API Reference

This page contains the API reference for pypomp.

Core Classes

• Pomp Class
  • Pomp
  • ys
  • theta
  • canonical_param_names
  • statenames
  • t0
  • rinit
  • rproc
  • dmeas
  • rmeas
  • par_trans
  • covars
  • accumvars
  • results_history
  • fresh_key
  • metadata
  • pypomp.Pomp.simulate
  • pypomp.Pomp.pfilter
  • pypomp.Pomp.mif
  • pypomp.Pomp.train
  • pypomp.Pomp.dpop_train
  • pypomp.Pomp.pmcmc
  • pypomp.Pomp.abc
  • pypomp.Pomp.results
  • pypomp.Pomp.traces
  • pypomp.Pomp.CLL
  • pypomp.Pomp.ESS
  • pypomp.Pomp.sample_params
  • pypomp.Pomp.to_struct
  • pypomp.Pomp.prune
  • pypomp.Pomp.time
  • pypomp.Pomp.arma
  • pypomp.Pomp.negbin
  • pypomp.Pomp.probe
  • pypomp.Pomp.print_summary
  • pypomp.Pomp.print_metadata
  • pypomp.Pomp.merge
  • pypomp.Pomp.plot_traces
  • pypomp.Pomp.plot_simulations
• PanelPomp Class
  • PanelPomp
  • ys
  • theta
  • unit_objects
  • canonical_param_names
  • canonical_shared_param_names
  • canonical_unit_param_names
  • results_history
  • fresh_key
  • metadata
  • pypomp.PanelPomp.simulate
  • pypomp.PanelPomp.pfilter
  • pypomp.PanelPomp.mif
  • pypomp.PanelPomp.train
  • pypomp.PanelPomp.dpop_train
  • pypomp.PanelPomp.results
  • pypomp.PanelPomp.CLL
  • pypomp.PanelPomp.ESS
  • pypomp.PanelPomp.traces
  • pypomp.PanelPomp.get_unit_names
  • pypomp.PanelPomp.get_unit_parameters
  • pypomp.PanelPomp.sample_params
  • pypomp.PanelPomp.to_struct
  • pypomp.PanelPomp.prune
  • pypomp.PanelPomp.mix_and_match
  • pypomp.PanelPomp.time
  • pypomp.PanelPomp.probe
  • pypomp.PanelPomp.arma
  • pypomp.PanelPomp.negbin
  • pypomp.PanelPomp.print_metadata
  • pypomp.PanelPomp.print_summary
  • pypomp.PanelPomp.merge
  • pypomp.PanelPomp.plot_traces
  • pypomp.PanelPomp.plot_simulations
• Parameters
  • PompParameters
  • pypomp.PompParameters.logLik
  • pypomp.PompParameters.to_jax_array
  • pypomp.PompParameters.num_replicates
  • pypomp.PompParameters.num_params
  • pypomp.PompParameters.subset
  • pypomp.PompParameters.get_param_names
  • pypomp.PompParameters.params
  • pypomp.PompParameters.set_params
  • pypomp.PompParameters.transformed
  • pypomp.PompParameters.pruned
  • pypomp.PompParameters.merge
  • PanelParameters
  • pypomp.PanelParameters.logLik
  • pypomp.PanelParameters.logLik_unit
  • pypomp.PanelParameters.params
  • pypomp.PanelParameters.set_params
  • pypomp.PanelParameters.num_replicates
  • pypomp.PanelParameters.get_param_names
  • pypomp.PanelParameters.get_shared_param_names
  • pypomp.PanelParameters.get_unit_param_names
  • pypomp.PanelParameters.get_unit_names
  • pypomp.PanelParameters.subset
  • pypomp.PanelParameters.to_jax_array
  • pypomp.PanelParameters.transformed
  • pypomp.PanelParameters.pruned
  • pypomp.PanelParameters.mixed_and_matched
  • pypomp.PanelParameters.merge
• Results
  • pypomp.core.results.Result
  • pypomp.core.results.ResultsHistory

Functional API

• Functional API
  • Data Structs
    • pypomp.functional.PompStruct
    • pypomp.functional.PanelPompStruct
  • Core Algorithms
    • pypomp.functional.pfilter
    • pypomp.functional.panel_pfilter
    • pypomp.functional.mif
    • pypomp.functional.panel_mif
    • pypomp.functional.simulate
    • pypomp.functional.pmcmc
    • pypomp.functional.abc
  • Differentiable Particle Filtering
    • pypomp.functional.train
    • pypomp.functional.panel_train
    • pypomp.functional.mop
    • pypomp.functional.dpop
  • Utilities
    • pypomp.functional.align_params

Configuration & Tuning

• Parameter Transformations
  • ParTrans
  • to_est
  • from_est
• Random Walk Standard Deviation
  • RWSigma
  • sigmas
  • init_names
  • not_init_names
  • all_names
  • cooling_fn
  • a
  • s
  • c
  • M
  • pypomp.RWSigma.geometric_cooling
  • pypomp.RWSigma.cosine_cooling
  • pypomp.RWSigma.hyperbolic_cooling
  • pypomp.RWSigma.custom_cooling
  • pypomp.RWSigma.copy
  • pypomp.RWSigma.cooled
  • pypomp.RWSigma.keys
  • pypomp.RWSigma.values
  • pypomp.RWSigma.items
  • pypomp.RWSigma.get
• Learning Rate
  • LearningRate
  • rates
  • pypomp.LearningRate.to_array
  • pypomp.LearningRate.cosine_decay
  • pypomp.LearningRate.geometric_decay
  • pypomp.LearningRate.linear_decay
• Optimizers
  • pypomp.core.optimizer.Optimizer
  • pypomp.SGD
  • pypomp.Adam
  • pypomp.FullMatrixAdam
  • pypomp.BFGS
  • pypomp.Newton
  • pypomp.WeightedNewton

Utilities

• Mathematical Utilities
  • pypomp.maths.logmeanexp
  • pypomp.maths.logmeanexp_se
  • pypomp.maths.expit
  • pypomp.maths.logit
• Fast Random Number Generation on GPUs
  • Random Variate Generators
  • Inverse Cumulative Distribution Functions (CDFs)
• Proposal Distributions
  • pypomp.proposals.mvn_diag_rw
  • pypomp.proposals.mvn_rw
  • pypomp.proposals.mvn_rw_adaptive
  • pypomp.proposals.MVNDiagRW
  • pypomp.proposals.MVNRWFull
  • pypomp.proposals.MVNRWAdaptive
• Monte Carlo Adjusted Profile
  • mcap()
  • MCAPResult
  • level
  • mle
  • ci
  • delta
  • se_stat
  • se_mc
  • se_total
  • fit
  • quadratic_max
  • quadratic_coef
  • vcov
• Type Aliases
  • StateDict
  • ParamDict
  • CovarDict
  • TimeFloat
  • StepSizeFloat
  • RNGKey
  • ObservationDict
  • InitialTimeFloat

Example Models

• Example Models
  • pypomp.models.dhaka
  • pypomp.models.LG
  • pypomp.models.sir
  • pypomp.models.spx
  • pypomp.models.UKMeasles