Index

A

any_negative() (in module episimlab.utils.variable)

apply_edges() (episimlab.compt_model.ComptModel method)

B

BaseFOI (class in episimlab.foi) BetaReduction (class in episimlab.models.vaccine)

binomial() (in module episimlab.models.vaccine) BruteForceFOI (class in episimlab.foi)

C

calc_k() (episimlab.compt_model.ComptModel method) clip_to_zero() (in module episimlab.utils.variable) coerce_to_da() (in module episimlab.utils.variable) ComptModel (class in episimlab.compt_model) contacts_coords (episimlab.partition.partition.Partition property) CONTACTS_DIMS (episimlab.partition.partition.Partition attribute) contacts_dims (episimlab.partition.partition.Partition property) ContactsFromCSV (class in episimlab.partition.contacts) coords (episimlab.models.example_sir.SetupPhi property) (episimlab.models.example_sir.SetupState property) (episimlab.models.example_sirv.SetupPhi property) (episimlab.models.example_sirv.SetupState property) (episimlab.models.partition_v1.SetupNuDefault property) (episimlab.models.partition_v1.SetupPiDefault property) (episimlab.models.partition_v1.SetupState property) (episimlab.models.vaccine.SetupNuDefault property) (episimlab.models.vaccine.SetupPiDefault property) (episimlab.models.vaccine.SetupState property) (episimlab.models.vaccine.SetupVaccineDoses property) (episimlab.partition.partition.Partition property) (episimlab.setup.state.SetupToyState property)

D

DATA_DIR (episimlab.models.partition_v1.PartitionFromTravel attribute) (episimlab.models.vaccine.Vaccine attribute) dims (episimlab.models.example_sir.SetupState property) (episimlab.models.example_sirv.SetupState property) DIMS (episimlab.models.partition_v1.SetupNuDefault attribute) dims (episimlab.models.partition_v1.SetupNuDefault property) DIMS (episimlab.models.partition_v1.SetupPiDefault attribute) dims (episimlab.models.partition_v1.SetupPiDefault property) (episimlab.models.partition_v1.SetupState property)

DIMS (episimlab.models.vaccine.SetupNuDefault attribute) dims (episimlab.models.vaccine.SetupNuDefault property) DIMS (episimlab.models.vaccine.SetupPiDefault attribute) dims (episimlab.models.vaccine.SetupPiDefault property) (episimlab.models.vaccine.SetupState property) DIMS (episimlab.models.vaccine.SetupVaccineDoses attribute) dims (episimlab.models.vaccine.SetupVaccineDoses property) discrete_time_approx() (in module episimlab.utils.datetime) dt64_to_day_of_week() (in module episimlab.utils.datetime)

E

edge_to_tm() (episimlab.compt_model.ComptModel method) edge_weight() (episimlab.compt_model.ComptModel method) edge_weight_name() (in module episimlab.utils.variable) edges_by_priority (episimlab.compt_model.ComptModel property) eligible_pop (episimlab.models.vaccine.SetupVaccineDoses property) EpiModel (class in episimlab.models.epi_model) episimlab module episimlab.compt_model module episimlab.foi module episimlab.models module episimlab.models.epi_model module episimlab.models.example_sir module episimlab.models.example_sirv module episimlab.models.partition_v1 module episimlab.models.vaccine module episimlab.partition module episimlab.partition.contacts module episimlab.partition.partition module episimlab.partition.travel_pat module episimlab.setup module episimlab.setup.coords module episimlab.setup.greek module episimlab.setup.greek.eta module

episimlab.setup.greek.gamma module episimlab.setup.greek.mu module episimlab.setup.greek.omega module episimlab.setup.greek.pi module episimlab.setup.greek.rho module episimlab.setup.greek.sigma module episimlab.setup.greek.tau module episimlab.setup.seed module episimlab.setup.state module episimlab.setup.sto module episimlab.utils module episimlab.utils.datetime module episimlab.utils.plot module episimlab.utils.profile module episimlab.utils.rng module episimlab.utils.tags module episimlab.utils.variable module ExampleSIR (class in episimlab.models.example_sir) ExampleSIRV (class in episimlab.models.example_sirv) extend_phi_dims() (episimlab.models.example_sir.SetupPhi method) (episimlab.models.example_sirv.SetupPhi method)

F

finalize() (episimlab.models.example_sir.SetupComptGraph method) (episimlab.models.example_sirv.SetupComptGraph method) finalize_step() (episimlab.compt_model.ComptModel method) fix_coord_dtypes() (in module episimlab.utils.variable) FOI (class in episimlab.models.example_sir) (class in episimlab.models.example_sirv)

foi (episimlab.foi.BaseFOI property) (episimlab.foi.BruteForceFOI property) foi_coords (episimlab.foi.BaseFOI property) foi_dims (episimlab.foi.BaseFOI property)

G

get_c_ijk() (episimlab.partition.partition.Partition method) get_compt_graph() (episimlab.models.example_sir.SetupComptGraph method) (episimlab.models.example_sirv.SetupComptGraph method) (episimlab.models.partition_v1.SetupComptGraph method) (episimlab.models.vaccine.SetupComptGraph method) get_contacts_da() (episimlab.partition.contacts.ContactsFromCSV method) get_contacts_df() (episimlab.partition.contacts.ContactsFromCSV method) get_date_mask() (episimlab.partition.travel_pat.TravelPatFromCSV method) get_df_coords() (episimlab.setup.coords.SetupCoordsFromTravel method) get_edge_weight() (episimlab.compt_model.ComptModel method) get_eta() (episimlab.setup.greek.eta.SetupDefaultEta method) (episimlab.setup.greek.eta.SetupEtaFromAsympRate method) get_gamma() (episimlab.setup.greek.gamma.SetupGammaIh method) get_gamma_Ia() (episimlab.setup.greek.gamma.SetupGammaIa method) get_in_ds() (episimlab.models.epi_model.EpiModel method) get_int_per_day() (in module episimlab.utils.datetime) get_mu() (episimlab.setup.greek.mu.SetupDefaultMu method) (episimlab.setup.greek.mu.SetupStaticMuIh2D method)

get_omega() (episimlab.setup.greek.omega.SetupDefaultOmega method) (episimlab.setup.greek.omega.SetupStaticOmega method) get_omega_a() (episimlab.setup.greek.omega.SetupStaticOmega method) get_omega_p() (episimlab.setup.greek.omega.SetupStaticOmega method) get_omega_pa() (episimlab.setup.greek.omega.SetupStaticOmega method) get_omega_py() (episimlab.setup.greek.omega.SetupStaticOmega method) get_omega_y() (episimlab.setup.greek.omega.SetupStaticOmega method) get_pi() (episimlab.setup.greek.pi.SetupDefaultPi method) (episimlab.setup.greek.pi.SetupStaticPi method) get_rng() (in module episimlab.utils.rng) get_sigma() (episimlab.setup.greek.sigma.SetupDefaultSigma method) (episimlab.setup.greek.sigma.SetupStaticSigmaFromExposedPara method) get_travel_da() (episimlab.partition.travel_pat.TravelPatFromCSV method) get_travel_df() (episimlab.partition.travel_pat.TravelPatFromCSV method) get_var_dims() (in module episimlab.utils.variable) group_dict_by_var() (in module episimlab.utils.variable)

H

hypergeometric() (in module episimlab.models.vaccine)

I

I (episimlab.foi.BaseFOI property) (episimlab.models.example_sir.RecoveryRate property) (episimlab.models.example_sirv.RecoveryRate property) (episimlab.models.partition_v1.RateS2E property) (episimlab.models.vaccine.RateS2E property) I_COMPT_LABELS (episimlab.foi.BaseFOI attribute) (episimlab.models.vaccine.RateV2Ev attribute) initialize() (episimlab.models.example_sir.SetupComptGraph method) (episimlab.models.example_sir.SetupCoords method) (episimlab.models.example_sir.SetupPhi method) (episimlab.models.example_sir.SetupState method) (episimlab.models.example_sirv.SetupComptGraph method) (episimlab.models.example_sirv.SetupCoords method) (episimlab.models.example_sirv.SetupPhi method) (episimlab.models.example_sirv.SetupState method) (episimlab.models.partition_v1.SetupComptGraph method) (episimlab.models.partition_v1.SetupCoords method) (episimlab.models.partition_v1.SetupNuDefault method) (episimlab.models.partition_v1.SetupPiDefault method) (episimlab.models.partition_v1.SetupState method) (episimlab.models.vaccine.SetupComptGraph method) (episimlab.models.vaccine.SetupCoords method) (episimlab.models.vaccine.SetupNuDefault method) (episimlab.models.vaccine.SetupPiDefault method) (episimlab.models.vaccine.SetupState method) (episimlab.models.vaccine.SetupVaccineDoses method) (episimlab.partition.contacts.ContactsFromCSV method) (episimlab.partition.travel_pat.TravelPatFromCSV method) (episimlab.setup.coords.SetupCoordsFromTravel method) (episimlab.setup.coords.SetupToyCoords method) (episimlab.setup.greek.eta.SetupDefaultEta method) (episimlab.setup.greek.gamma.SetupDefaultGamma method) (episimlab.setup.greek.gamma.SetupGammaIa method) (episimlab.setup.greek.gamma.SetupGammaIh method) (episimlab.setup.greek.gamma.SetupGammaIy method) (episimlab.setup.greek.mu.SetupDefaultMu method) (episimlab.setup.greek.mu.SetupStaticMuIh2D method) (episimlab.setup.greek.omega.SetupDefaultOmega method) (episimlab.setup.greek.pi.SetupDefaultPi method) (episimlab.setup.greek.rho.SetupDefaultRho method) (episimlab.setup.greek.rho.SetupRhoIa method) (episimlab.setup.greek.rho.SetupRhoIy method) (episimlab.setup.greek.sigma.SetupDefaultSigma method) (episimlab.setup.greek.tau.SetupDefaultTau method) (episimlab.setup.greek.tau.SetupTauFromAsympRate method) (episimlab.setup.seed.SeedGenerator method) (episimlab.setup.state.SetupStateFromCensusCSV method) (episimlab.setup.state.SetupToyState method) (episimlab.setup.sto.SetupStochasticFromToggle method)

input_vars_from_config() (episimlab.models.epi_model.EpiModel method) IntPerDay (class in episimlab.utils.datetime)

L

load_travel_df() (episimlab.setup.coords.SetupCoordsFromTravel method)

M

module episimlab episimlab.compt_model episimlab.foi episimlab.models episimlab.models.epi_model episimlab.models.example_sir episimlab.models.example_sirv episimlab.models.partition_v1 episimlab.models.vaccine episimlab.partition episimlab.partition.contacts episimlab.partition.partition episimlab.partition.travel_pat episimlab.setup episimlab.setup.coords episimlab.setup.greek episimlab.setup.greek.eta episimlab.setup.greek.gamma episimlab.setup.greek.mu episimlab.setup.greek.omega episimlab.setup.greek.pi episimlab.setup.greek.rho episimlab.setup.greek.sigma episimlab.setup.greek.tau episimlab.setup.seed episimlab.setup.state episimlab.setup.sto episimlab.utils episimlab.utils.datetime episimlab.utils.plot episimlab.utils.profile episimlab.utils.rng episimlab.utils.tags episimlab.utils.variable

N

normalize_index() (episimlab.foi.BaseFOI method)

P

parse_input_vars() (episimlab.models.epi_model.EpiModel method) Partition (class in episimlab.partition.partition) PartitionFromTravel (class in episimlab.models.partition_v1) phi_coords (episimlab.models.example_sir.SetupPhi property) (episimlab.models.example_sirv.SetupPhi property) (episimlab.partition.partition.Partition property) PHI_DIMS (episimlab.foi.BaseFOI attribute) phi_dims (episimlab.foi.BaseFOI property) PHI_DIMS (episimlab.foi.BruteForceFOI attribute) (episimlab.models.example_sir.FOI attribute) phi_dims (episimlab.models.example_sir.SetupPhi property) PHI_DIMS (episimlab.models.example_sirv.FOI attribute) phi_dims (episimlab.models.example_sirv.SetupPhi property) PHI_DIMS (episimlab.models.partition_v1.RateS2E attribute) (episimlab.models.vaccine.RateS2E attribute)

phi_dims (episimlab.partition.partition.Partition property) plot() (episimlab.models.example_sir.ExampleSIR method) (episimlab.models.example_sirv.ExampleSIRV method) (episimlab.models.partition_v1.PartitionFromTravel method) (episimlab.models.vaccine.Vaccine method) plot_rate_V2I() (episimlab.models.example_sirv.ExampleSIRV method) plot_vacc() (episimlab.models.example_sirv.ExampleSIRV method) plotter() (in module episimlab.utils.plot) poisson() (episimlab.compt_model.ComptModel method) PROCESSES (episimlab.models.epi_model.EpiModel attribute) (episimlab.models.example_sir.ExampleSIR attribute) (episimlab.models.example_sirv.ExampleSIRV attribute) (episimlab.models.partition_v1.PartitionFromTravel attribute) (episimlab.models.vaccine.Vaccine attribute) profiler() (in module episimlab.utils.profile)

R

RAISE_NULL (episimlab.partition.travel_pat.TravelPatFromCSV attribute) RANDOM_PHI_DATA (episimlab.models.example_sir.SetupPhi attribute) (episimlab.models.example_sirv.SetupPhi attribute) RateE2P (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateE2Pa (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateE2Py (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateEv2P (class in episimlab.models.vaccine) RateEv2Pa (class in episimlab.models.vaccine) RateEv2Py (class in episimlab.models.vaccine) RateIa2R (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateIh2D (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateIh2R (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateIy2Ih (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateIy2R (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RatePa2Ia (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RatePy2Iy (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateS2E (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) RateS2V (class in episimlab.models.example_sirv) (class in episimlab.models.vaccine) RateV2Ev (class in episimlab.models.vaccine) RateV2I (class in episimlab.models.example_sirv) read_census_csv() (episimlab.setup.state.SetupStateFromCensusCSV method) realistic_state_basic() (episimlab.setup.state.SetupToyState method) RecoveryRate (class in episimlab.models.example_sir) (class in episimlab.models.example_sirv) rng (episimlab.compt_model.ComptModel property) run() (episimlab.models.epi_model.EpiModel method) run_step() (episimlab.compt_model.ComptModel method) (episimlab.foi.BruteForceFOI method) (episimlab.models.example_sir.FOI method) (episimlab.models.example_sir.RecoveryRate method) (episimlab.models.example_sir.VaccRate method) (episimlab.models.example_sirv.FOI method) (episimlab.models.example_sirv.RateS2V method) (episimlab.models.example_sirv.RateV2I method) (episimlab.models.example_sirv.RecoveryRate method) (episimlab.models.example_sirv.SetupComptGraph method) (episimlab.models.partition_v1.RateE2P method) (episimlab.models.partition_v1.RateE2Pa method) (episimlab.models.partition_v1.RateE2Py method) (episimlab.models.partition_v1.RateIa2R method) (episimlab.models.partition_v1.RateIh2D method) (episimlab.models.partition_v1.RateIh2R method) (episimlab.models.partition_v1.RateIy2Ih method) (episimlab.models.partition_v1.RateIy2R method) (episimlab.models.partition_v1.RatePa2Ia method) (episimlab.models.partition_v1.RatePy2Iy method) (episimlab.models.partition_v1.RateS2E method) (episimlab.models.vaccine.BetaReduction method) (episimlab.models.vaccine.RateE2P method) (episimlab.models.vaccine.RateE2Pa method) (episimlab.models.vaccine.RateE2Py method) (episimlab.models.vaccine.RateEv2P method) (episimlab.models.vaccine.RateEv2Pa method) (episimlab.models.vaccine.RateEv2Py method) (episimlab.models.vaccine.RateIa2R method) (episimlab.models.vaccine.RateIh2D method) (episimlab.models.vaccine.RateIh2R method) (episimlab.models.vaccine.RateIy2Ih method) (episimlab.models.vaccine.RateIy2R method) (episimlab.models.vaccine.RatePa2Ia method) (episimlab.models.vaccine.RatePy2Iy method) (episimlab.models.vaccine.RateS2E method) (episimlab.models.vaccine.RateS2V method) (episimlab.models.vaccine.RateV2Ev method) (episimlab.models.vaccine.SetupVaccineDoses method) (episimlab.partition.partition.Partition method) (episimlab.partition.travel_pat.TravelPatFromCSV method) (episimlab.partition.travel_pat.TravelPatRepeatDaily method) (episimlab.setup.greek.gamma.SetupGammaIy method) (episimlab.setup.greek.mu.SetupDynamicMuIh2D method) (episimlab.setup.greek.omega.SetupDynamicOmega method) (episimlab.setup.greek.pi.SetupDynamicPi method) (episimlab.setup.greek.sigma.SetupDynamicSigmaFromExposedPara method) (episimlab.setup.seed.SeedGenerator method) (episimlab.setup.sto.SetupStochasticFromToggle method) (episimlab.utils.datetime.IntPerDay method)

RUNNER_DEFAULTS (episimlab.models.epi_model.EpiModel attribute) (episimlab.models.example_sir.ExampleSIR attribute) (episimlab.models.example_sirv.ExampleSIRV attribute) (episimlab.models.partition_v1.PartitionFromTravel attribute) (episimlab.models.vaccine.Vaccine attribute)

S

S (episimlab.foi.BaseFOI property) (episimlab.models.example_sir.VaccRate property) (episimlab.models.partition_v1.RateS2E property) (episimlab.models.vaccine.RateS2E property) (episimlab.models.vaccine.SetupVaccineDoses property) S_COMPT_LABELS (episimlab.foi.BaseFOI attribute) (episimlab.models.example_sirv.RateV2I attribute) (episimlab.models.vaccine.RateV2Ev attribute) SeedGenerator (class in episimlab.setup.seed) set_ia() (episimlab.setup.state.SetupStateFromCensusCSV method) SetupComptGraph (class in episimlab.models.example_sir) (class in episimlab.models.example_sirv) (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) SetupCoords (class in episimlab.models.example_sir) (class in episimlab.models.example_sirv) (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) SetupCoordsFromTravel (class in episimlab.setup.coords) SetupDefaultEta (class in episimlab.setup.greek.eta) SetupDefaultGamma (class in episimlab.setup.greek.gamma) SetupDefaultMu (class in episimlab.setup.greek.mu) SetupDefaultOmega (class in episimlab.setup.greek.omega) SetupDefaultPi (class in episimlab.setup.greek.pi) SetupDefaultRho (class in episimlab.setup.greek.rho) SetupDefaultSigma (class in episimlab.setup.greek.sigma) SetupDefaultTau (class in episimlab.setup.greek.tau) SetupDynamicMuIh2D (class in episimlab.setup.greek.mu) SetupDynamicOmega (class in episimlab.setup.greek.omega) SetupDynamicPi (class in episimlab.setup.greek.pi) SetupDynamicSigmaFromExposedPara (class in episimlab.setup.greek.sigma)

SetupEtaFromAsympRate (class in episimlab.setup.greek.eta) SetupGammaIa (class in episimlab.setup.greek.gamma) SetupGammaIh (class in episimlab.setup.greek.gamma) SetupGammaIy (class in episimlab.setup.greek.gamma) SetupNuDefault (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) SetupPhi (class in episimlab.models.example_sir) (class in episimlab.models.example_sirv) SetupPiDefault (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) SetupRhoIa (class in episimlab.setup.greek.rho) SetupRhoIy (class in episimlab.setup.greek.rho) SetupState (class in episimlab.models.example_sir) (class in episimlab.models.example_sirv) (class in episimlab.models.partition_v1) (class in episimlab.models.vaccine) SetupStateFromCensusCSV (class in episimlab.setup.state) SetupStaticMuIh2D (class in episimlab.setup.greek.mu) SetupStaticOmega (class in episimlab.setup.greek.omega) SetupStaticPi (class in episimlab.setup.greek.pi) SetupStaticSigmaFromExposedPara (class in episimlab.setup.greek.sigma) SetupStochasticFromToggle (class in episimlab.setup.sto) SetupTauFromAsympRate (class in episimlab.setup.greek.tau) SetupToyCoords (class in episimlab.setup.coords) SetupToyState (class in episimlab.setup.state) SetupVaccineDoses (class in episimlab.models.vaccine) spawn_next() (episimlab.setup.seed.SeedGenerator method) state_coords (episimlab.setup.state.SetupToyState property) STATE_DIMS (episimlab.compt_model.ComptModel attribute) state_dims (episimlab.setup.state.SetupToyState property) stochastic_draw() (episimlab.compt_model.ComptModel method) suffixed_dims() (in module episimlab.utils.variable)

T

tag() (in module episimlab.utils.tags) TAGS (episimlab.compt_model.ComptModel attribute) (episimlab.foi.BaseFOI attribute) (episimlab.foi.BruteForceFOI attribute) (episimlab.models.epi_model.EpiModel attribute) (episimlab.models.example_sir.ExampleSIR attribute) (episimlab.models.example_sir.FOI attribute) (episimlab.models.example_sirv.ExampleSIRV attribute) (episimlab.models.example_sirv.FOI attribute) (episimlab.models.partition_v1.PartitionFromTravel attribute) (episimlab.models.vaccine.RateS2E attribute) (episimlab.models.vaccine.RateV2Ev attribute) (episimlab.models.vaccine.Vaccine attribute) (episimlab.partition.contacts.ContactsFromCSV attribute) (episimlab.partition.partition.Partition attribute) (episimlab.partition.travel_pat.TravelPatFromCSV attribute) (episimlab.partition.travel_pat.TravelPatRepeatDaily attribute) (episimlab.setup.coords.SetupCoordsFromTravel attribute) (episimlab.setup.coords.SetupToyCoords attribute) (episimlab.setup.greek.omega.SetupDefaultOmega attribute) (episimlab.setup.greek.pi.SetupDefaultPi attribute) (episimlab.setup.greek.sigma.SetupDefaultSigma attribute)

travel_pat_coords (episimlab.partition.partition.Partition property) TRAVEL_PAT_DIMS (episimlab.partition.partition.Partition attribute) travel_pat_dims (episimlab.partition.partition.Partition property) TravelPatFromCSV (class in episimlab.partition.travel_pat) TravelPatRepeatDaily (class in episimlab.partition.travel_pat) trim_data_to_coords() (in module episimlab.utils.variable)

U

uniform_state_basic() (episimlab.setup.state.SetupToyState method)

unsuffixed_coords() (episimlab.partition.partition.Partition method) unsuffixed_dims() (in module episimlab.utils.variable)

V

Vaccine (class in episimlab.models.vaccine) VaccRate (class in episimlab.models.example_sir) vis() (episimlab.models.partition_v1.SetupComptGraph method) (episimlab.models.vaccine.SetupComptGraph method)

visualize() (episimlab.models.example_sir.SetupComptGraph method) (episimlab.models.example_sirv.SetupComptGraph method) visualize_compt_graph() (in module episimlab.utils.plot)

X

xr_plot() (in module episimlab.utils.plot)