metawards.Infections

class metawards.Infections

This class holds the arrays that record the infections as they are occuring during the outbreak

__init__() → None

Methods

__init__()
aggregate([profiler])	Aggregate all of the infection data from the demographic sub-networks
build(network, …)	Construct and return the Infections object that will track infections during a model run on the passed Network (or Networks)
clear(nthreads)	Clear all of the infections (resets all to zero)
get_stage_mapping()	Return the mapping from disease stages in this sub-network to disease stages in the overall network.
get_work_index()	Return the mapping from the index in this sub-networks work matrix to the mapping in the overall network’s work matrix
has_different_stage_mapping()	Return whether or not the sub-network disease stages are different to that of the overall network, and must thus be mapped
has_different_work_matrix()	Return whether or not the sub-network work matrix is different to that of the overall network

Attributes

N_INF_CLASSES	The total number of stages in the disease
nlinks	Return the number of work links
nnodes	The total number of nodes (wards)
nsubnets	Return the number of demographic subnetworks
play	The infections caused by random (play) movements.
subinfs	The infections for the multi-demographic subnets
work	The infections caused by fixed (work) movements.

N_INF_CLASSES

The total number of stages in the disease

aggregate(profiler=None, nthreads: int = 1) → None

Aggregate all of the infection data from the demographic sub-networks

Parameters:

• network (Network) – Network that was used to initialise these infections
• profiler (Profiler, optional) – Profiler used to profile the calculation, by default None
• nthreads (int, optional) – Number of threads to use, by default 1

static build(network: Union[metawards._network.Network, metawards._networks.Networks] = None, overall: metawards._network.Network = None)

Construct and return the Infections object that will track infections during a model run on the passed Network (or Networks)

Parameters:

• network (Network or Networks) – The network or networks that will be run
• overall (Network) – The overall network to which this subnet belongs

Returns:

infections – The space for the work and play infections for the network (including space for all of the demographics)

Return type:

Infections

clear(nthreads: int = 1)

Clear all of the infections (resets all to zero)

Parameters:nthreads (int) – Optionally parallelise this reset by specifying the number of threads to use

get_stage_mapping()

Return the mapping from disease stages in this sub-network to disease stages in the overall network. This returns a list where mapping[i] gives the index of stage i in the subnetwork to stage j in the overall network

get_work_index()

Return the mapping from the index in this sub-networks work matrix to the mapping in the overall network’s work matrix

has_different_stage_mapping()

Return whether or not the sub-network disease stages are different to that of the overall network, and must thus be mapped

has_different_work_matrix()

Return whether or not the sub-network work matrix is different to that of the overall network

nlinks

Return the number of work links

nnodes

The total number of nodes (wards)

nsubnets

Return the number of demographic subnetworks

play = None

The infections caused by random (play) movements. This is a list of int arrays, size play[N_INF_CLASSES][nnodes+1]

subinfs = None

The infections for the multi-demographic subnets

work = None

The infections caused by fixed (work) movements. This is a list of int arrays, size work[N_INF_CLASSES][nlinks+1]