base

base

The v3 contact layers (cv.Layer, now a Starsim network, and cv.Contacts), and the v3 cv.Result (now Starsim’s).

Classes

Name	Description
Contacts	The contact layers (i.e. networks), keyed by name, e.g. sim.people.contacts['h'].
FlexDict	A dict that allows more flexible element access: in addition to obj[‘a’],
Layer	A v3 contact layer: a static Starsim network, i.e. one whose edges don’t change unless modified,

Contacts

base.Contacts(data=None, layer_keys=None, sim=None, **kwargs)

The contact layers (i.e. networks), keyed by name, e.g. sim.people.contacts['h'].

sim.people.contacts is made from the sim’s networks each time it is read. Adding a layer adds a network to the sim (after it has been initialized, but before it has been run); layers can’t be removed from or replaced in a sim this way, so pass networks to cv.Sim() instead.

Parameters

Name	Type	Description	Default
data	dict	a dictionary of layers (or of dicts of p1, p2, and beta arrays)	None
layer_keys	list	if provided, create an empty Contacts object with these layers	None
sim	Sim	if provided, the sim whose networks these are	None
kwargs	dict	additional layer(s), merged with data	{}

New in version 4.0.0: the layers are Starsim networks; sim argument.

Methods

Name	Description
add_layer	Small method to add one or more layers to the contacts. Layers should
from_sim	Create the contacts from the sim’s networks
pop_layer	Remove the layer(s) from the contacts. Layers can’t be removed from a sim, so this
to_graph	Convert all layers to a networkx MultiDiGraph

add_layer

base.Contacts.add_layer(**kwargs)

Small method to add one or more layers to the contacts. Layers should be provided as keyword arguments.

Example::

hospitals_layer = cv.Layer(label='hosp')
sim.people.contacts.add_layer(hospitals=hospitals_layer)

from_sim

base.Contacts.from_sim(sim)

Create the contacts from the sim’s networks

pop_layer

base.Contacts.pop_layer(*args)

Remove the layer(s) from the contacts. Layers can’t be removed from a sim, so this is only for contacts that aren’t from a sim.

Example::

contacts = cv.Contacts(a=dict(p1=[0,1], p2=[1,2], beta=[1,1]), b=dict(p1=[2], p2=[3], beta=[1]))
contacts.pop_layer('b')

to_graph

base.Contacts.to_graph()

Convert all layers to a networkx MultiDiGraph

Example::

import networkx as nx
sim = cv.Sim(pop_size=50, pop_type='hybrid').run()
G = sim.people.contacts.to_graph()
nx.draw(G)

FlexDict

base.FlexDict()

A dict that allows more flexible element access: in addition to obj[‘a’], also allow obj[0]. Lightweight implementation of the Sciris odict class.

Layer

base.Layer()

A v3 contact layer: a static Starsim network, i.e. one whose edges don’t change unless modified, e.g. by an intervention. See ss.Network for details.

Example::

n = 10_000
n_people = 1000
p1 = np.random.randint(n_people, size=n)
p2 = np.random.randint(n_people, size=n)
beta = np.ones(n)
layer = cv.Layer(p1=p1, p2=p2, beta=beta, label='rand')

Methods

Name	Description
keys	v3: a layer was a dict of its edge arrays (p1, p2, beta, and any others), so e.g. cv.Layer(**layer) copies it
step	The edges are static

keys

base.Layer.keys()

v3: a layer was a dict of its edge arrays (p1, p2, beta, and any others), so e.g. cv.Layer(**layer) copies it

step

base.Layer.step()

The edges are static