tlo.methods.copd module

class Copd(name=None, resourcefilepath=None)

The module responsible for determining Chronic Obstructive Pulmonary Diseases (COPD) status and outcomes. and initialises parameters and properties associated with COPD plus functions and events related to COPD.

Bases: tlo.core.Module

PARAMETERS:

Item	Type	Description
prob_progress_to_next_cat	REAL	probability of changing from a lower lung function category to a higher lung function category
prob_mod_exacerb	LIST	probability of moderate exacerbation given lung function, for each lungfunction category.
prob_sev_exacerb	LIST	probability of severe exacerbation given lung function, for each lungfunction category.
prob_will_die_sev_exacerbation	REAL	probability that a person will die of severe exacerbation
prob_will_survive_given_oxygen	REAL	probability that an individual with severe copd will not die when given oxygen

PROPERTIES:

Item	Type	Description
ch_lungfunction	CATEGORICAL	Lung function of the person.NaN for those under 15; on a 7-point scale for others, from 0 (Perfect) to 6 (End-Stage COPD).. Possible values are: [0, 1, 2, 3, 4, 5, 6, ]
ch_will_die_this_episode	BOOL	Whether this person will die during a current severe exacerbation
ch_has_inhaler	BOOL	Whether the person is currently using an inhaler

Class attributes:

ADDITIONAL_DEPENDENCIES : set()

CAUSES_OF_DEATH : {‘COPD’: <tlo.methods.causes.Cause object at 0x7fd214b9e8b0>}

CAUSES_OF_DISABILITY : {‘COPD’: <tlo.methods.causes.Cause object at 0x7fd214b9e910>}

INIT_DEPENDENCIES : {‘SymptomManager’}

METADATA : {<Metadata.DISEASE_MODULE: 1>, <Metadata.USES_HEALTHSYSTEM: 3>, <Metadata.USES_HEALTHBURDEN: 4>, <Metadata.USES_SYMPTOMMANAGER: 2>}

gbd_causes_of_copd_represented_in_this_module : {‘Other chronic respiratory diseases’}

Functions (defined or overridden in class Copd):

__init__(name=None, resourcefilepath=None)

Construct a new disease module ready to be included in a simulation.

Initialises an empty parameters dictionary and module-specific random number generator.

Parameters

name – the name to use for this module. Defaults to the concrete subclass’ name.

read_parameters(data_folder)

Read all parameters and define symptoms (if any)

pre_initialise_population()

Things to do before processing the population: * Generate the models

initialise_population(population)

Set initial values of properties values for all individuals

initialise_simulation(sim)

Get ready for simulation start: * Schedule the main polling event * Look-up item codes for consumables

on_birth(mother_id, child_id)

Initialise COPD properties for a newborn individual.

report_daly_values()

Return disability weight for alive persons, based on the current status of ch_lungfunction.

define_symptoms()

Define and register Symptoms

lookup_item_codes()

Look-up the item-codes for the consumables needed in the HSI Events for this module.

do_logging()

Log current states.

give_inhaler(person_id: int, hsi_event: HSI_Event)

Give inhaler if person does not already have one

do_when_present_with_breathless(person_id: int, hsi_event: HSI_Event)

What to do when a person presents at the generic first appt HSI with a symptom of breathless_severe or breathless_moderate. * If severe –> give the inhaler and schedule the HSI for Treatment * Otherwise –> just give inhaler.

class CopdPollEvent(module)

An event that controls the COPD infection process and logs current states. It repeats every 3 months.

Bases: tlo.events.RegularEvent, tlo.events.Event, tlo.events.PopulationScopeEventMixin

Functions (defined or overridden in class CopdPollEvent):

__init__(module)

Create a new regular event.

Parameters

• module – the module that created this event

• frequency (pandas.tseries.offsets.DateOffset) – the interval from one occurrence to the next (must be supplied as a keyword argument)

apply(population)

• Progress persons to higher categories of ch_lungfunction

• Schedules Exacerbation (Moderate / Severe) events.

• Log current states.

gen_random_date_in_next_three_months()

Returns a datetime for a day that is chosen randomly to be within the next 3 months.

static increment_category(ser: Series) → Series

Returns a pd.Series with same index as ser but with the categories shifted to next higher one.

progress_to_next_lung_function(df)

make individuals progress to a next higher lung function

class CopdExacerbationEvent(module, person_id, severe: bool = False)

An Exacerbation, which may be ‘Severe’ (severe=True) or ‘Moderate’ (severe=False). * A Moderate Exacerbation will not cause death but may cause non-emergency healthcare seeking; * A Severe Exacerbation may cause death and may cause emergency healthcare seeking.

Bases: tlo.events.Event, tlo.events.IndividualScopeEventMixin

Functions (defined or overridden in class CopdExacerbationEvent):

__init__(module, person_id, severe: bool = False)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters

• module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

• priority – a keyword-argument to set the priority (see Priority enum)

apply(person_id)

Apply this event to the given person.

Must be implemented by subclasses.

Parameters

person_id – the person the event happens to

class CopdDeath(module, person_id)

This event will cause the person to die to ‘COPD’ if the person’s property ch_will_die_this_episode is True. It is scheduled when a Severe Exacerbation is lethal, but can be cancelled if a subsequent treatment is successful.

Bases: tlo.events.Event, tlo.events.IndividualScopeEventMixin

Functions (defined or overridden in class CopdDeath):

__init__(module, person_id)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters

• module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

• priority – a keyword-argument to set the priority (see Priority enum)

apply(person_id)

Apply this event to the given person.

Must be implemented by subclasses.

Parameters

person_id – the person the event happens to

class HSI_Copd_TreatmentOnSevereExacerbation(module, person_id)

Bases: tlo.methods.healthsystem.HSI_Event, tlo.events.IndividualScopeEventMixin

Functions (defined or overridden in class HSI_Copd_TreatmentOnSevereExacerbation):

__init__(module, person_id)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters

module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

apply(person_id, squeeze_factor)

What to do when someone presents for care with an exacerbation. * Provide treatment: whatever is available at this facility at this time (no referral).