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Fixing recurrence of HSIs in RTI #1408

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merged 6 commits into from
Jul 10, 2024
Merged

Fixing recurrence of HSIs in RTI #1408

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e17d663
Fixing recurrence of HSIs. Reworked logic
thewati Jul 1, 2024
f1c478f
Rollback to is_cons_available and is_tetanus_available. Removing look…
thewati Jul 2, 2024
099e60f
roll back incidental formatting changes
tbhallett Jul 8, 2024
362433b
roll back positin of df.loc and logger.debug statment to match curren…
tbhallett Jul 8, 2024
fb7c04e
add logic to `HSI_RTI_Major_Surgeries`
tbhallett Jul 8, 2024
35085e5
add logic to `HSI_RTI_Minor_Surgeries`
tbhallett Jul 8, 2024
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4 changes: 2 additions & 2 deletions resources/ResourceFile_RTI.xlsx
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130 changes: 86 additions & 44 deletions src/tlo/methods/rti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1016,6 +1016,10 @@ def __init__(self, name=None, resourcefilepath=None):
Types.INT,
"A cut-off score above which an injuries will be considered severe enough to cause mortality in those who"
"have not sought care."
),
'maximum_number_of_times_HSI_events_should_run': Parameter(
Types.INT,
"limit on the number of times an HSI event can run"
)

}
Expand Down Expand Up @@ -1526,6 +1530,7 @@ def initialise_simulation(self, sim):
# Begin logging the RTI events
sim.schedule_event(RTI_Logging_Event(self), sim.date + DateOffset(months=1))


def rti_do_when_diagnosed(self, person_id):
"""
This function is called by the generic first appointments when an injured person has been diagnosed
Expand Down Expand Up @@ -3825,9 +3830,12 @@ def __init__(self, module, person_id):
self.TREATMENT_ID = 'Rti_ShockTreatment'
self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({'AccidentsandEmerg': 1})
self.ACCEPTED_FACILITY_LEVEL = '1b'
self._number_of_times_this_event_has_run = 0
self._maximum_number_times_event_should_run = self.module.parameters['maximum_number_of_times_HSI_events_should_run']
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def apply(self, person_id, squeeze_factor):
df = self.sim.population.props
self._number_of_times_this_event_has_run += 1
# determine if this is a child
if df.loc[person_id, 'age_years'] < 15:
is_child = True
Expand All @@ -3845,27 +3853,26 @@ def apply(self, person_id, squeeze_factor):
get_item_code('Blood, one unit'): 2,
get_item_code("Oxygen, 1000 liters, primarily with oxygen cylinders"): 23_040
}
is_cons_available = self.get_consumables(
self.module.item_codes_for_consumables_required['shock_treatment_child']
)
is_cons_available = self.get_consumables(item_codes=
self.module.item_codes_for_consumables_required['shock_treatment_child'])
else:
self.module.item_codes_for_consumables_required['shock_treatment_adult'] = {
get_item_code("ringer's lactate (Hartmann's solution), 1000 ml_12_IDA"): 2000,
get_item_code('Cannula iv (winged with injection pot) 18_each_CMST'): 1,
get_item_code('Blood, one unit'): 2,
get_item_code("Oxygen, 1000 liters, primarily with oxygen cylinders"): 23_040
}
is_cons_available = self.get_consumables(
self.module.item_codes_for_consumables_required['shock_treatment_adult']
)
is_cons_available = self.get_consumables(item_codes=
self.module.item_codes_for_consumables_required['shock_treatment_adult'])

if is_cons_available:
logger.debug(key='rti_general_message',
data=f"Hypovolemic shock treatment available for person {person_id}")
df.at[person_id, 'rt_in_shock'] = False
self.add_equipment({'Infusion pump', 'Drip stand', 'Oxygen cylinder, with regulator', 'Nasal Prongs'})
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
return self.make_appt_footprint({})
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def did_not_run(self):
Expand Down Expand Up @@ -3918,11 +3925,15 @@ def __init__(self, module, person_id):
self.TREATMENT_ID = 'Rti_FractureCast'
self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({'AccidentsandEmerg': 1})
self.ACCEPTED_FACILITY_LEVEL = '1b'
self._number_of_times_this_event_has_run = 0
self._maximum_number_times_event_should_run = self.module.parameters[
'maximum_number_of_times_HSI_events_should_run']

def apply(self, person_id, squeeze_factor):
# Get the population and health system
df = self.sim.population.props
p = df.loc[person_id]
self._number_of_times_this_event_has_run += 1
# if the person isn't alive return a blank footprint
if not df.at[person_id, 'is_alive']:
return self.make_appt_footprint({})
Expand Down Expand Up @@ -4017,12 +4028,13 @@ def apply(self, person_id, squeeze_factor):
df.loc[person_id, 'rt_injuries_to_cast'].clear()
df.loc[person_id, 'rt_date_death_no_med'] = pd.NaT
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
logger.debug(key='rti_general_message',
data=f"Person {person_id} has {fracturecastcounts + slingcounts} fractures without treatment"
)
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
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I think this needs to be un-indented, so that it's not inside the clause to do with the number of times the HSI has run. i.e. this need to happen, irrespective of whether or not we're rescheduling the HSI

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logger.debug(key='rti_general_message',
data=f"Person {person_id} has {fracturecastcounts + slingcounts}"
f" fractures without treatment")
return self.make_appt_footprint({})

def did_not_run(self):
Expand Down Expand Up @@ -4057,9 +4069,13 @@ def __init__(self, module, person_id):
self.TREATMENT_ID = 'Rti_OpenFractureTreatment'
self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({'MinorSurg': 1})
self.ACCEPTED_FACILITY_LEVEL = '1b'
self._number_of_times_this_event_has_run = 0
self._maximum_number_times_event_should_run = self.module.parameters[
'maximum_number_of_times_HSI_events_should_run']

def apply(self, person_id, squeeze_factor):
df = self.sim.population.props
self._number_of_times_this_event_has_run += 1
if not df.at[person_id, 'is_alive']:
return self.make_appt_footprint({})
road_traffic_injuries = self.sim.modules['RTI']
Expand Down Expand Up @@ -4131,12 +4147,13 @@ def apply(self, person_id, squeeze_factor):
if code[0] in df.loc[person_id, 'rt_injuries_for_open_fracture_treatment']:
df.loc[person_id, 'rt_injuries_for_open_fracture_treatment'].remove(code[0])
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
logger.debug(key='rti_general_message',
data=f"Person {person_id}'s has {open_fracture_counts} open fractures without treatment",
)
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
logger.debug(key='rti_general_message',
data=f"Person {person_id}'s has {open_fracture_counts} open fractures without treatment",
)
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as per the comment above, I think this need to be outside of the new clause we're introducing about the rescheduling (or not) the HSI event.

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def did_not_run(self):
person_id = self.target
Expand Down Expand Up @@ -4174,10 +4191,15 @@ def __init__(self, module, person_id):
self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({
('Under5OPD' if self.sim.population.props.at[person_id, "age_years"] < 5 else 'Over5OPD'): 1})
self.ACCEPTED_FACILITY_LEVEL = '1b'
self._number_of_times_this_event_has_run = 0
self._maximum_number_times_event_should_run = self.module.parameters[
'maximum_number_of_times_HSI_events_should_run']

def apply(self, person_id, squeeze_factor):
get_item_code = self.sim.modules['HealthSystem'].get_item_code_from_item_name
df = self.sim.population.props
self._number_of_times_this_event_has_run += 1

if not df.at[person_id, 'is_alive']:
return self.make_appt_footprint({})
road_traffic_injuries = self.sim.modules['RTI']
Expand Down Expand Up @@ -4222,11 +4244,12 @@ def apply(self, person_id, squeeze_factor):
assert df.loc[person_id, date_to_remove_daly_column] > self.sim.date
df.loc[person_id, 'rt_date_death_no_med'] = pd.NaT
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
logger.debug(key='rti_general_message',
data="This facility has no treatment for open wounds available.")
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
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same comment as above, about moving this outside the new clause

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Suggested change
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)

logger.debug(key='rti_general_message',
data="This facility has no treatment for open wounds available.")
return self.make_appt_footprint({})

def did_not_run(self):
Expand Down Expand Up @@ -4269,11 +4292,15 @@ def __init__(self, module, person_id):

p = self.module.parameters
self.prob_mild_burns = p['prob_mild_burns']
self._number_of_times_this_event_has_run = 0
self._maximum_number_times_event_should_run = p['maximum_number_of_times_HSI_events_should_run']


def apply(self, person_id, squeeze_factor):
get_item_code = self.sim.modules['HealthSystem'].get_item_code_from_item_name
df = self.sim.population.props
self._number_of_times_this_event_has_run += 1

if not df.at[person_id, 'is_alive']:
return self.make_appt_footprint({})
road_traffic_injuries = self.sim.modules['RTI']
Expand Down Expand Up @@ -4346,11 +4373,12 @@ def apply(self, person_id, squeeze_factor):
)
df.loc[person_id, 'rt_date_death_no_med'] = pd.NaT
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
logger.debug(key='rti_general_message',
data="This facility has no treatment for burns available.")
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
if pd.isnull(df.loc[person_id, 'rt_date_death_no_med']):
df.loc[person_id, 'rt_date_death_no_med'] = self.sim.date + DateOffset(days=7)
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same comment as above about moving this outside the new clause.

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logger.debug(key='rti_general_message',
data="This facility has no treatment for burns available.")

def did_not_run(self):
person_id = self.target
Expand All @@ -4373,9 +4401,14 @@ def __init__(self, module, person_id):
self.TREATMENT_ID = 'Rti_TetanusVaccine'
self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({'EPI': 1})
self.ACCEPTED_FACILITY_LEVEL = '1b'
self._number_of_times_this_event_has_run = 0
self._maximum_number_times_event_should_run = self.module.parameters[
'maximum_number_of_times_HSI_events_should_run']

def apply(self, person_id, squeeze_factor):
df = self.sim.population.props
self._number_of_times_this_event_has_run += 1

if not df.at[person_id, 'is_alive']:
return self.make_appt_footprint({})
person_injuries = df.loc[[person_id], RTI.INJURY_COLUMNS]
Expand Down Expand Up @@ -4404,9 +4437,10 @@ def apply(self, person_id, squeeze_factor):
logger.debug(key='rti_general_message',
data=f"Tetanus vaccine requested for person {person_id} and given")
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
logger.debug(key='rti_general_message',
data=f"Tetanus vaccine requested for person {person_id}, not given")
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
logger.debug(key='rti_general_message',
data=f"Tetanus vaccine requested for person {person_id}, not given")
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return self.make_appt_footprint({})

def did_not_run(self):
Expand Down Expand Up @@ -4434,9 +4468,14 @@ def __init__(self, module, person_id):
self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({
('Under5OPD' if self.sim.population.props.at[person_id, "age_years"] < 5 else 'Over5OPD'): 1})
self.ACCEPTED_FACILITY_LEVEL = '1b'
self._number_of_times_this_event_has_run = 0
self._maximum_number_times_event_should_run = self.module.parameters[
'maximum_number_of_times_HSI_events_should_run']

def apply(self, person_id, squeeze_factor):
df = self.sim.population.props
self._number_of_times_this_event_has_run += 1

if not df.at[person_id, 'is_alive']:
return self.make_appt_footprint({})
# Check that the person sent here is alive, has been through A&E and RTI_Med_int
Expand Down Expand Up @@ -4545,10 +4584,11 @@ def apply(self, person_id, squeeze_factor):
data=dict_to_output,
description='Pain medicine successfully provided to the person')
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
logger.debug(key='rti_general_message',
data=f"This facility has no pain management available for their mild pain, person "
f"{person_id}.")
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
logger.debug(key='rti_general_message',
data=f"This facility has no pain management available for their mild pain, person "
f"{person_id}.")
return self.make_appt_footprint({})

if pain_level == "moderate":
Expand Down Expand Up @@ -4576,10 +4616,11 @@ def apply(self, person_id, squeeze_factor):
data=dict_to_output,
description='Pain medicine successfully provided to the person')
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
logger.debug(key='rti_general_message',
data=f"This facility has no pain management available for moderate pain for person "
f"{person_id}.")
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
logger.debug(key='rti_general_message',
data=f"This facility has no pain management available for moderate pain for person "
f"{person_id}.")
return self.make_appt_footprint({})

if pain_level == "severe":
Expand Down Expand Up @@ -4608,10 +4649,11 @@ def apply(self, person_id, squeeze_factor):
data=dict_to_output,
description='Pain medicine successfully provided to the person')
else:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
logger.debug(key='rti_general_message',
data=f"This facility has no pain management available for severe pain for person "
f"{person_id}.")
if self._number_of_times_this_event_has_run < self._maximum_number_times_event_should_run:
self.sim.modules['RTI'].schedule_hsi_event_for_tomorrow(self)
logger.debug(key='rti_general_message',
data=f"This facility has no pain management available for severe pain for person "
f"{person_id}.")
return self.make_appt_footprint({})

def did_not_run(self):
Expand Down