tlo.methods.postnatal_supervisor module

class PostnatalSupervisor(name=None, resourcefilepath=None)

This module is responsible for the key conditions/complications experienced by a mother and by a neonate following labour and the immediate postpartum period (this period, from birth to day +1, is covered by the labour module).

For mothers: This module applies risk of complications across the postnatal period, which is defined as birth until day 42 post-delivery. PostnatalWeekOneMaternalEvent represents the first week post birth where risk of complications remains high. The primary mortality causing complications here are infection/sepsis, secondary postpartum haemorrhage and hypertension. Women with or without complications may/may not seek Postnatal Care within the Labour module for assessment and treatment of any complications assigned in this module. Additionally the PostnatalSupervisorEvent applies risk of complications in the following 3 weeks of the postnatal period.

For neonates: This module applies risk of complications during the neonatal period, from birth until day 28. The PostnatalWeekOneNeonatalEvent Event applies risk of early onset neonatal sepsis (sepsis onsetting prior to day 7 of life). Care may be sought (as described above) and neonates can be admitted for treatment. The PostnatalSupervisor Event applies risk of late onset neonatal sepsis from week 2-4 (ending on day 28). This event also determines additional care seeking for neonates who are unwell during this time period. All neonatal variables are reset on day 28.

Bases: tlo.core.Module

PARAMETERS:

Item	Type	Description
prob_obstetric_fistula	LIST	probability of a woman developing an obstetric fistula after birth
rr_obstetric_fistula_obstructed_labour	LIST	relative risk of obstetric fistula in women who experienced obstructed labour
prevalence_type_of_fistula	LIST	prevalence of 1.) vesicovaginal 2.)rectovaginal fistula
prob_secondary_pph	LIST	baseline probability of secondary PPH
rr_secondary_pph_endometritis	LIST	relative risk of secondary postpartum haemorrhage in women with sepsis secondary to endometritis
prob_secondary_pph_severity	LIST	probability of mild, moderate or severe secondary PPH
cfr_secondary_postpartum_haemorrhage	LIST	case fatality rate for secondary pph
prob_htn_resolves	LIST	Weekly probability of resolution of hypertension
weekly_prob_gest_htn_pn	LIST	weekly probability of a woman developing gestational hypertension during the postnatal period
rr_gest_htn_obesity	LIST	Relative risk of gestational hypertension for women who are obese
prob_pre_eclampsia_per_month	LIST	underlying risk of pre-eclampsia per month without the impact of risk factors
weekly_prob_pre_eclampsia_pn	LIST	weekly probability of a woman developing mild pre-eclampsia during the postnatal period
rr_pre_eclampsia_obesity	LIST	Relative risk of pre-eclampsia for women who are obese
rr_pre_eclampsia_chronic_htn	LIST	Relative risk of pre-eclampsia in women who are chronically hypertensive
rr_pre_eclampsia_diabetes_mellitus	LIST	Relative risk of pre-eclampsia in women who have diabetes mellitus
probs_for_mgh_matrix_pn	LIST	probability of mild gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia
probs_for_sgh_matrix_pn	LIST	probability of severe gestational hypertension moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia
probs_for_mpe_matrix_pn	LIST	probability of mild pre-eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia
probs_for_spe_matrix_pn	LIST	probability of severe pre-eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia
probs_for_ec_matrix_pn	LIST	probability of eclampsia moving between states: gestational hypertension, severe gestational hypertension, mild pre-eclampsia, severe pre-eclampsia, eclampsia
cfr_eclampsia	LIST	case fatality rate of eclampsia in the postnatal period
cfr_severe_pre_eclampsia	LIST	case fatality rate of severe pre-eclampsia in the postnatal period
weekly_prob_death_severe_gest_htn	LIST	weekly risk of death from severe hypertension in the postnatal period
baseline_prob_anaemia_per_week	LIST	Weekly probability of anaemia in pregnancy
rr_anaemia_maternal_malaria	LIST	relative risk of anaemia secondary to malaria infection
rr_anaemia_recent_haemorrhage	LIST	relative risk of anaemia secondary to recent haemorrhage
rr_anaemia_hiv_no_art	LIST	relative risk of anaemia for a woman with HIV not on ART
prob_type_of_anaemia_pn	LIST	probability of a woman with anaemia having mild, moderate or severe anaemia
prob_late_sepsis_endometritis	LIST	probability of developing sepsis following postpartum endometritis infection
rr_sepsis_endometritis_post_cs	LIST	relative risk of endometritis following caesarean delivery
prob_late_sepsis_urinary_tract	LIST	probability of developing sepsis following postpartum UTI
prob_late_sepsis_skin_soft_tissue	LIST	probability of developing sepsis following postpartum skin/soft tissue infection
rr_sepsis_sst_post_cs	LIST	relative risk of skin/soft tissue sepsis following caesarean delivery
cfr_postpartum_sepsis	LIST	case fatality rate for postnatal sepsis
prob_early_onset_neonatal_sepsis_week_1	LIST	Baseline probability of a newborn developing sepsis in week one of life
rr_eons_maternal_chorio	LIST	relative risk of EONS in newborns whose mothers have chorioamnionitis
rr_eons_maternal_prom	LIST	relative risk of EONS in newborns whose mothers have PROM
rr_eons_preterm_neonate	LIST	relative risk of EONS in preterm newborns
cfr_early_onset_neonatal_sepsis	LIST	case fatality for early onset neonatal sepsis
prob_late_onset_neonatal_sepsis	LIST	probability of late onset neonatal sepsis (all cause)
cfr_late_neonatal_sepsis	LIST	Risk of death from late neonatal sepsis
prob_sepsis_disabilities	LIST	Probabilities of varying disability levels after neonatal sepsis
prob_care_seeking_postnatal_emergency	LIST	baseline probability of emergency care seeking for women in the postnatal period
prob_care_seeking_postnatal_emergency_neonate	LIST	baseline probability care will be sought for a neonate with a complication
odds_care_seeking_fistula_repair	LIST	odds of a woman seeking care for treatment of obstetric fistula
aor_cs_fistula_age_15_19	LIST	odds ratio for care seeking for treatment of obstetric fistula in 15-19 year olds
aor_cs_fistula_age_lowest_education	LIST	odds ratio for care seeking for treatment of obstetric fistula in women in the lowest education quantile
treatment_effect_early_init_bf	LIST	effect of early initiation of breastfeeding on neonatal sepsis rates
treatment_effect_iron_folic_acid_anaemia	LIST	effect of iron and folic acid supplementation on anaemia risk
treatment_effect_abx_prom	LIST	effect of early antibiotics given to a mother with PROM on neonatal sepsis rates
treatment_effect_clean_birth	LIST	Treatment effect of clean birth practices on early onset neonatal sepsis risk
treatment_effect_cord_care	LIST	Treatment effect of chlorhexidine cord care on early onset neonatal sepsis risk
treatment_effect_anti_htns_progression_pn	LIST	Treatment effect of oral anti hypertensives on progression from mild/mod to severe gestationalhypertension

PROPERTIES:

Item	Type	Description
pn_postnatal_period_in_weeks	REAL	The number of weeks a woman is in the postnatal period (1-6)
pn_htn_disorders	CATEGORICAL	Hypertensive disorders of the postnatal period. Possible values are: [none, resolved, gest_htn, severe_gest_htn, mild_pre_eclamp, severe_pre_eclamp, eclampsia, ]
pn_postpartum_haem_secondary	BOOL	Whether this woman is experiencing a secondary postpartum haemorrhage
pn_sepsis_late_postpartum	BOOL	Whether this woman is experiencing postnatal (day7+) sepsis
pn_obstetric_fistula	CATEGORICAL	Type of fistula developed after birth. Possible values are: [none, vesicovaginal, rectovaginal, ]
pn_sepsis_early_neonatal	BOOL	Whether this neonate has developed early onset neonatal sepsis during week one of life
pn_sepsis_late_neonatal	BOOL	Whether this neonate has developed late neonatal sepsis following discharge
pn_anaemia_following_pregnancy	CATEGORICAL	severity of anaemia following pregnancy. Possible values are: [none, mild, moderate, severe, ]
pn_emergency_event_mother	BOOL	Whether a mother is experiencing an emergency complication postnatally

Class attributes:

ADDITIONAL_DEPENDENCIES : {‘NewbornOutcomes’, ‘Labour’, ‘Lifestyle’, ‘PregnancySupervisor’}

CAUSES_OF_DEATH : {‘secondary_postpartum_haemorrhage’: <tlo.methods.causes.Cause object at 0x12a3c3fd0>, ‘postpartum_sepsis’: <tlo.methods.causes.Cause object at 0x12a3c1d10>, ‘severe_pre_eclampsia’: <tlo.methods.causes.Cause object at 0x12a3c17d0>, ‘eclampsia’: <tlo.methods.causes.Cause object at 0x12a3c1610>, ‘severe_gestational_hypertension’: <tlo.methods.causes.Cause object at 0x12a3c0150>, ‘early_onset_sepsis’: <tlo.methods.causes.Cause object at 0x12a3c3c10>, ‘late_onset_sepsis’: <tlo.methods.causes.Cause object at 0x12a3c3410>}

CAUSES_OF_DISABILITY : {‘maternal’: <tlo.methods.causes.Cause object at 0x12a3c3450>}

INIT_DEPENDENCIES : {‘Demography’, ‘HealthSystem’}

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

Functions (defined or overridden in class PostnatalSupervisor):

__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 parameter values from file, if required.

Must be implemented by subclasses.

Parameters:

data_folder – path of a folder supplied to the Simulation containing data files. Typically, modules would read a particular file within here.

initialise_population(population)

Set our property values for the initial population.

Must be implemented by subclasses.

This method is called by the simulation when creating the initial population, and is responsible for assigning initial values, for every individual, of those properties ‘owned’ by this module, i.e. those declared in its PROPERTIES dictionary.

TODO: We probably need to declare somehow which properties we ‘read’ here, so the simulation knows what order to initialise modules in!

Parameters:

population – the population of individuals

initialise_simulation(sim)

Get ready for simulation start.

Must be implemented by subclasses.

This method is called just before the main simulation loop begins, and after all modules have read their parameters and the initial population has been created. It is a good place to add initial events to the event queue.

on_birth(mother_id, child_id)

Initialise our properties for a newborn individual.

Must be implemented by subclasses.

This is called by the simulation whenever a new person is born.

Parameters:

• mother_id – the person id for the mother of this child (can be -1 if the mother is not identified).

• child_id – the person id of new child

further_on_birth_postnatal_supervisor(mother_id)

This function is called by the on_birth function of NewbornOutcomes module or following an intrapartum stillbirth in the Labour Module. This function contains additional code related to the postnatal supervisor module that should be ran on_birth. These additional on_birth functions ensure each modules (pregnancy,antenatal care, labour, newborn, postnatal) on_birth code is ran in the correct sequence (as this can vary depending on how modules are registered) :param mother_id: mothers individual id

on_hsi_alert(person_id, treatment_id)

report_daly_values()

apply_linear_model(lm, df)

Helper function will apply the linear model (lm) on the dataframe (df) to get a probability of some event happening to each individual. It then returns a series with same index with bools indicating the outcome based on the toss of the biased coin. :param lm: The linear model :param df: The dataframe :return: Series with same index containing outcomes (bool)

set_postnatal_complications_mothers(week)

This function is called by the PostnatalSupervisor event. It applies risk of key complications to a subset of women during each week of the postnatal period starting from week 2. Currently this includes sepsis, anaemia and hypertension :param week: week in the postnatal period used to select women in the data frame.

apply_risk_of_neonatal_complications_in_week_one(child_id, mother_id)

This function is called by PostnatalWeekOneEvent for newborns to determine risk of complications. Currently this is limited to early onset neonatal sepsis :param child_id: childs individual id :param mother_id: mothers individual id :return:

set_postnatal_complications_neonates(upper_and_lower_day_limits)

This function is called by the PostnatalSupervisor event. It applies risk of key complication to neonates during each week of the neonatal period after week one (weeks 2, 3 & 4). This is currently limited to sepsis but may be expanded at a later date :param upper_and_lower_day_limits: 2 value list of the first and last day of each week of the neonatal period

apply_risk_of_maternal_or_neonatal_death_postnatal(mother_or_child, individual_id)

This function is called to calculate an individuals risk of death following the onset of a complication. For individuals who dont seek care this is immediately after the onset of complications. For those who seek care it is called at the end of the HSI to allow for treatment effects. Either a mother or a child can be passed to the function. :param mother_or_child: Person of interest for the effect of this function - pass ‘mother’ or ‘child’ to

apply risk of death correctly

Parameters:

individual_id – individual_id

class PostnatalSupervisorEvent(module)

This is the PostnatalSupervisorEvent. This event runs every week and is responsible for applying risk of complications to mothers and newborns in the postnatal and neonatal periods. Risk is applied after the first week of

life as this is managed via PostnatalWeekOneMaternalEvent and PostnatalWeekOneNeonatalEvent. In addition this

event ensures that the relevant postnatal/neonatal variables are reset for those who survive.

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class PostnatalSupervisorEvent):

__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)

Apply this event to the given target.

This is a no-op; subclasses should override this method.

Parameters:

target – the target of the event

class PostnatalWeekOneMaternalEvent(module, individual_id)

This is PostnatalWeekOneMaternalEvent. It is scheduled for all mothers who survive labour and the first 48 hours after birth. This event applies risk of key complications that can occur in the first week after birth. This event also schedules postnatal care for those women predicted to attend after 48 hours or in the situation where they have developed a complication. For women who dont seek care for themselves risk of death is applied.

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

Functions (defined or overridden in class PostnatalWeekOneMaternalEvent):

__init__(module, individual_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(individual_id)

Apply this event to the given target.

Must be implemented by subclasses.

Parameters:

target – the target of the event

class PostnatalWeekOneNeonatalEvent(module, individual_id)

This is PostnatalWeekOneNeonatalEvent. It is scheduled for all newborns who survive labour and the first 48 hours

after birth. This event applies risk of key complications that can occur in the first week after birth. This event also schedules postnatal care for those newborns predicted to attend after 48 hours or in the situation where they

have developed a complication. For newborns who don’t seek care for themselves risk of death is applied.

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

Functions (defined or overridden in class PostnatalWeekOneNeonatalEvent):

__init__(module, individual_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(individual_id)

Apply this event to the given target.

Must be implemented by subclasses.

Parameters:

target – the target of the event

class HSI_PostnatalSupervisor_TreatmentForObstetricFistula(module, person_id)

This is HSI_PostnatalSupervisor_TreatmentForObstetricFistula. It is scheduled by the on_birth function of this

module for women have developed obstetric fistula and choose to seek care. Treatment delivered in this event

includes surgical correction of obstetric fistula

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_PostnatalSupervisor_TreatmentForObstetricFistula):

__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)

Apply this event to the population.

Must be implemented by subclasses.