tlo.methods.breast_cancer module
Breast Cancer Disease Module
Limitations to note: * Footprints of HSI – pending input from expert on resources required.
- class BreastCancer(name=None, resourcefilepath=None)[source]
Breast Cancer Disease Module
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.
Bases:
tlo.core.Module
,tlo.methods.hsi_generic_first_appts.GenericFirstAppointmentsMixin
PARAMETERS:
Item
Type
Description
init_prop_breast_cancer_stage
LIST
initial proportions in cancer categories for woman aged 15-29
init_prop_breast_lump_discernible_breast_cancer_by_stage
LIST
initial proportions of those with cancer categories that have the symptom breast_lump_discernible
init_prop_with_breast_lump_discernible_diagnosed_breast_cancer_by_stage
LIST
initial proportions of people that have breast_lump_discernible that have been diagnosed
init_prop_treatment_status_breast_cancer
LIST
initial proportions of people with breast cancer previously treated
init_prob_palliative_care
REAL
initial probability of being under palliative care if in stage 4
r_stage1_none
REAL
probabilty per 3 months of incident stage 1 breast, amongst people with no breast cancer
rr_stage1_none_age3049
REAL
rate ratio for stage1 breast cancer for age 30-49
rr_stage1_none_agege50
REAL
rate ratio for stage1 breast cancer for age 50+
r_stage2_stage1
REAL
probabilty per 3 months of stage 2 breast cancer amongst people with stage 1
rr_stage2_undergone_curative_treatment
REAL
rate ratio for stage 2 breast cancer for people with stage 1 breast cancer if had curative treatment at stage 1
r_stage3_stage2
REAL
probabilty per 3 months of stage 3 breast cancer amongst people with stage 2
rr_stage3_undergone_curative_treatment
REAL
rate ratio for stage 3 breast cancer for people with stage 2 breast cancer if had curative treatment at stage 2
r_stage4_stage3
REAL
probabilty per 3 months of stage 4 breast cancer amongst people with stage 3
rr_stage4_undergone_curative_treatment
REAL
rate ratio for stage 4 breast cancer for people with stage 3 breast cancer if had curative treatment at stage 3
r_death_breast_cancer
REAL
probabilty per 3 months of death from breast cancer amongst people with stage 4 breast cancer
r_breast_lump_discernible_stage1
REAL
rate ratio for breast_lump_discernible if have stage 1 breast cancer
rr_breast_lump_discernible_stage2
REAL
rate ratio for breast_lump_discernible if have stage 2 breast cancer
rr_breast_lump_discernible_stage3
REAL
rate ratio for breast_lump_discernible if have stage 3 breast cancer
rr_breast_lump_discernible_stage4
REAL
rate ratio for breast_lump_discernible if have stage 4 breast cancer
rp_breast_cancer_age3049
REAL
relative prevalence at baseline of breast cancer if age3049
rp_breast_cancer_agege50
REAL
relative prevalence at baseline of breast cancer if agege50
sensitivity_of_biopsy_for_stage1_breast_cancer
REAL
sensitivity of biopsy_for diagnosis of stage 1 breast cancer
sensitivity_of_biopsy_for_stage2_breast_cancer
REAL
sensitivity of biopsy_for diagnosis of stage 2 breast cancer
sensitivity_of_biopsy_for_stage3_breast_cancer
REAL
sensitivity of biopsy_for diagnosis of stage 3 breast cancer
sensitivity_of_biopsy_for_stage4_breast_cancer
REAL
sensitivity of biopsy_for diagnosis of stage 4 breast cancer
PROPERTIES:
Item
Type
Description
brc_status
CATEGORICAL
Current status of the health condition, breast cancer. Possible values are: [none, stage1, stage2, stage3, stage4, ]
brc_date_diagnosis
DATE
the date of diagnosis of the breast_cancer (pd.NaT if never diagnosed)
brc_date_treatment
DATE
date of first receiving attempted curative treatment (pd.NaT if never started treatment)
brc_breast_lump_discernible_investigated
BOOL
whether a breast_lump_discernible has been investigated, and cancer missed
brc_stage_at_which_treatment_given
CATEGORICAL
the cancer stage at which treatment is given (because the treatment only has an effect during the stageat which it is given).. Possible values are: [none, stage1, stage2, stage3, stage4, ]
brc_date_palliative_care
DATE
date of first receiving palliative care (pd.NaT is never had palliative care)
brc_date_death
DATE
date of brc death
brc_new_stage_this_month
BOOL
new_stage_this month
Class attributes:
CAUSES_OF_DEATH : {‘BreastCancer’: <tlo.methods.causes.Cause object at 0x129523ad0>}
CAUSES_OF_DISABILITY : {‘BreastCancer’: <tlo.methods.causes.Cause object at 0x129523c10>}
INIT_DEPENDENCIES : {‘SymptomManager’, ‘Demography’, ‘HealthSystem’}
METADATA : {<Metadata.USES_HEALTHSYSTEM: 3>, <Metadata.USES_SYMPTOMMANAGER: 2>, <Metadata.USES_HEALTHBURDEN: 4>, <Metadata.DISEASE_MODULE: 1>}
OPTIONAL_INIT_DEPENDENCIES : {‘HealthBurden’}
__annotations__ : {}
Functions (defined or overridden in class BreastCancer):
- __init__(name=None, resourcefilepath=None)[source]
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)[source]
Setup parameters used by the module, now including disability weights
- initialise_simulation(sim)[source]
Schedule the main polling event
Schedule the main logging event
Define the LinearModels
Define the Diagnostic used
Define the Disability-weights
Schedule the palliative care appointments for those that are on palliative care at initiation
- on_birth(mother_id, child_id)[source]
Initialise properties for a newborn individual. :param mother_id: the mother for this child :param child_id: the new child
- do_at_generic_first_appt(person_id: int, individual_properties: IndividualProperties, symptoms: List[str], schedule_hsi_event: HSIEventScheduler, **kwargs) None [source]
Actions to take during a non-emergency generic health system interaction (HSI).
Derived classes should overwrite this method so that they are compatible with the
HealthSystem
module, and can schedule HSI events when a individual presents symptoms indicative of the corresponding illness or condition.When overwriting, arguments that are not required can be left out of the definition. If done so, the method must take a
**kwargs
input to avoid errors when looping over all disease modules and running their generic HSI methods.HSI events should be scheduled by the
Module
subclass implementing this method using theschedule_hsi_event
argument.Implementations of this method should not make any updates to the population dataframe directly - if the target individuals properties need to be updated this should be performed by updating the
individual_properties
argument.- Parameters:
person_id – Row index (ID) of the individual target of the HSI event in the population dataframe.
individual_properties – Properties of individual target as provided in the population dataframe. Updates to individual properties may be written to this object.
symptoms – List of symptoms the patient is experiencing.
schedule_hsi_event – A function that can schedule subsequent HSI events.
diagnosis_function – A function that can run diagnosis tests based on the patient’s symptoms.
consumables_checker – A function that can query the health system to check for available consumables.
facility_level – The level of the facility that the patient presented at.
treatment_id – The treatment id of the HSI event triggering the generic appointment.
- class BreastCancerMainPollingEvent(module)[source]
Regular event that updates all breast cancer properties for population: * Acquisition and progression of breast Cancer * Symptom Development according to stage of breast Cancer * Deaths from breast Cancer for those in stage4
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)
Bases:
tlo.events.RegularEvent
,tlo.events.Event
,tlo.events.PopulationScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class BreastCancerMainPollingEvent):
- class HSI_BreastCancer_Investigation_Following_breast_lump_discernible(module, person_id)[source]
This event is scheduled by HSI_GenericFirstApptAtFacilityLevel1 following presentation for care with the symptom breast_lump_discernible. This event begins the investigation that may result in diagnosis of breast Cancer and the scheduling of treatment or palliative care. It is for people with the symptom breast_lump_discernible.
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.
Bases:
tlo.methods.hsi_event.HSI_Event
,tlo.events.IndividualScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class HSI_BreastCancer_Investigation_Following_breast_lump_discernible):
- __init__(module, person_id)[source]
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.
- class HSI_BreastCancer_StartTreatment(module, person_id)[source]
This event is scheduled by HSI_BreastCancer_Investigation_Following_breast_lump_discernible following a diagnosis of breast Cancer. It initiates the treatment of breast Cancer. It is only for persons with a cancer that is not in stage4 and who have been diagnosed.
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.
Bases:
tlo.methods.hsi_event.HSI_Event
,tlo.events.IndividualScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class HSI_BreastCancer_StartTreatment):
- __init__(module, person_id)[source]
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.
- class HSI_BreastCancer_PostTreatmentCheck(module, person_id)[source]
This event is scheduled by HSI_BreastCancer_StartTreatment and itself. It is only for those who have undergone treatment for breast Cancer. If the person has developed cancer to stage4, the patient is initiated on palliative care; otherwise a further appointment is scheduled for one year.
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.
Bases:
tlo.methods.hsi_event.HSI_Event
,tlo.events.IndividualScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class HSI_BreastCancer_PostTreatmentCheck):
- __init__(module, person_id)[source]
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.
- class HSI_BreastCancer_PalliativeCare(module, person_id)[source]
- This is the event for palliative care. It does not affect the patients progress but does affect the disability
weight and takes resources from the healthsystem.
This event is scheduled by either: * HSI_BreastCancer_Investigation_Following_breast_lump_discernible following a diagnosis of breast Cancer at stage4. * HSI_BreastCancer_PostTreatmentCheck following progression to stage4 during treatment. * Itself for the continuance of care. It is only for persons with a cancer in stage4.
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.
Bases:
tlo.methods.hsi_event.HSI_Event
,tlo.events.IndividualScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class HSI_BreastCancer_PalliativeCare):
- __init__(module, person_id)[source]
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.
- class BreastCancerLoggingEvent(module)[source]
The only logging event for this module
schedule logging to repeat every 1 month
Bases:
tlo.events.RegularEvent
,tlo.events.Event
,tlo.events.PopulationScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class BreastCancerLoggingEvent):