diagnostics.py

PCR

All symptomatic particles be tested with sensitivity of 90% and a 2 days delay for results.

SEROLOGICAL

All symptomatic particles be tested with sensitivity of 86%.

diagnostic

This class stores the attributes for a disease policy and the methods for its progression.

Attributes:

Name	Type	Description
name	str	Name of the diagnostic.
id	int	Id of the diagnostic (same as diag_type).
filter	str	Parsed filter to select particles to diagnose.
start_day	int	Day to start this diagnostic.
end_day	int	Day to end this diagnostic.
sensitivity	float	Sensitivity of the diagnostic (fraction of the positives that it is able to correctly identify).
specificity	float	Specificity of the diagnostic (fraction of the negatives that it is able to correctly identify).
tests_per_hour	np.array	Array with the number of tests to apply in each hour of the day.

__call__(self) special

Runs methods related to apply this diagnostic.

__init__(self, diag_param, comm, randgen) special

Initialize diagnostics object.

Parameters:

Name	Type	Description	Default
diag_param	dict	Parameters related to the diagnostic.	required
comm	community	The community object.	required
randgen	Generator	Random number generator used in diagnostics.	required

apply(self)

Apply this diagnostic.

can_be_tested(self)

Returns a mask of the particles that can be tested at the moment.

Returns:

Type	Description
np.array	Mask of the particles that can be tested at the moment.

init_diagnostics(parameters, comm)

Initialize diagnostics policies.

Parameters:

Name	Type	Description	Default
parameters	dict	Parameters for the simulation.	required
comm	community	The community object.	required

Returns:

Type	Description
List	List of the disease objects.

window_filter(start_state, start_time, end_state, end_time)

Generates a filter to be used in the 'filter_infected' parameter to diagnose in a time window.

Parameters:

Name	Type	Description	Default
start_state	int	State to mark the start of the window.	required
start_time	float	Relative time from the transition to the start_state	required
end_state	int	State to mark the end of the window.	required
end_time	float	Relative time from the transition to the end_state	required

Returns:

Type	Description
tuple	[description]