episimlab.setup.greek package

Submodules

episimlab.setup.greek.eta module

class episimlab.setup.greek.eta.SetupDefaultEta

Bases: object

Return a default value for eta.

etaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : eta

get_eta()

initialize()

class episimlab.setup.greek.eta.SetupEtaFromAsympRate(*, t_onset_to_Ih)

Bases: episimlab.setup.greek.eta.SetupDefaultEta

Given a static scalar time until hospitalization, calculate eta.

etaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : eta

t_onset_to_Ihattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

• static : True

get_eta()

episimlab.setup.greek.gamma module

class episimlab.setup.greek.gamma.SetupDefaultGamma

Bases: object

Provide default values for gamma for compartments Ia, Iy, and Ih.

gamma_Ihattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : gamma_Ih

gamma_Iaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : gamma_Ia

gamma_Iyattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : gamma_Iy

initialize()

class episimlab.setup.greek.gamma.SetupGammaIa(*, tri_Iy2R_para, stochastic, seed_state)

Bases: object

Draws gamma for compartments Ia from a triangular distribution defined by 3-length array tri_Iy2R_para.

gamma_Iaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : gamma_Ia

tri_Iy2R_paraattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : (‘value’,)

• static : True

stochasticattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : stochastic

seed_stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : seed_state

get_gamma_Ia() → float

Sample from triangular distributions if stochastic, or return the mean if deterministic.

initialize()

Note that because seed_state is same for both rng, gamma_Ia and gamma_Iy are exactly the same at each timestep.

class episimlab.setup.greek.gamma.SetupGammaIh(*, tri_Ih2R, stochastic, seed_state)

Bases: object

Draws gamma for compartment Ih from a triangular distribution defined by 3-length array tri_Ih2R.

gamma_Ihattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : gamma_Ih

tri_Ih2Rattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : (‘value’,)

• static : True

stochasticattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : stochastic

seed_stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : seed_state

get_gamma() → xarray.core.dataarray.DataArray

initialize()

class episimlab.setup.greek.gamma.SetupGammaIy(*, gamma_Ia)

Bases: object

Set gamma for Iy equal to gamma for Ia

gamma_Iaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : gamma_Ia

gamma_Iyattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : gamma_Iy

initialize()

run_step()

episimlab.setup.greek.mu module

class episimlab.setup.greek.mu.SetupDefaultMu

Bases: object

Returns a static, scalar default value for mu.

muattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : mu

get_mu()

initialize()

class episimlab.setup.greek.mu.SetupDynamicMuIh2D(*, tri_Ih2D, stochastic, seed_state)

Bases: episimlab.setup.greek.mu.SetupStaticMuIh2D

Like SetupStaticMuIh2D, but the triangular distibution is sampled to calculate mu at every step.

tri_Ih2Dattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : (‘value’,)

• static : True

stochasticattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : stochastic

seed_stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : seed_state

muattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : mu

run_step()

class episimlab.setup.greek.mu.SetupStaticMuIh2D(*, tri_Ih2D, stochastic, seed_state)

Bases: object

Given a length 3 iterable input tri_Ih2D, calculate mu after sampling once from this triangular distibution, at the beginning of the simulation.

tri_Ih2Dattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : (‘value’,)

• static : True

stochasticattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : stochastic

seed_stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : seed_state

muattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : mu

get_mu()

Sample from triangular distribution if stochastic, or return the mean if deterministic.

initialize()

episimlab.setup.greek.nu module

episimlab.setup.greek.omega module

class episimlab.setup.greek.omega.SetupDefaultOmega

Bases: object

omegaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : omega

TAGS = ('deprecated',)

get_omega()

initialize()

class episimlab.setup.greek.omega.SetupDynamicOmega(*, prop_trans_in_p, symp_h_ratio, asymp_relative_infect, gamma, eta, rho, tau)

Bases: episimlab.setup.greek.omega.SetupStaticOmega

Like SetupStaticOmega, but recalculate at every step.

omegaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : omega

prop_trans_in_pattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

• static : True

symp_h_ratioattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : (‘age_group’,)

• static : True

asymp_relative_infectattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

• static : True

gammaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : gamma

etaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : eta

rhoattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : rho

tauattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : tau

run_step()

class episimlab.setup.greek.omega.SetupStaticOmega(*, prop_trans_in_p, symp_h_ratio, asymp_relative_infect, gamma, eta, rho, tau)

Bases: episimlab.setup.greek.omega.SetupDefaultOmega

Calculate omega once at the beginning of the simulation.

omegaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : omega

prop_trans_in_pattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

• static : True

symp_h_ratioattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : (‘age_group’,)

• static : True

asymp_relative_infectattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

• static : True

gammaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : gamma

etaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : eta

rhoattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : rho

tauattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : tau

get_omega() → xarray.core.dataarray.DataArray

get_omega_a() → xarray.core.dataarray.DataArray

get_omega_p() → xarray.core.dataarray.DataArray

get_omega_pa() → xarray.core.dataarray.DataArray

get_omega_py() → xarray.core.dataarray.DataArray

get_omega_y() → xarray.core.dataarray.DataArray

episimlab.setup.greek.pi module

class episimlab.setup.greek.pi.SetupDefaultPi

Bases: object

piattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : pi

TAGS = ('deprecated',)

get_pi()

initialize()

class episimlab.setup.greek.pi.SetupDynamicPi(*, symp_h_ratio_w_risk, gamma, eta)

Bases: episimlab.setup.greek.pi.SetupStaticPi

Like SetupStaticPi, but recalculate at every step

piattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : pi

symp_h_ratio_w_riskattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : (‘risk_group’, ‘age_group’)

• static : True

gammaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : gamma

etaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : eta

run_step()

class episimlab.setup.greek.pi.SetupStaticPi(*, symp_h_ratio_w_risk, gamma, eta)

Bases: episimlab.setup.greek.pi.SetupDefaultPi

Calculate pi after sampling once from this triangular distibution, at the beginning of the simulation.

piattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : pi

symp_h_ratio_w_riskattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : (‘risk_group’, ‘age_group’)

• static : True

gammaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : gamma

etaattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : eta

get_pi() → xarray.core.dataarray.DataArray

episimlab.setup.greek.rho module

class episimlab.setup.greek.rho.SetupDefaultRho

Bases: object

Provide a default value for rho_Ia and rho_Iy.

rho_Iaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : rho_Ia

rho_Iyattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : rho_Iy

initialize()

class episimlab.setup.greek.rho.SetupRhoIa(*, tri_Pa2Ia)

Bases: object

Calculate rho for compartment Ia.

tri_Pa2Iaattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• global name : tri_Pa2Ia

• dimensions : ()

• static : True

rho_Iaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : rho_Ia

initialize()

class episimlab.setup.greek.rho.SetupRhoIy(*, tri_Py2Iy)

Bases: object

Calculate rho for compartment Iy.

tri_Py2Iyattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• global name : tri_Py2Iy

• dimensions : ()

• static : True

rho_Iyattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : rho_Iy

initialize()

episimlab.setup.greek.sigma module

class episimlab.setup.greek.sigma.SetupDefaultSigma

Bases: object

Returns a static, scalar default value for sigma.

sigmaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : sigma

TAGS = ('example',)

get_sigma()

initialize()

class episimlab.setup.greek.sigma.SetupDynamicSigmaFromExposedPara(*, tri_exposed_para, stochastic, seed_state)

Bases: episimlab.setup.greek.sigma.SetupStaticSigmaFromExposedPara

Like SetupStaticSigmaFromExposedPara, but the triangular distibution is sampled to calculate sigma at every step.

sigmaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : sigma

tri_exposed_paraattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• global name : tri_exposed_para

• dimensions : (‘value’,)

• static : True

stochasticattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : stochastic

seed_stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : seed_state

run_step()

class episimlab.setup.greek.sigma.SetupStaticSigmaFromExposedPara(*, tri_exposed_para, stochastic, seed_state)

Bases: episimlab.setup.greek.sigma.SetupDefaultSigma

Given a length 3 iterable input tri_exposed_para, calculate sigma after sampling once from this triangular distibution, at the beginning of the simulation.

sigmaattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : sigma

tri_exposed_paraattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• global name : tri_exposed_para

• dimensions : (‘value’,)

• static : True

stochasticattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : stochastic

seed_stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : in

• global name : seed_state

get_sigma()

Sample from triangular distribution if stochastic, or return the mean if deterministic.

episimlab.setup.greek.tau module

class episimlab.setup.greek.tau.SetupDefaultTau

Bases: object

Return a default value for tau.

tauattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : tau

initialize()

class episimlab.setup.greek.tau.SetupTauFromAsympRate(*, asymp_rate)

Bases: object

Given a static scalar input asymptomatic ratio, calculate tau.

asymp_rateattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

• static : True

tauattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : tau

initialize()

Module contents