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b/resources/cmd/ResourceFile_cmd_events_hsi/ever_stroke.csv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:a63a296565e1e403af488aad84a446de620e6347595b3f6b56834f284ac18fe9 -size 328 +oid sha256:69cd6c66093439ee8c4211acc82106094a37ee3cc2074112991cf4a2898ba7db +size 463 diff --git a/resources/cmd/ResourceFile_cmd_events_symptoms/ever_heart_attack.csv b/resources/cmd/ResourceFile_cmd_events_symptoms/ever_heart_attack.csv index dea909ccf6..f47951d51a 100644 --- a/resources/cmd/ResourceFile_cmd_events_symptoms/ever_heart_attack.csv +++ b/resources/cmd/ResourceFile_cmd_events_symptoms/ever_heart_attack.csv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:12db4315913ec105f75270160cbca5bf7091610309d603a4991eebad44a84814 -size 45 +oid sha256:57a355df5e11be4289357c4443ad13195465b6fa3def06852db8f622ee2a5074 +size 110 diff --git a/resources/cmd/ResourceFile_cmd_events_symptoms/ever_stroke.csv b/resources/cmd/ResourceFile_cmd_events_symptoms/ever_stroke.csv index b191d9fabb..4d8a9027e0 100644 --- a/resources/cmd/ResourceFile_cmd_events_symptoms/ever_stroke.csv +++ b/resources/cmd/ResourceFile_cmd_events_symptoms/ever_stroke.csv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d01ce6b375ec1e6678fa1e5471cae1d59a772a299bf197fdf222fe063a53e0f0 -size 39 +oid sha256:9b4deadfea79902ae4e7c3ab0c4cc1ec6cf7600d60482ae5cc56d7d56736cda4 +size 104 diff --git a/resources/cmd/ResourceFile_cmd_parameters.csv b/resources/cmd/ResourceFile_cmd_parameters.csv deleted file mode 100644 index d98e5d9ae6..0000000000 --- a/resources/cmd/ResourceFile_cmd_parameters.csv +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f40e80c51061fb032b6f7971aedab287a8fc5b387e52233df8a8b3c707a0d72b -size 70 diff --git a/resources/cmd/parameter_values.csv b/resources/cmd/parameter_values.csv new file mode 100644 index 0000000000..e3ed4e0f6d --- /dev/null +++ b/resources/cmd/parameter_values.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7e375fc4921ff456b477d4b59ce4f8ad65cf2a849844d6a717ad8261936c7149 +size 1249 diff --git a/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py b/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py index 59c04ea02c..c46aca4520 100644 --- a/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py +++ b/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py @@ -190,8 +190,8 @@ def convert_output(output_path): # get prevalence + lower and upper values prev_range = read_csv_files(resourcefilepath / "cmd" / "ResourceFile_cmd_condition_prevalence", files=None) - baseline_error = [(prev_range[f'{condition}']['value'].values - prev_range[f'{condition}']['lower'].values), - (prev_range[f'{condition}']['upper'].values - prev_range[f'{condition}']['value'].values)] + baseline_error = [(prev_range[f'{condition}']['value'].values - prev_range[f'{condition}']['prior_min'].values), + (prev_range[f'{condition}']['prior_max'].values - prev_range[f'{condition}']['value'].values)] if 'gbd_value' in prev_range[f'{condition}']: gbd_error = [(prev_range[f'{condition}']['gbd_value'].values - prev_range[f'{condition}'][ 'gbd_lower'].values), @@ -498,8 +498,8 @@ def make_incidence_plot(condition, type): files=None) else: inc_range = read_csv_files(resourcefilepath / "cmd" / f"ResourceFile_cmd_event_{type}", files=None) - asymptomatic_error = [(inc_range[f'{condition}']['value'].values - inc_range[f'{condition}']['lower'].values), - (inc_range[f'{condition}']['upper'].values - inc_range[f'{condition}']['value'].values)] + asymptomatic_error = [(inc_range[f'{condition}']['value'].values - inc_range[f'{condition}']['prior_min'].values), + (inc_range[f'{condition}']['prior_max'].values - inc_range[f'{condition}']['value'].values)] bar_width = 0.75 opacity = 0.25 diff --git a/src/tlo/methods/cardio_metabolic_disorders.py b/src/tlo/methods/cardio_metabolic_disorders.py index 0d52f3fa80..a05a4d403d 100644 --- a/src/tlo/methods/cardio_metabolic_disorders.py +++ b/src/tlo/methods/cardio_metabolic_disorders.py @@ -137,19 +137,59 @@ class CardioMetabolicDisorders(Module, GenericFirstAppointmentsMixin): initial_prev_param_dicts = { f"{p}_initial_prev": Parameter(Types.DICT, 'initial prevalence of condition') for p in conditions } - other_params_dict = { - 'interval_between_polls': Parameter(Types.INT, 'months between the main polling event'), - 'pr_bmi_reduction': Parameter(Types.INT, 'probability of an individual having a reduction in BMI following ' - 'weight loss treatment') - } + PARAMETERS = { **onset_conditions_param_dicts, **removal_conditions_param_dicts, **hsi_conditions_param_dicts, **onset_events_param_dicts, **death_conditions_param_dicts, **death_events_param_dicts, - **hsi_events_param_dicts, **initial_prev_param_dicts, **other_params_dict, + **hsi_events_param_dicts, **initial_prev_param_dicts, 'prob_care_provided_given_seek_emergency_care': Parameter( Types.REAL, "The probability that correct care is fully provided to persons that have sought emergency care" - " for a Cardio-metabolic disorder.") + " for a Cardio-metabolic disorder."), + 'interval_between_polls': + Parameter(Types.INT, 'months between the main polling event'), + 'emergency_care_symptom_max_days': + Parameter(Types.INT, 'max days of symptoms for person to seek emergency care in days'), + 'community_testing_schedule_buffer_days': + Parameter(Types.INT, 'buffer days for community testing schedule to ensure testing ' + 'occurs before next polling event'), + 'community_testing_deadline_buffer_days': + Parameter(Types.INT, 'buffer days for community testing deadline to ensure testing ' + 'occurs before next polling event'), + 'symptom_onset_buffer_days': + Parameter(Types.INT, 'buffer days for symptom onset to ensure it occurs ' + 'before next polling event'), + 'event_buffer_days': + Parameter(Types.INT, 'buffer days for event to ensure it occurs ' + 'before next polling event'), + 'death_outcome_delay_days': + Parameter(Types.INT, 'delay days for death outcome'), + 'weight_loss_min_wait_months': + Parameter(Types.INT, 'minimum time for individual to loose weight in months'), + 'weight_loss_max_wait_months': + Parameter(Types.INT, 'maximum time for individual to loose weight in months'), + 'medication_refill_interval_months': + Parameter(Types.INT, 'interval for medication refill in months'), + 'medication_refill_deadline_window_days': + Parameter(Types.INT, 'buffer window to complete medication refill in days'), + 'retry_appointment_start_delay_days': + Parameter(Types.INT, 'days to wait before starting retry appointment window'), + 'retry_appointment_deadline_days': + Parameter(Types.INT, 'maximum days allowed for retry appointment'), + 'min_age_for_assessment_years': + Parameter(Types.INT, 'minimum age for assessment of CMD in years'), + 'bmi_threshold_for_risk_score': + Parameter(Types.INT, 'BMI threshold for risk score calculation'), + 'min_risk_factors_for_scheduled_weight_loss': + Parameter(Types.INT, 'minimum number of risk factors for individual ' + 'to be recommended weight loss'), + 'bmi_threshold_weight_loss_advice': + Parameter(Types.INT, 'BMI threshold for weight loss advice'), + 'tests_per_year': + Parameter(Types.INT, 'tests to be undergone per year for conditions that require investigation'), + 'pr_bmi_reduction': + Parameter(Types.REAL, 'probability of an individual having a ' + 'reduction in BMI following weight loss treatment') } # Convert conditions and events to dicts and merge together into PROPERTIES @@ -287,7 +327,7 @@ def read_parameters(self, resourcefilepath: Optional[Path] = None): events_symptoms = read_csv_files(cmd_path / "ResourceFile_cmd_events_symptoms", files=None) events_hsi = read_csv_files(cmd_path / "ResourceFile_cmd_events_hsi", files=None) - self.load_parameters_from_dataframe(pd.read_csv(cmd_path / "ResourceFile_cmd_parameters.csv")) + self.load_parameters_from_dataframe(pd.read_csv(cmd_path / "parameter_values.csv")) def get_values(params, value): """replaces nans in the 'value' key with specified value""" @@ -313,12 +353,6 @@ def get_values(params, value): p[f'{event}_symptoms'] = get_values(events_symptoms[event], 1) p[f'{event}_hsi'] = get_values(events_hsi[event], 1) - # Set the interval (in months) between the polls - p['interval_between_polls'] = 3 - # Set the probability of an individual losing weight in the CardioMetabolicDisordersWeightLossEvent (this value - # doesn't vary by condition) - p['pr_bmi_reduction'] = 0.1 - # Check that every value has been read-in successfully for param_name in self.PARAMETERS: assert self.parameters[param_name] is not None, f'Parameter "{param_name}" has not been set.' @@ -755,9 +789,10 @@ def update_risk_score(self): Generates or updates the risk score for individuals at initialisation of population or at each polling event """ df = self.sim.population.props + p = self.parameters df.loc[df.is_alive, 'nc_risk_score'] = (df[[ 'li_low_ex', 'li_high_salt', 'li_high_sugar', 'li_tob', 'li_ex_alc']] > 0).sum(1) - df.loc[df['li_bmi'] >= 3, ['nc_risk_score']] += 1 + df.loc[df['li_bmi'] >= p['bmi_threshold_for_risk_score'], ['nc_risk_score']] += 1 def report_daly_values(self): """Report disability weight (average values for the last month) to the HealthBurden module""" @@ -828,7 +863,8 @@ def do_at_generic_first_appt( # A maximum of one instance of `HSI_CardioMetabolicDisorders_Investigations` # is created for the person, during which multiple conditions can # be investigated. - if individual_properties["age_years"] <= 5: + p = self.parameters + if individual_properties["age_years"] <= p['min_age_for_assessment_years']: return # The list of conditions that will be investigated in follow-up HSI @@ -845,7 +881,7 @@ def do_at_generic_first_appt( date_of_last_test = individual_properties[f"nc_{condition}_date_last_test"] next_test_due = ( pd.isnull(date_of_last_test) - or (self.sim.date - date_of_last_test).days > DAYS_IN_YEAR / 2 + or (self.sim.date - date_of_last_test).days > DAYS_IN_YEAR / p['tests_per_year'] ) p_assess_if_no_symptom = self.parameters[f"{condition}_hsi"].get( "pr_assessed_other_symptoms" @@ -889,6 +925,7 @@ def do_at_generic_first_appt_emergency( # based on the duration of time since symptoms have appeared. A maximum of one # instance of `HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment` # is created for the person, during which multiple events can be investigated. + p = self.parameters ev_to_investigate = [] for ev in self.events: # If the person has symptoms of damage from within the last 3 days, schedule @@ -897,7 +934,7 @@ def do_at_generic_first_appt_emergency( ( self.sim.date - individual_properties[f"nc_{ev}_date_last_event"] ).days - <= 3 + <= p['emergency_care_symptom_max_days'] ): ev_to_investigate.append(ev) @@ -964,6 +1001,7 @@ def apply(self, population): """ df = population.props m = self.module + p = self.module.parameters rng = m.rng # Function to schedule deaths on random day throughout polling period @@ -987,8 +1025,10 @@ def schedule_death_to_occur_before_next_poll(p_id, cond): hsi_event=HSI_CardioMetabolicDisorders_CommunityTestingForHypertension(person_id=person_id, module=self.module), priority=1, - topen=random_date(self.sim.date, self.sim.date + self.frequency - pd.DateOffset(days=2), m.rng), - tclose=self.sim.date + self.frequency - pd.DateOffset(days=1) # (to occur before next polling) + topen=random_date(self.sim.date, self.sim.date + + self.frequency - pd.DateOffset(days=p['community_testing_schedule_buffer_days']), m.rng), + tclose=self.sim.date + self.frequency - + pd.DateOffset(days=p['community_testing_deadline_buffer_days']) # (to occur before next polling) ) # ------------------------------ DETERMINE ONSET / REMOVAL OF CONDITIONS ------------------------------------- @@ -1019,7 +1059,9 @@ def schedule_death_to_occur_before_next_poll(p_id, cond): # Schedule symptom onset some time before next polling event for symptom in self.module.prob_symptoms[condition].keys(): date_onset = random_date( - self.sim.date, self.sim.date + self.frequency - pd.DateOffset(days=1), m.rng) + self.sim.date, + self.sim.date + self.frequency - pd.DateOffset(days=p['symptom_onset_buffer_days']), + m.rng) self.sim.modules['SymptomManager'].change_symptom( person_id=idx_symptom_onset.tolist(), symptom_string=f'{symptom}', @@ -1066,7 +1108,7 @@ def schedule_death_to_occur_before_next_poll(p_id, cond): for person_id in idx_has_event: self.sim.schedule_event(CardioMetabolicDisordersEvent(self.module, person_id, event), random_date(self.sim.date, self.sim.date + self.frequency - - pd.DateOffset(days=1), m.rng)) + pd.DateOffset(days=p['event_buffer_days']), m.rng)) # Add cases to either incident or prevalent list of cases if df.at[person_id, f'nc_{event}']: @@ -1088,6 +1130,8 @@ def __init__(self, module, person_id, event): def apply(self, person_id): df = self.sim.population.props + p = self.module.parameters + if not df.at[person_id, 'is_alive']: return @@ -1106,7 +1150,7 @@ def apply(self, person_id): # ------------------------------------ DETERMINE OUTCOME OF THIS EVENT ---------------------------------------- prob_death = self.module.lms_event_death[self.event].predict(df.loc[[person_id]]) # Schedule a future death event for 7 days' time - date_of_outcome = self.sim.date + DateOffset(days=7) + date_of_outcome = self.sim.date + DateOffset(days=p['death_outcome_delay_days']) if self.module.rng.random_sample() < prob_death[person_id]: df.at[person_id, f'nc_{self.event}_scheduled_date_death'] = date_of_outcome self.sim.schedule_event(CardioMetabolicDisordersDeathEvent(self.module, person_id, @@ -1518,6 +1562,7 @@ def do_for_each_condition(self, _c) -> bool: def apply(self, person_id, squeeze_factor): df = self.sim.population.props hs = self.sim.modules['HealthSystem'] + p = self.module.parameters # Ignore this event if the person is no longer alive: if not df.at[person_id, 'is_alive']: @@ -1534,14 +1579,14 @@ def apply(self, person_id, squeeze_factor): # If no follow-up treatment scheduled but the person has at least 2 risk factors, start weight loss treatment if ( (not any(hsi_scheduled)) - and (df.at[person_id, 'nc_risk_score'] >= 2) + and (df.at[person_id, 'nc_risk_score'] >= p['min_risk_factors_for_scheduled_weight_loss']) and (not df.at[person_id, 'nc_ever_weight_loss_treatment']) ): df.at[person_id, 'nc_ever_weight_loss_treatment'] = True # Schedule a post-weight loss event for 6-12 months for individual to potentially lose weight: self.sim.schedule_event(CardioMetabolicDisordersWeightLossEvent(self.module, person_id), - random_date(self.sim.date + pd.DateOffset(months=6), - self.sim.date + pd.DateOffset(months=12), + random_date(self.sim.date + pd.DateOffset(months=p['weight_loss_min_wait_months']), + self.sim.date + pd.DateOffset(months=p['weight_loss_max_wait_months']), self.module.rng)) # If the person did have any symptoms, and the main condition to investigate was not `hypertension`, @@ -1597,16 +1642,19 @@ def apply(self, person_id, squeeze_factor): df = self.sim.population.props person = df.loc[person_id] m = self.sim.modules['CardioMetabolicDisorders'] + p = self.module.parameters # Don't advise those with CKD to lose weight, but do so for all other conditions if BMI is higher than normal - if self.condition != 'chronic_kidney_disease' and (df.at[person_id, 'li_bmi'] > 2): + if (self.condition != 'chronic_kidney_disease' and + (df.at[person_id, 'li_bmi'] > p['bmi_threshold_weight_loss_advice'])): self.add_equipment({'Weighing scale'}) self.sim.population.props.at[person_id, 'nc_ever_weight_loss_treatment'] = True # Schedule a post-weight loss event for individual to potentially lose weight in next 6-12 months: self.sim.schedule_event(CardioMetabolicDisordersWeightLossEvent(m, person_id), - random_date(self.sim.date + pd.DateOffset(months=6), - self.sim.date + pd.DateOffset(months=12), m.rng)) + random_date(self.sim.date + pd.DateOffset(months=p['weight_loss_min_wait_months']), + self.sim.date + + pd.DateOffset(months=p['weight_loss_max_wait_months']), m.rng)) # If person is already on medication, do not do anything if person[f'nc_{self.condition}_on_medication']: @@ -1640,8 +1688,9 @@ def apply(self, person_id, squeeze_factor): hsi_event=HSI_CardioMetabolicDisorders_Refill_Medication(person_id=person_id, module=self.module, condition=self.condition), priority=1, - topen=self.sim.date + DateOffset(months=1), - tclose=self.sim.date + DateOffset(months=1) + DateOffset(days=7) + topen=self.sim.date + DateOffset(months=p['medication_refill_interval_months']), + tclose=self.sim.date + DateOffset(months=p['medication_refill_interval_months']) + + DateOffset(days=p['medication_refill_deadline_window_days']) ) else: # If person 'decides to' seek another appointment, schedule a new HSI appointment for tomorrow. @@ -1651,8 +1700,8 @@ def apply(self, person_id, squeeze_factor): m.parameters[f'{self.condition}_hsi'].get('pr_seeking_further_appt_if_drug_not_available')): self.sim.modules['HealthSystem'].schedule_hsi_event( hsi_event=self, - topen=self.sim.date + pd.DateOffset(days=1), - tclose=self.sim.date + pd.DateOffset(days=15), + topen=self.sim.date + pd.DateOffset(days=p['retry_appointment_start_delay_days']), + tclose=self.sim.date + pd.DateOffset(days=p['retry_appointment_deadline_days']), priority=1 ) @@ -1679,6 +1728,7 @@ def apply(self, person_id, squeeze_factor): df = self.sim.population.props person = df.loc[person_id] m = self.sim.modules['CardioMetabolicDisorders'] + p = self.module.parameters assert person[f'nc_{self.condition}_ever_diagnosed'], "The person is not diagnosed and so should not be " \ "receiving an HSI." @@ -1727,8 +1777,8 @@ def apply(self, person_id, squeeze_factor): m.parameters[f'{self.condition}_hsi'].get('pr_seeking_further_appt_if_drug_not_available')): self.sim.modules['HealthSystem'].schedule_hsi_event( hsi_event=self, - topen=self.sim.date + pd.DateOffset(days=1), - tclose=self.sim.date + pd.DateOffset(days=15), + topen=self.sim.date + pd.DateOffset(days=p['retry_appointment_start_delay_days']), + tclose=self.sim.date + pd.DateOffset(days=p['retry_appointment_deadline_days']), priority=1 )