypfilt.examples.predation) default_style() (in module pypfilt.plot) DELETE_KEY (class in pypfilt.scenario)

descriptor (pypfilt.build.Context attribute) (pypfilt.scenario.Instance attribute) display_names (pypfilt.scenario.ObsModelParams attribute) distribution() (pypfilt.examples.lorenz.ObsLorenz63 method) (pypfilt.examples.predation.ObsModel method) (pypfilt.examples.simple.GaussianObs method) (pypfilt.examples.sir.SirObs method) (pypfilt.examples.sirv.Incidence method) (pypfilt.obs.Univariate method) draw_samples() (pypfilt.sampler.Base method) (pypfilt.sampler.LatinHypercube method) dt (pypfilt.time.TimeStep attribute) dtype() (pypfilt.time.Time method)

E

earlier_states() (in module pypfilt.state) encode() (pypfilt.summary.Metadata method) encode_settings() (pypfilt.summary.Metadata method) end (pypfilt.time.TimeStep attribute) end() (pypfilt.io.Lookup method) end_sim() (pypfilt.summary.BackcastMonitor method) (pypfilt.summary.Monitor method) end_time() (pypfilt.build.Context method) EnsembleSnapshot (class in pypfilt.summary) event_handler (pypfilt.build.Context attribute) example_obs_x_data() (in module pypfilt.examples.predation) example_obs_x_datetime_data() (in module pypfilt.examples.predation) example_obs_y_data() (in module pypfilt.examples.predation) example_obs_y_datetime_data() (in module pypfilt.examples.predation)

example_toml_data() (in module pypfilt.examples.predation) example_toml_datetime_data() (in module pypfilt.examples.predation) expand_x_lims() (pypfilt.plot.Grid method) (pypfilt.plot.Plot method) (pypfilt.plot.Single method) (pypfilt.plot.Wrap method) expand_y_lims() (pypfilt.plot.Grid method) (pypfilt.plot.Plot method) (pypfilt.plot.Single method) (pypfilt.plot.Wrap method) expect() (in module pypfilt.obs) (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) external_prior_samples() (pypfilt.build.Context method)

F

field_names() (pypfilt.model.Model method) field_types() (pypfilt.examples.lorenz.Lorenz63 method) (pypfilt.examples.predation.LotkaVolterra method) (pypfilt.examples.simple.GaussianWalk method) (pypfilt.examples.sir.SirCtmc method) (pypfilt.examples.sir.SirDtmc method) (pypfilt.examples.sir.SirOdeEuler method) (pypfilt.examples.sir.SirOdeRk method) (pypfilt.examples.sir.SirSde method) (pypfilt.examples.sirv.FinalSize method) (pypfilt.examples.sirv.SirvOde method) (pypfilt.model.Model method) (pypfilt.summary.BackcastPredictiveCIs method) (pypfilt.summary.EnsembleSnapshot method) (pypfilt.summary.ForecastSnapshot method) (pypfilt.summary.ModelCIs method) (pypfilt.summary.ParamCovar method) (pypfilt.summary.PartitionModelCIs method) (pypfilt.summary.PartitionPredictiveCIs method) (pypfilt.summary.PredictiveCIs method) (pypfilt.summary.SimulatedObs method) (pypfilt.summary.Table method)

fields_dtype() (in module pypfilt.io) FinalSize (class in pypfilt.examples.sirv) finished() (pypfilt.examples.sirv.FinalSize method) (pypfilt.summary.BackcastPredictiveCIs method) (pypfilt.summary.Table method) fit() (in module pypfilt) fit_effective_fraction() (in module pypfilt.adaptive) fixed_exponents() (in module pypfilt.adaptive) forecast() (in module pypfilt) (in module pypfilt.examples.predation) forecast_times() (pypfilt.pfilter.Results method) ForecastSnapshot (class in pypfilt.summary) from_dtype() (pypfilt.time.Time method) from_file() (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) from_unicode() (pypfilt.time.Time method)

G

gaussian_walk_instance() (in module pypfilt.examples.simple) gaussian_walk_toml_data() (in module pypfilt.examples.simple) GaussianObs (class in pypfilt.examples.simple) GaussianWalk (class in pypfilt.examples.simple)

get_chained() (in module pypfilt.build) get_setting() (pypfilt.build.Context method) git_data() (pypfilt.summary.Metadata method) global_settings (pypfilt.scenario.Specification attribute) Grid (class in pypfilt.plot)

H

HDF5 (class in pypfilt.summary)

History (class in pypfilt.state) history_matrix() (in module pypfilt.state)

I

Incidence (class in pypfilt.examples.sirv) init() (pypfilt.examples.sir.SirCtmc method) (pypfilt.examples.sir.SirDtmc method) (pypfilt.examples.sir.SirOdeEuler method) (pypfilt.examples.sir.SirOdeRk method) (pypfilt.examples.sir.SirSde method) (pypfilt.examples.sirv.SirvOde method) (pypfilt.model.Model method)

install_event_handler() (pypfilt.build.Context method) Instance (class in pypfilt.scenario) instances() (in module pypfilt.scenario) is_history_matrix() (in module pypfilt.state) is_instance() (pypfilt.time.Time method) is_state_vec_matrix() (in module pypfilt.state) is_valid() (pypfilt.model.Model method)

L

LatinHypercube (class in pypfilt.sampler) legend() (pypfilt.plot.Plot method) llhd_in() (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) load_dataset() (in module pypfilt.io) load_instances() (in module pypfilt) (in module pypfilt.scenario) load_rng_states() (in module pypfilt.cache) load_specifications() (in module pypfilt.scenario) load_state() (in module pypfilt.cache) (pypfilt.state.History static method) (pypfilt.summary.BackcastMonitor method) (pypfilt.summary.ForecastSnapshot method) (pypfilt.summary.Monitor method) (pypfilt.summary.SimulatedObs method) (pypfilt.summary.Table method) load_summary_table() (in module pypfilt.io)

load_toml() (in module pypfilt.scenario) log_llhd() (in module pypfilt.obs) (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) log_llhds (pypfilt.event.LogLikelihood attribute) LogLikelihood (class in pypfilt.event) Lookup (class in pypfilt.io) lookup() (in module pypfilt.io) (pypfilt.io.Lookup method) lookup_times() (in module pypfilt.io) lookup_values_count() (in module pypfilt.io) Lorenz63 (class in pypfilt.examples.lorenz) lorenz63_all_scenarios_toml() (in module pypfilt.examples.lorenz) lorenz63_forecast_regularised_toml() (in module pypfilt.examples.lorenz) lorenz63_forecast_toml() (in module pypfilt.examples.lorenz) lorenz63_simulate_toml() (in module pypfilt.examples.lorenz) LotkaVolterra (class in pypfilt.examples.predation)

M

Metadata (class in pypfilt.summary) ministeps() (in module pypfilt.model) Model (class in pypfilt.model) ModelCIs (class in pypfilt.summary) module pypfilt pypfilt.adaptive pypfilt.build pypfilt.cache pypfilt.crps pypfilt.event pypfilt.examples pypfilt.examples.lorenz pypfilt.examples.predation pypfilt.examples.simple pypfilt.examples.sir pypfilt.examples.sirv pypfilt.io pypfilt.model pypfilt.obs pypfilt.pfilter pypfilt.plot pypfilt.resample pypfilt.sampler pypfilt.scenario pypfilt.state pypfilt.stats pypfilt.summary pypfilt.time

Monitor (class in pypfilt.summary) monitor() (pypfilt.summary.Monitor method)

N

n_colours() (in module pypfilt.plot) n_rows() (pypfilt.examples.sirv.FinalSize method) (pypfilt.summary.BackcastPredictiveCIs method) (pypfilt.summary.EnsembleSnapshot method) (pypfilt.summary.ForecastSnapshot method) (pypfilt.summary.ModelCIs method) (pypfilt.summary.ParamCovar method) (pypfilt.summary.PartitionModelCIs method) (pypfilt.summary.PartitionPredictiveCIs method) (pypfilt.summary.PredictiveCIs method) (pypfilt.summary.SimulatedObs method) (pypfilt.summary.Table method)

native_dtype() (pypfilt.time.Time method) new_infections() (pypfilt.examples.sir.SirObs method) (pypfilt.examples.sirv.Incidence method)

O

Obs (class in pypfilt.obs) obs (pypfilt.event.LogLikelihood attribute) obs_into_row() (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) obs_list (pypfilt.event.AfterTimeStep attribute) observation_model_parameter_combinations() (in module pypfilt.scenario) observations (pypfilt.time.TimeStepWithObservations attribute)

observations() (in module pypfilt.plot) ObsLorenz63 (class in pypfilt.examples.lorenz) ObsModel (class in pypfilt.examples.predation) ObsModelParams (class in pypfilt.scenario) OdeModel (class in pypfilt.model) override_dict() (in module pypfilt.scenario) override_settings() (pypfilt.build.Context method)

P

ParamCovar (class in pypfilt.summary) particle_count() (pypfilt.build.Context method) partition (pypfilt.event.AfterRegularisation attribute) (pypfilt.event.AfterResample attribute) (pypfilt.event.BeforeRegularisation attribute) (pypfilt.event.BeforeResample attribute) PartitionModelCIs (class in pypfilt.summary) PartitionPredictiveCIs (class in pypfilt.summary) pkg_version() (pypfilt.summary.Metadata method) Plot (class in pypfilt.plot) plot() (in module pypfilt.examples.predation) plot_forecasts() (in module pypfilt.examples.predation) plot_params() (in module pypfilt.examples.predation) post_regularise() (in module pypfilt.resample) predation_datetime_instance() (in module pypfilt.examples.predation) predation_instance() (in module pypfilt.examples.predation) predation_scalar_instance() (in module pypfilt.examples.predation) PredictiveCIs (class in pypfilt.summary) prepare() (pypfilt.summary.BackcastMonitor method) (pypfilt.summary.Monitor method) previous_snapshot() (pypfilt.state.History method) prior_table() (pypfilt.build.Context method) pypfilt module pypfilt.adaptive module pypfilt.build module pypfilt.cache module pypfilt.crps module pypfilt.event module pypfilt.examples module

pypfilt.examples.lorenz module pypfilt.examples.predation module pypfilt.examples.simple module pypfilt.examples.sir module pypfilt.examples.sirv module pypfilt.io module pypfilt.model module pypfilt.obs module pypfilt.pfilter module pypfilt.plot module pypfilt.resample module pypfilt.sampler module pypfilt.scenario module pypfilt.state module pypfilt.stats module pypfilt.summary module pypfilt.time module

Q

qtl_wt() (in module pypfilt.stats) quantiles() (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method)

quantiles_tolerance() (pypfilt.obs.Univariate method)

R

reached_window_end() (pypfilt.state.History method) read_fields() (in module pypfilt.io) read_lookup_table() (in module pypfilt.io) read_table() (in module pypfilt.io) repack() (in module pypfilt.state) require_history_matrix() (in module pypfilt.state) require_state_vec_matrix() (in module pypfilt.state) resample() (in module pypfilt.resample) resample_ensemble() (in module pypfilt.pfilter) resample_ixs() (in module pypfilt.resample)

resample_mask (pypfilt.event.AfterTimeStep attribute) resample_weights() (in module pypfilt.resample) Result (class in pypfilt.pfilter) Results (class in pypfilt.pfilter) resume_from_cache() (pypfilt.model.Model method) reweight_ensemble() (in module pypfilt.pfilter) reweight_partition() (in module pypfilt.pfilter) row_into_obs() (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) run() (in module pypfilt.pfilter) run_cmd() (pypfilt.summary.Metadata method)

S

save() (pypfilt.plot.Plot method) save_dataset() (in module pypfilt.io) save_forecasts() (pypfilt.summary.HDF5 method) save_lorenz63_scenario_files() (in module pypfilt.examples.lorenz) save_rng_states() (in module pypfilt.cache) save_scalar_observations() (in module pypfilt.examples.predation) save_state() (in module pypfilt.cache) (pypfilt.state.History method) (pypfilt.summary.BackcastMonitor method) (pypfilt.summary.ForecastSnapshot method) (pypfilt.summary.Monitor method) (pypfilt.summary.SimulatedObs method) (pypfilt.summary.Table method) Scalar (class in pypfilt.time) scale_x_date() (pypfilt.plot.Plot method) scale_y_date() (pypfilt.plot.Plot method) Scenario (class in pypfilt.scenario) scenario_id (pypfilt.build.Context attribute) (pypfilt.scenario.Instance attribute) (pypfilt.scenario.Scenario attribute) scenario_observation_model_combinations() (in module pypfilt.scenario) scenario_observation_model_parameters() (in module pypfilt.scenario) scenario_settings (pypfilt.scenario.Specification attribute) scenarios() (in module pypfilt.scenario) select_next_event() (pypfilt.examples.sir.SirCtmc method) series() (in module pypfilt.plot) set_chained() (in module pypfilt.build) set_chained_default() (in module pypfilt.build) set_period() (pypfilt.time.Datetime method) (pypfilt.time.Scalar method) set_resampled() (pypfilt.state.History method) set_time_step() (pypfilt.state.History method) set_xlabel() (pypfilt.plot.Plot method) set_ylabel() (pypfilt.plot.Plot method) settings (pypfilt.build.Context attribute) (pypfilt.scenario.Instance attribute) (pypfilt.scenario.Scenario attribute) shift_window_back() (pypfilt.state.History method) simulate() (in module pypfilt.obs) (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) simulate_from_model() (in module pypfilt)

simulated_field_types() (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) simulated_obs() (pypfilt.obs.Obs method) (pypfilt.obs.Univariate method) simulated_obs_crps() (in module pypfilt.crps) SimulatedObs (class in pypfilt.summary) Single (class in pypfilt.plot) sir_toml_data() (in module pypfilt.examples.sir) SirCtmc (class in pypfilt.examples.sir) SirDtmc (class in pypfilt.examples.sir) SirObs (class in pypfilt.examples.sir) SirOdeEuler (class in pypfilt.examples.sir) SirOdeRk (class in pypfilt.examples.sir) SirSde (class in pypfilt.examples.sir) sirv_toml_data() (in module pypfilt.examples.sirv) SirvOde (class in pypfilt.examples.sirv) sliced() (pypfilt.state.Snapshot method) Snapshot (class in pypfilt.state) snapshot (pypfilt.event.AfterReweight attribute) (pypfilt.event.AfterTimeStep attribute) snapshot() (pypfilt.state.History method) source (pypfilt.build.Context attribute) (pypfilt.scenario.Instance attribute) (pypfilt.scenario.Scenario attribute) (pypfilt.scenario.Specification attribute) Specification (class in pypfilt.scenario) start (pypfilt.time.TimeStep attribute) start() (pypfilt.io.Lookup method) start_time() (pypfilt.build.Context method) stat_info() (pypfilt.model.Model method) step() (in module pypfilt.pfilter) step_count() (pypfilt.time.Time method) step_number (pypfilt.time.TimeStepWithObservations attribute) step_of() (pypfilt.time.Time method) steps() (pypfilt.time.Time method) string_field() (in module pypfilt.io) subplots() (pypfilt.plot.Grid method) (pypfilt.plot.Plot method) (pypfilt.plot.Single method) (pypfilt.plot.Wrap method) summary_count() (pypfilt.build.Context method) summary_times() (pypfilt.build.Context method) summary_window() (pypfilt.state.History method)

T

Table (class in pypfilt.summary) Time (class in pypfilt.time) time (pypfilt.event.AfterResample attribute) (pypfilt.event.BeforeResample attribute) time_field() (in module pypfilt.io) time_of_obs() (pypfilt.time.Time method) time_scale() (pypfilt.scenario.Instance method) time_step (pypfilt.time.TimeStepWithObservations attribute)

time_step_of_next_observation() (pypfilt.time.Datetime method) (pypfilt.time.Scalar method) time_steps() (pypfilt.build.Context method) time_units() (pypfilt.build.Context method) times() (pypfilt.io.Lookup method) TimeStep (class in pypfilt.time) TimeStepWithObservations (class in pypfilt.time) to_dtype() (pypfilt.time.Time method) to_unicode() (pypfilt.time.Time method)

U

unit (pypfilt.scenario.ObsModelParams attribute) Univariate (class in pypfilt.obs) update() (pypfilt.examples.simple.GaussianWalk method) (pypfilt.examples.sir.SirCtmc method) (pypfilt.examples.sir.SirDtmc method) (pypfilt.examples.sir.SirOdeEuler method) (pypfilt.examples.sir.SirSde method) (pypfilt.examples.sirv.SirvOde method) (pypfilt.model.Model method) (pypfilt.model.OdeModel method)

V

value_count() (pypfilt.io.Lookup method) value_format (pypfilt.scenario.ObsModelParams attribute) values (pypfilt.scenario.ObsModelParams attribute)

vec (pypfilt.event.AfterRegularisation attribute) (pypfilt.event.AfterResample attribute) (pypfilt.event.BeforeRegularisation attribute) (pypfilt.event.BeforeResample attribute)

W

weights (pypfilt.event.LogLikelihood attribute) window (pypfilt.summary.BackcastMonitor attribute) with_observation_tables() (pypfilt.time.Datetime method) (pypfilt.time.Scalar method)

Wrap (class in pypfilt.plot) write_example_files() (in module pypfilt.examples.predation) write_table() (in module pypfilt.io)