Model

Model#

Hospital Admissions#

class HospModelSample(Rt: float | None = None, latent_infections: ArrayLike | None = None, infection_hosp_rate: float | None = None, latent_hosp_admissions: ArrayLike | None = None, observed_hosp_admissions: ArrayLike | None = None)[source]#

Bases: NamedTuple

A container for holding the output from model.HospitalAdmissionsModel.sample().

Rt#

The reproduction number over time. Defaults to None.

Type:

float | None, optional

latent_infections#

The estimated number of new infections over time. Defaults to None.

Type:

ArrayLike | None, optional

infection_hosp_rate#

The infected hospitalization rate. Defaults to None.

Type:

float | None, optional

latent_hosp_admissions#

The estimated latent hospitalizations. Defaults to None.

Type:

ArrayLike | None, optional

observed_hosp_admissions#

The sampled or observed hospital admissions. Defaults to None.

Type:

ArrayLike | None, optional

Rt: float | None#

Alias for field number 0

infection_hosp_rate: float | None#

Alias for field number 2

latent_hosp_admissions: Union[Array, ndarray, bool, number, bool, int, float, complex, None]#

Alias for field number 3

latent_infections: Union[Array, ndarray, bool, number, bool, int, float, complex, None]#

Alias for field number 1

observed_hosp_admissions: Union[Array, ndarray, bool, number, bool, int, float, complex, None]#

Alias for field number 4

class HospitalAdmissionsModel(latent_hosp_admissions_rv, latent_infections_rv, gen_int_rv, I0_rv, Rt_process_rv, hosp_admission_obs_process_rv)[source]#

Bases: Model

Hospital Admissions Model (BasicRenewal + HospitalAdmissions)

This class inherits from pyrenew.models.Model. It extends the basic renewal model by adding a hospital admissions module, e.g., pyrenew.observations.HospitalAdmissions.

sample(n_timepoints_to_simulate=None, data_observed_hosp_admissions=None, padding=0, **kwargs)[source]#

Sample from the HospitalAdmissions model

Parameters:

  • n_timepoints_to_simulate (int, optional) – Number of timepoints to sample (passed to the basic renewal model).

  • data_observed_hosp_admissions (ArrayLike, optional) – The observed hospitalization data (passed to the basic renewal model). Defaults to None (simulation, rather than fit).

  • padding (int, optional) – Number of padding timepoints to add to the beginning of the simulation. Defaults to 0.

  • **kwargs (dict, optional) – Additional keyword arguments passed through to internal sample() calls, should there be any.

Return type:

HospModelSample

See also

basic_renewal.sample

For sampling the basic renewal model

sample_observed_admissions

For sampling observed hospital admissions

static validate(latent_hosp_admissions_rv, hosp_admission_obs_process_rv)[source]#

Verifies types and status (RV) of latent and observed hospital admissions

Parameters:

  • latent_hosp_admissions_rv (RandomVariable) – The latent process for the hospital admissions.

  • hosp_admission_obs_process_rv (RandomVariable) – The observed hospital admissions.

Return type:

None

See also

_assert_sample_and_rtype

Perform type-checking and verify RV

Reproduction Number Renewal Infections#

class RtInfectionsRenewalModel(latent_infections_rv, gen_int_rv, I0_rv, Rt_process_rv, infection_obs_process_rv=None)[source]#

Bases: Model

Basic Renewal Model (Infections + Rt)

The basic renewal model consists of a sampler of two steps: Sample from Rt and then used that to sample the infections.

sample(n_timepoints_to_simulate=None, data_observed_infections=None, padding=0, **kwargs)[source]#

Sample from the Basic Renewal Model

Parameters:

  • n_timepoints_to_simulate (int, optional) – Number of timepoints to sample.

  • data_observed_infections (ArrayLike | None, optional) – Observed infections. Defaults to None.

  • padding (int, optional) – Number of padding timepoints to add to the beginning of the simulation. Defaults to 0.

  • **kwargs (dict, optional) – Additional keyword arguments passed through to internal sample() calls, if any

Notes

Either data_observed_infections or n_timepoints_to_simulate must be specified, not both.

Return type:

RtInfectionsRenewalSample

static validate(gen_int_rv, I0_rv, latent_infections_rv, infection_obs_process_rv, Rt_process_rv)[source]#

Verifies types and status (RV) of the generation interval, initial infections, latent and observed infections, and the Rt process.

Parameters:

  • gen_int_rv (any) – The generation interval. Expects RandomVariable.

  • I0_rv (any) – The initial infections. Expects RandomVariable.

  • latent_infections_rv (any) – Infections latent process. Expects RandomVariable.

  • infection_obs_process_rv (any) – Infections observation process. Expects RandomVariable.

  • Rt_process_rv (any) – The sample function of the process should return a tuple where the first element is the drawn Rt. Expects RandomVariable.

Return type:

None

See also

_assert_sample_and_rtype

Perform type-checking and verify RV

class RtInfectionsRenewalSample(Rt: ArrayLike | None = None, latent_infections: ArrayLike | None = None, observed_infections: ArrayLike | None = None)[source]#

Bases: NamedTuple

A container for holding the output from model.RtInfectionsRenewalModel.sample().

Rt#

The reproduction number over time. Defaults to None.

Type:

ArrayLike | None, optional

latent_infections#

The estimated latent infections. Defaults to None.

Type:

ArrayLike | None, optional

observed_infections#

The sampled infections. Defaults to None.

Type:

ArrayLike | None, optional

Rt: Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], None]#

Alias for field number 0

latent_infections: Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], None]#

Alias for field number 1

observed_infections: Union[Buffer, _SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], None]#

Alias for field number 2

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