episimlab.setup package

Subpackages

• episimlab.setup.greek package
  • Submodules
  • episimlab.setup.greek.eta module
  • episimlab.setup.greek.gamma module
  • episimlab.setup.greek.mu module
  • episimlab.setup.greek.nu 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
  • Module contents

Submodules

episimlab.setup.coords module

class episimlab.setup.coords.SetupCoordsFromTravel(*, travel_fp)

Bases: episimlab.setup.coords.SetupToyCoords

comptattr.Attribute

No description given

Variable properties:

• type : variable

• intent : out

• global name : compt_coords

• dimensions : ()

• groups : coords

ageattr.Attribute

No description given

Variable properties:

• type : variable

• intent : out

• global name : age_coords

• dimensions : ()

• groups : coords

riskattr.Attribute

No description given

Variable properties:

• type : variable

• intent : out

• global name : risk_coords

• dimensions : ()

• groups : coords

vertexattr.Attribute

No description given

Variable properties:

• type : variable

• intent : out

• global name : vertex_coords

• dimensions : ()

• groups : coords

travel_fpattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

TAGS = ('deprecated', 'coords')

get_df_coords() → dict

initialize()

load_travel_df()

class episimlab.setup.coords.SetupToyCoords

Bases: object

Initialize state coordinates

comptattr.Attribute

No description given

Variable properties:

• type : variable

• intent : out

• global name : compt_coords

• dimensions : ()

• groups : coords

ageattr.Attribute

No description given

Variable properties:

• type : variable

• intent : out

• global name : age_coords

• dimensions : ()

• groups : coords

riskattr.Attribute

No description given

Variable properties:

• type : variable

• intent : out

• global name : risk_coords

• dimensions : ()

• groups : coords

vertexattr.Attribute

No description given

Variable properties:

• type : variable

• intent : out

• global name : vertex_coords

• dimensions : ()

• groups : coords

TAGS = ('coords', 'model::SIRV', 'example')

initialize()

episimlab.setup.seed module

class episimlab.setup.seed.SeedGenerator(*, seed_entropy)

Bases: object

Handles the seed_state variable, which is a pseudo-randomly generated integer seed that changes at every step of the simulation. Generation is handled by a numpy SeedSequence, which itself is seeded by an input integer seed seed_entropy.

seed_entropyattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

• static : True

seed_stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : seed_state

initialize()

run_step()

spawn_next(seed_seq)

episimlab.setup.state module

class episimlab.setup.state.SetupStateFromCensusCSV(*, coords={}, census_state_csv)

Bases: episimlab.setup.state.SetupToyState

Initializes state from a census.gov formatted CSV file.

stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : state

_coordsattr.Attribute

Mapping of all variables that belong to group ‘coords’

Variable properties:

• type : group_dict

• intent : in

• default value : {}

census_state_csvattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• dimensions : ()

initialize()

read_census_csv() → xarray.core.dataarray.DataArray

set_ia()

Sets Ia compt to 50 for all vertices.

class episimlab.setup.state.SetupToyState(*, coords={})

Bases: object

stateattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : state

_coordsattr.Attribute

Mapping of all variables that belong to group ‘coords’

Variable properties:

• type : group_dict

• intent : in

• default value : {}

property coords

initialize()

realistic_state_basic()

property state_coords

property state_dims

uniform_state_basic(value=0.0)

episimlab.setup.sto module

class episimlab.setup.sto.SetupStochasticFromToggle(*, sto_toggle)

Bases: object

Switches on stochasticity after simulation has run sto_toggle steps.

sto_toggleattr.Attribute

No description given

Variable properties:

• type : variable

• intent : in

• global name : sto_toggle

• dimensions : ()

• static : True

stochasticattr.Attribute

No description given

Variable properties:

• type : global

• intent : out

• global name : stochastic

initialize()

Ensures that stochastic is set during initialization

run_step(step)

Module contents