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Minor refactor to setting PrEP start date and cumulative use columns.
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@pineapple-cat
pineapple-cat committed Nov 8, 2024
1 parent a4dcf3e commit 09f8538
Showing 1 changed file with 30 additions and 55 deletions.
85 changes: 30 additions & 55 deletions src/hivpy/prep.py
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Original file line number Diff line number Diff line change
Expand Up @@ -520,20 +520,14 @@ def tested_start_prep(self, pop: Population, prep_eligible_pop, prep_type,
pop.set_present_variable(col.PREP_TYPE, prep_type, starting_prep_pop)
pop.set_present_variable(col.EVER_PREP, True, starting_prep_pop)
pop.set_present_variable(col.PREP_JUST_STARTED, True, starting_prep_pop)
# set start dates
pop.set_present_variable(col.LAST_PREP_START_DATE, pop.date, starting_prep_pop)
pop.set_present_variable(first_start_col, pop.date, starting_prep_pop)
# set continuous use
pop.set_present_variable(col.CONT_ON_PREP, time_step, starting_prep_pop)
pop.set_present_variable(col.CONT_ACTIVE_ON_PREP, time_step, starting_prep_pop)
# increment cumulative use
self.set_prep_cumulative_cont(
pop, starting_prep_pop, PrEPType.Oral, col.CUMULATIVE_PREP_ORAL, time_step)
self.set_prep_cumulative_cont(
pop, starting_prep_pop, PrEPType.Cabotegravir, col.CUMULATIVE_PREP_CAB, time_step)
self.set_prep_cumulative_cont(
pop, starting_prep_pop, PrEPType.Lenacapavir, col.CUMULATIVE_PREP_LEN, time_step)
self.set_prep_cumulative_cont(
pop, starting_prep_pop, PrEPType.VaginalRing, col.CUMULATIVE_PREP_VR, time_step)
self.set_all_prep_cumulative(pop, starting_prep_pop, time_step)

def general_start_prep(self, pop: Population, prep_eligible_pop, time_step):
"""
Expand All @@ -553,38 +547,45 @@ def general_start_prep(self, pop: Population, prep_eligible_pop, time_step):
pop.set_present_variable(col.PREP_TYPE, prep_types, starting_prep_pop)
pop.set_present_variable(col.EVER_PREP, True, starting_prep_pop)
pop.set_present_variable(col.PREP_JUST_STARTED, True, starting_prep_pop)

# set start dates
pop.set_present_variable(col.LAST_PREP_START_DATE, pop.date, starting_prep_pop)
self.set_prep_first_start_date(pop, starting_prep_pop, PrEPType.Oral, col.FIRST_ORAL_START_DATE)
self.set_prep_first_start_date(pop, starting_prep_pop, PrEPType.Cabotegravir, col.FIRST_CAB_START_DATE)
self.set_prep_first_start_date(pop, starting_prep_pop, PrEPType.Lenacapavir, col.FIRST_LEN_START_DATE)
self.set_prep_first_start_date(pop, starting_prep_pop, PrEPType.VaginalRing, col.FIRST_VR_START_DATE)
self.set_all_prep_start_dates(pop, starting_prep_pop)
# set continuous use
pop.set_present_variable(col.CONT_ON_PREP, time_step, starting_prep_pop)
pop.set_present_variable(col.CONT_ACTIVE_ON_PREP, time_step, starting_prep_pop)
# increment cumulative use
self.set_prep_cumulative_cont(
pop, starting_prep_pop, PrEPType.Oral, col.CUMULATIVE_PREP_ORAL, time_step)
self.set_prep_cumulative_cont(
pop, starting_prep_pop, PrEPType.Cabotegravir, col.CUMULATIVE_PREP_CAB, time_step)
self.set_prep_cumulative_cont(
pop, starting_prep_pop, PrEPType.Lenacapavir, col.CUMULATIVE_PREP_LEN, time_step)
self.set_prep_cumulative_cont(
pop, starting_prep_pop, PrEPType.VaginalRing, col.CUMULATIVE_PREP_VR, time_step)
self.set_all_prep_cumulative(pop, starting_prep_pop, time_step)

def set_all_prep_start_dates(self, pop: Population, starting_prep_pop):
"""
Set current PrEP start date and all first PrEP start date columns.
"""
pop.set_present_variable(col.LAST_PREP_START_DATE, pop.date, starting_prep_pop)
self.set_prep_first_start_date(pop, starting_prep_pop, PrEPType.Oral, col.FIRST_ORAL_START_DATE)
self.set_prep_first_start_date(pop, starting_prep_pop, PrEPType.Cabotegravir, col.FIRST_CAB_START_DATE)
self.set_prep_first_start_date(pop, starting_prep_pop, PrEPType.Lenacapavir, col.FIRST_LEN_START_DATE)
self.set_prep_first_start_date(pop, starting_prep_pop, PrEPType.VaginalRing, col.FIRST_VR_START_DATE)

def set_prep_first_start_date(self, pop: Population, starting_prep_pop, prep_type, first_start_date_col):
"""
Set a specific start date column for the population starting a
corresponding PrEP type for the first time.
Set a specific start date column for the population starting a corresponding
PrEP type for the first time. Only overwrites if first start date is None.
"""
pop.set_present_variable(
first_start_date_col, pop.date,
pop.get_sub_pop_intersection(
starting_prep_pop, pop.get_sub_pop(AND(COND(col.PREP_TYPE, op.eq, prep_type),
COND(first_start_date_col, op.eq, None)))))

def set_prep_cumulative_cont(self, pop: Population, using_prep_pop, prep_type, cumulative_col, time_step):
def set_all_prep_cumulative(self, pop: Population, using_prep_pop, time_step):
"""
Increment all cumulative PrEP usage columns for active PrEP users.
"""
self.set_prep_cumulative(pop, using_prep_pop, PrEPType.Oral, col.CUMULATIVE_PREP_ORAL, time_step)
self.set_prep_cumulative(pop, using_prep_pop, PrEPType.Cabotegravir, col.CUMULATIVE_PREP_CAB, time_step)
self.set_prep_cumulative(pop, using_prep_pop, PrEPType.Lenacapavir, col.CUMULATIVE_PREP_LEN, time_step)
self.set_prep_cumulative(pop, using_prep_pop, PrEPType.VaginalRing, col.CUMULATIVE_PREP_VR, time_step)

def set_prep_cumulative(self, pop: Population, using_prep_pop, prep_type, cumulative_col, time_step):
"""
Increment a specific cumulative PrEP usage column for the population using a
corresponding PrEP type. Applies to those starting, continuing, or switching PrEP.
Expand Down Expand Up @@ -683,25 +684,14 @@ def continue_prep(self, pop: Population, time_step):
# set new prep types
pop.set_present_variable(col.PREP_TYPE, prep_types, switching_prep_pop)
# set start dates
pop.set_present_variable(col.LAST_PREP_START_DATE, pop.date, switching_prep_pop)
self.set_prep_first_start_date(pop, switching_prep_pop, PrEPType.Oral, col.FIRST_ORAL_START_DATE)
self.set_prep_first_start_date(pop, switching_prep_pop, PrEPType.Cabotegravir, col.FIRST_CAB_START_DATE)
self.set_prep_first_start_date(pop, switching_prep_pop, PrEPType.Lenacapavir, col.FIRST_LEN_START_DATE)
self.set_prep_first_start_date(pop, switching_prep_pop, PrEPType.VaginalRing, col.FIRST_VR_START_DATE)
self.set_all_prep_start_dates(pop, switching_prep_pop)
# reset continuous use
pop.set_present_variable(col.CONT_ON_PREP, time_step, switching_prep_pop)
pop.set_present_variable(col.CONT_ACTIVE_ON_PREP, time_step, switching_prep_pop)

if len(using_prep_pop) > 0:
# increment cumulative use
self.set_prep_cumulative_cont(
pop, using_prep_pop, PrEPType.Oral, col.CUMULATIVE_PREP_ORAL, time_step)
self.set_prep_cumulative_cont(
pop, using_prep_pop, PrEPType.Cabotegravir, col.CUMULATIVE_PREP_CAB, time_step)
self.set_prep_cumulative_cont(
pop, using_prep_pop, PrEPType.Lenacapavir, col.CUMULATIVE_PREP_LEN, time_step)
self.set_prep_cumulative_cont(
pop, using_prep_pop, PrEPType.VaginalRing, col.CUMULATIVE_PREP_VR, time_step)
self.set_all_prep_cumulative(pop, using_prep_pop, time_step)

if len(stopping_prep_pop) > 0:
# stop continuous use
Expand Down Expand Up @@ -750,27 +740,12 @@ def restart_prep(self, pop: Population, time_step):
pop.set_present_variable(col.PREP_TYPE, prep_types, restarting_prep_pop)
pop.set_present_variable(col.PREP_JUST_STARTED, True, restarting_prep_pop)
# set start dates
pop.set_present_variable(col.LAST_PREP_START_DATE, pop.date, restarting_prep_pop)
self.set_prep_first_start_date(
pop, restarting_prep_pop, PrEPType.Oral, col.FIRST_ORAL_START_DATE)
self.set_prep_first_start_date(
pop, restarting_prep_pop, PrEPType.Cabotegravir, col.FIRST_CAB_START_DATE)
self.set_prep_first_start_date(
pop, restarting_prep_pop, PrEPType.Lenacapavir, col.FIRST_LEN_START_DATE)
self.set_prep_first_start_date(
pop, restarting_prep_pop, PrEPType.VaginalRing, col.FIRST_VR_START_DATE)
self.set_all_prep_start_dates(pop, restarting_prep_pop)
# set continuous use
pop.set_present_variable(col.CONT_ON_PREP, time_step, restarting_prep_pop)
pop.set_present_variable(col.CONT_ACTIVE_ON_PREP, time_step, restarting_prep_pop)
# increment cumulative use
self.set_prep_cumulative_cont(
pop, restarting_prep_pop, PrEPType.Oral, col.CUMULATIVE_PREP_ORAL, time_step)
self.set_prep_cumulative_cont(
pop, restarting_prep_pop, PrEPType.Cabotegravir, col.CUMULATIVE_PREP_CAB, time_step)
self.set_prep_cumulative_cont(
pop, restarting_prep_pop, PrEPType.Lenacapavir, col.CUMULATIVE_PREP_LEN, time_step)
self.set_prep_cumulative_cont(
pop, restarting_prep_pop, PrEPType.VaginalRing, col.CUMULATIVE_PREP_VR, time_step)
self.set_all_prep_cumulative(pop, restarting_prep_pop, time_step)
# unset stop date
pop.set_present_variable(col.LAST_PREP_STOP_DATE, None, restarting_prep_pop)

Expand Down

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