Index

A

AbstractRegressionPrediction (class in pyrenew.regression) AbsTransform (class in pyrenew.transformation) AffineTransform (class in pyrenew.transformation)

arg_constraints (CensoredNormal attribute) ARProcess (class in pyrenew.process) assert_valid_differencing_order() (DifferencedProcess static method)

C

call_with_intermediates() (ComposeTransform method) (Transform method) CensoredNormal (class in pyrenew.distributions) CholeskyTransform (class in pyrenew.transformation) codomain (AbsTransform attribute) (AffineTransform property) (CholeskyTransform attribute) (ComposeTransform property) (CorrCholeskyTransform attribute) (CorrMatrixCholeskyTransform attribute) (ExpTransform property) (L1BallTransform attribute) (LowerCholeskyAffine attribute) (LowerCholeskyTransform attribute) (PermuteTransform attribute) (PowerTransform attribute) (RealFastFourierTransform property) (ReshapeTransform attribute) (ScaledUnitLowerCholeskyTransform attribute) (SigmoidTransform attribute) (SimplexToOrderedTransform attribute) (SoftplusLowerCholeskyTransform attribute) (SoftplusTransform attribute) (StickBreakingTransform attribute) (Transform attribute) (UnpackTransform attribute) (ZeroSumTransform property)

coefficients (GLMPredictionSample attribute), [1] ComposeTransform (class in pyrenew.transformation) compute_delay_ascertained_incidence() (in module pyrenew.convolve) compute_infections_from_rt() (in module pyrenew.latent.infection_functions) compute_infections_from_rt_with_feedback() (in module pyrenew.latent.infection_functions) CorrCholeskyTransform (class in pyrenew.transformation) CorrMatrixCholeskyTransform (class in pyrenew.transformation)

D

DayOfWeekEffect (class in pyrenew.process) DeterministicPMF (class in pyrenew.deterministic) DeterministicVariable (class in pyrenew.deterministic) DifferencedProcess (class in pyrenew.process) DistributionalVariable() (in module pyrenew.randomvariable) domain (AbsTransform attribute) (CholeskyTransform attribute) (ComposeTransform property) (CorrCholeskyTransform attribute) (CorrMatrixCholeskyTransform attribute) (L1BallTransform attribute) (LowerCholeskyAffine attribute) (LowerCholeskyTransform attribute) (PermuteTransform attribute) (PowerTransform attribute) (RealFastFourierTransform property) (ReshapeTransform attribute) (ScaledUnitLowerCholeskyTransform attribute) (SimplexToOrderedTransform attribute) (SoftplusLowerCholeskyTransform attribute) (SoftplusTransform attribute) (StickBreakingTransform attribute) (Transform attribute) (UnpackTransform attribute) (ZeroSumTransform property)

DynamicDistributionalVariable (class in pyrenew.randomvariable)

E

expand_by() (DynamicDistributionalVariable method) (StaticDistributionalVariable method)

ExpTransform (class in pyrenew.transformation) extend_axis() (ZeroSumTransform method) extend_axis_rev() (ZeroSumTransform method)

F

forward_shape() (AffineTransform method) (ComposeTransform method) (CorrCholeskyTransform method) (LowerCholeskyAffine method) (LowerCholeskyTransform method) (PowerTransform method) (RealFastFourierTransform method) (ReshapeTransform method) (SimplexToOrderedTransform method) (SoftplusLowerCholeskyTransform method) (StickBreakingTransform method) (Transform method) (UnpackTransform method) (ZeroSumTransform method)

G

get_asymptotic_growth_rate() (in module pyrenew.math) get_asymptotic_growth_rate_and_age_dist() (in module pyrenew.math) get_leslie_matrix() (in module pyrenew.math)

get_stable_age_distribution() (in module pyrenew.math) GLMPrediction (class in pyrenew.regression) GLMPredictionSample (class in pyrenew.regression)

H

HospitalAdmissions (class in pyrenew.latent.hospitaladmissions) HospitalAdmissionsModel (class in pyrenew.model.admissionsmodel)

HospitalAdmissionsSample (class in pyrenew.latent.hospitaladmissions) HospModelSample (class in pyrenew.model.admissionsmodel)

I

IdentityTransform (class in pyrenew.transformation) IIDRandomSequence (class in pyrenew.process) infection_hosp_rate (HospitalAdmissionsSample attribute), [1] (HospModelSample attribute), [1] InfectionInitializationMethod (class in pyrenew.latent.infection_initialization_method) InfectionInitializationProcess (class in pyrenew.latent.infection_initialization_process) Infections (class in pyrenew.latent.infections) InfectionsSample (class in pyrenew.latent.infections) initialize_infections() (InfectionInitializationMethod method) (InitializeInfectionsExponentialGrowth method) (InitializeInfectionsFromVec method) (InitializeInfectionsZeroPad method) InitializeInfectionsExponentialGrowth (class in pyrenew.latent.infection_initialization_method) InitializeInfectionsFromVec (class in pyrenew.latent.infection_initialization_method) InitializeInfectionsZeroPad (class in pyrenew.latent.infection_initialization_method) integrate_discrete() (in module pyrenew.math)

intercept (GLMPredictionSample attribute), [1] inv (Transform property) inverse_shape() (AffineTransform method) (ComposeTransform method) (CorrCholeskyTransform method) (LowerCholeskyAffine method) (LowerCholeskyTransform method) (PowerTransform method) (RealFastFourierTransform method) (ReshapeTransform method) (SimplexToOrderedTransform method) (SoftplusLowerCholeskyTransform method) (StickBreakingTransform method) (Transform method) (UnpackTransform method) (ZeroSumTransform method)

K

kernel (Model attribute)

L

L1BallTransform (class in pyrenew.transformation) latent_hosp_admissions (HospModelSample attribute), [1] latent_hospital_admissions (HospitalAdmissionsSample attribute), [1] latent_infections (HospModelSample attribute), [1] (RtInfectionsRenewalSample attribute), [1] load_generation_interval() (in module pyrenew.datasets.generation_interval) load_infection_admission_interval() (in module pyrenew.datasets.infection_admission_interval) load_wastewater() (in module pyrenew.datasets.wastewater) log_abs_det_jacobian() (AffineTransform method) (CholeskyTransform method) (ComposeTransform method) (CorrCholeskyTransform method) (CorrMatrixCholeskyTransform method) (ExpTransform method) (IdentityTransform method) (L1BallTransform method) (LowerCholeskyAffine method) (LowerCholeskyTransform method) (PermuteTransform method) (PowerTransform method) (RealFastFourierTransform method) (ReshapeTransform method) (ScaledUnitLowerCholeskyTransform method) (SigmoidTransform method) (SimplexToOrderedTransform method) (SoftplusLowerCholeskyTransform method) (SoftplusTransform method) (StickBreakingTransform method) (Transform method) (UnpackTransform method) (ZeroSumTransform method)

log_prob() (CensoredNormal method) logistic_susceptibility_adjustment() (in module pyrenew.latent.infection_functions) LowerCholeskyAffine (class in pyrenew.transformation) LowerCholeskyTransform (class in pyrenew.transformation)

M

mcmc (Model attribute) Model (class in pyrenew.metaclass) model() (Model method) module pyrenew.convolve pyrenew.datasets.generation_interval pyrenew.datasets.infection_admission_interval pyrenew.datasets.wastewater pyrenew.deterministic pyrenew.distributions pyrenew.distutil pyrenew.latent.hospitaladmissions pyrenew.latent.infection_functions pyrenew.latent.infection_initialization_method pyrenew.latent.infection_initialization_process pyrenew.latent.infections pyrenew.math pyrenew.metaclass pyrenew.model.admissionsmodel pyrenew.model.rtinfectionsrenewalmodel pyrenew.observation.negativebinomial pyrenew.observation.poisson pyrenew.process pyrenew.randomvariable pyrenew.regression pyrenew.transformation

multiplier (HospitalAdmissionsSample attribute), [1]

N

NegativeBinomialObservation (class in pyrenew.observation.negativebinomial) new_convolve_scanner() (in module pyrenew.convolve)

new_double_convolve_scanner() (in module pyrenew.convolve) NullObservation (class in pyrenew.deterministic) NullVariable (class in pyrenew.deterministic)

O

observed_hosp_admissions (HospModelSample attribute), [1]

observed_infections (RtInfectionsRenewalSample attribute), [1]

P

PeriodicEffect (class in pyrenew.process) PermuteTransform (class in pyrenew.transformation) PoissonObservation (class in pyrenew.observation.poisson) post_initialization_infections (InfectionsSample attribute), [1] posterior_predictive() (Model method) PowerTransform (class in pyrenew.transformation) predict() (AbstractRegressionPrediction method) (GLMPrediction method) prediction (GLMPredictionSample attribute), [1] print_summary() (Model method) prior_predictive() (Model method) pyrenew.convolve module pyrenew.datasets.generation_interval module pyrenew.datasets.infection_admission_interval module pyrenew.datasets.wastewater module pyrenew.deterministic module pyrenew.distributions module pyrenew.distutil module pyrenew.latent.hospitaladmissions module pyrenew.latent.infection_functions module

pyrenew.latent.infection_initialization_method module pyrenew.latent.infection_initialization_process module pyrenew.latent.infections module pyrenew.math module pyrenew.metaclass module pyrenew.model.admissionsmodel module pyrenew.model.rtinfectionsrenewalmodel module pyrenew.observation.negativebinomial module pyrenew.observation.poisson module pyrenew.process module pyrenew.randomvariable module pyrenew.regression module pyrenew.transformation module pytree_data_fields (CensoredNormal attribute)

R

RandomVariable (class in pyrenew.metaclass) RandomWalk (class in pyrenew.process) RealFastFourierTransform (class in pyrenew.transformation) ReshapeTransform (class in pyrenew.transformation) reverse_discrete_dist_vector() (in module pyrenew.distutil) Rt (HospModelSample attribute), [1] (RtInfectionsRenewalSample attribute), [1]

RtInfectionsRenewalModel (class in pyrenew.model.rtinfectionsrenewalmodel) RtInfectionsRenewalSample (class in pyrenew.model.rtinfectionsrenewalmodel) RtPeriodicDiffARProcess (class in pyrenew.process) RtWeeklyDiffARProcess (class in pyrenew.process) run() (Model method)

S

sample() (AbstractRegressionPrediction method) (ARProcess method) (CensoredNormal method) (DeterministicPMF method) (DeterministicVariable method) (DifferencedProcess method) (DynamicDistributionalVariable method) (GLMPrediction method) (HospitalAdmissions method) (HospitalAdmissionsModel method) (IIDRandomSequence method) (InfectionInitializationProcess method) (Infections method) (Model method) (NegativeBinomialObservation method) (NullObservation method) (NullVariable method) (PeriodicEffect method) (PoissonObservation method) (RandomVariable method) (RtInfectionsRenewalModel method) (RtPeriodicDiffARProcess method) (StaticDistributionalVariable method) (TransformedVariable method)

sample_length() (TransformedVariable method) ScaledLogitTransform() (in module pyrenew.transformation) ScaledUnitLowerCholeskyTransform (class in pyrenew.transformation) SigmoidTransform (class in pyrenew.transformation) sign (AffineTransform property) (ComposeTransform property) (ExpTransform attribute) (IdentityTransform attribute) (PowerTransform property) (ReshapeTransform attribute) (SigmoidTransform attribute) (SoftplusTransform attribute) (Transform property) SimplexToOrderedTransform (class in pyrenew.transformation) size() (DeterministicPMF method) SoftplusLowerCholeskyTransform (class in pyrenew.transformation) SoftplusTransform (class in pyrenew.transformation) StandardNormalRandomWalk (class in pyrenew.process) StandardNormalSequence (class in pyrenew.process) StaticDistributionalVariable (class in pyrenew.randomvariable) StickBreakingTransform (class in pyrenew.transformation) support (CensoredNormal property)

T

Transform (class in pyrenew.transformation) TransformedVariable (class in pyrenew.randomvariable) tree_flatten() (AffineTransform method) (ComposeTransform method) (ExpTransform method) (LowerCholeskyAffine method) (PermuteTransform method) (PowerTransform method) (RealFastFourierTransform method) (ReshapeTransform method) (SimplexToOrderedTransform method) (UnpackTransform method) (ZeroSumTransform method)

tree_unflatten() (Transform class method)

U

UnpackTransform (class in pyrenew.transformation)

V

validate() (ARProcess static method) (DayOfWeekEffect static method) (DeterministicPMF static method) (DeterministicVariable static method) (DifferencedProcess method) (DynamicDistributionalVariable static method) (HospitalAdmissions static method) (HospitalAdmissionsModel static method) (IIDRandomSequence static method) (InfectionInitializationMethod static method) (InfectionInitializationProcess static method) (Infections static method) (Model static method) (NegativeBinomialObservation static method) (NullObservation static method) (NullVariable static method) (PeriodicEffect static method) (PoissonObservation static method) (RandomVariable static method) (RtInfectionsRenewalModel static method) (RtPeriodicDiffARProcess static method) (StaticDistributionalVariable static method) (TransformedVariable method)

validate_discrete_dist_vector() (in module pyrenew.distutil)

Z

ZeroSumTransform (class in pyrenew.transformation)