Index

A

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

AffineTransform (class in pyrenew.transformation) ARProcess (class in pyrenew.process.ar)

C

call_with_intermediates() (ComposeTransform method) (Transform method) 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)

ComposeTransform (class in pyrenew.transformation) 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

DistributionalRV (class in pyrenew.metaclass) DistributionalRVSample (class in pyrenew.metaclass) 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)

E

ExpTransform (class in pyrenew.transformation)

extend_axis() (ZeroSumTransform method) extend_axis_rev() (ZeroSumTransform method)

F

FirstDifferenceARProcess (class in pyrenew.process.firstdifferencear) 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)

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) infection_hosp_rate (HospitalAdmissionsSample attribute), [1] (HospModelSample attribute), [1] Infections (class in pyrenew.latent.infections) InfectionSeedingProcess (class in pyrenew.latent.infection_seeding_process) InfectionSeedMethod (class in pyrenew.latent.infection_seeding_method) InfectionsSample (class in pyrenew.latent.infections) 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)

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) module pyrenew.convolve pyrenew.datasets.generation_interval pyrenew.datasets.infection_admission_interval pyrenew.datasets.wastewater pyrenew.distutil pyrenew.latent.hospitaladmissions pyrenew.latent.infection_functions pyrenew.latent.infection_seeding_method pyrenew.latent.infection_seeding_process pyrenew.latent.infections pyrenew.math pyrenew.mcmcutils pyrenew.metaclass pyrenew.model.admissionsmodel pyrenew.model.rtinfectionsrenewalmodel pyrenew.observation.negativebinomial pyrenew.observation.poisson pyrenew.process.ar pyrenew.process.firstdifferencear pyrenew.process.rtrandomwalk pyrenew.process.simplerandomwalk pyrenew.regression pyrenew.transformation

N

NegativeBinomialObservation (class in pyrenew.observation.negativebinomial)

new_convolve_scanner() (in module pyrenew.convolve) new_double_convolve_scanner() (in module pyrenew.convolve)

O

observed_hosp_admissions (HospModelSample attribute), [1]

observed_infections (RtInfectionsRenewalSample attribute), [1]

P

PermuteTransform (class in pyrenew.transformation) plot_posterior() (in module pyrenew.mcmcutils) (Model method) PoissonObservation (class in pyrenew.observation.poisson) post_seed_infections (InfectionsSample attribute), [1] posterior_predictive() (Model method) PowerTransform (class in pyrenew.transformation) predict() (AbstractRegressionPrediction method) (GLMPrediction method) 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.distutil module pyrenew.latent.hospitaladmissions module pyrenew.latent.infection_functions module pyrenew.latent.infection_seeding_method module pyrenew.latent.infection_seeding_process module

pyrenew.latent.infections module pyrenew.math module pyrenew.mcmcutils module pyrenew.metaclass module pyrenew.model.admissionsmodel module pyrenew.model.rtinfectionsrenewalmodel module pyrenew.observation.negativebinomial module pyrenew.observation.poisson module pyrenew.process.ar module pyrenew.process.firstdifferencear module pyrenew.process.rtrandomwalk module pyrenew.process.simplerandomwalk module pyrenew.regression module pyrenew.transformation module

R

RandomVariable (class in pyrenew.metaclass) 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) RtRandomWalkProcess (class in pyrenew.process.rtrandomwalk) run() (Model method)

S

sample() (AbstractRegressionPrediction method) (ARProcess method) (DistributionalRV method) (FirstDifferenceARProcess method) (GLMPrediction method) (HospitalAdmissions method) (HospitalAdmissionsModel method) (Infections method) (InfectionSeedingProcess method) (Model method) (NegativeBinomialObservation method) (PoissonObservation method) (RandomVariable method) (RtInfectionsRenewalModel method) (RtRandomWalkProcess method) (SimpleRandomWalkProcess method)

ScaledLogitTransform() (in module pyrenew.transformation) ScaledUnitLowerCholeskyTransform (class in pyrenew.transformation) seed_infections() (InfectionSeedMethod method) (SeedInfectionsExponential method) (SeedInfectionsFromVec method) (SeedInfectionsZeroPad method) SeedInfectionsExponential (class in pyrenew.latent.infection_seeding_method) SeedInfectionsFromVec (class in pyrenew.latent.infection_seeding_method) SeedInfectionsZeroPad (class in pyrenew.latent.infection_seeding_method) SigmoidTransform (class in pyrenew.transformation) SimpleRandomWalkProcess (class in pyrenew.process.simplerandomwalk) SimplexToOrderedTransform (class in pyrenew.transformation) SoftplusLowerCholeskyTransform (class in pyrenew.transformation) SoftplusTransform (class in pyrenew.transformation) spread_draws() (in module pyrenew.mcmcutils) (Model method) StickBreakingTransform (class in pyrenew.transformation)

T

Transform (class in pyrenew.transformation) 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) (DistributionalRV static method) (FirstDifferenceARProcess static method) (HospitalAdmissions static method) (HospitalAdmissionsModel static method) (Infections static method) (InfectionSeedingProcess static method) (InfectionSeedMethod static method) (Model static method) (NegativeBinomialObservation static method) (PoissonObservation static method) (RandomVariable static method) (RtInfectionsRenewalModel static method) (RtRandomWalkProcess static method) (SimpleRandomWalkProcess static method)

validate_discrete_dist_vector() (in module pyrenew.distutil) value (DistributionalRVSample attribute), [1]

Z

ZeroSumTransform (class in pyrenew.transformation)