def get_prescriptions_repartition(self,
limit_date,
start_date,
include_null_dates=None):
active_list = ActiveList(self.fuchia_database)
visits = active_list.filter_visits_by_category(
limit_date,
start_date=start_date,
include_null_dates=include_null_dates)
last_visits = visits.groupby('patient_id')['visit_date'].idxmax()
drugs = visits.loc[last_visits].groupby(
'arv_received')['patient_id'].count()
return drugs.sort_values(ascending=False)
def filter_patients_dataframe(self, limit_date, start_date=None,
include_null_dates=False):
followed = FollowedPatients(
self.fuchia_database
).get_filtered_patients_dataframe(
limit_date,
start_date=start_date,
include_null_dates=include_null_dates
)
visits = self.filter_visits_by_category(
limit_date,
start_date=None,
include_null_dates=include_null_dates
)
c1 = (visits['visit_date'] >= start_date)
c2 = (visits['visit_date'] <= limit_date)
visits = visits[c1 & c2]
visits = visits[visits['patient_id'].isin(followed.index)]
cd4 = visits['cd4'] <= 500
oms = visits['stade_oms'] >= 2
visits = visits[cd4 | oms]
patient_ids = visits['patient_id'].unique()
active_list = ActiveList(
self.fuchia_database
).get_filtered_patients_dataframe(
limit_date,
start_date=start_date,
include_null_dates=include_null_dates
)
ids = pd.Index(patient_ids).difference(active_list.index)
return followed.loc[ids], None
def filter_patients_dataframe(self,
limit_date,
start_date=None,
include_null_dates=False):
stopped_prev = ArvStopped(self.fuchia_database)
n_limit = limit_date - relativedelta(months=1)
n_start = start_date - relativedelta(months=1)
stopped_prev_patients = stopped_prev.get_filtered_patients_dataframe(
getLastDayOfPeriod(n_limit.month, n_limit.year),
start_date=getFirstDayOfPeriod(n_start.month, n_start.year),
include_null_dates=include_null_dates)
al = ActiveList(self.fuchia_database)
active_list = al.get_filtered_patients_dataframe(
limit_date,
start_date=start_date,
include_null_dates=include_null_dates)
idx = stopped_prev_patients.index.intersection(active_list.index)
return active_list.loc[idx], None
def filter_patients_dataframe(self,
limit_date,
start_date=None,
include_null_dates=False):
tb_treatment = UnderTbTreatmentPatients(self.fuchia_database)
active_list = ActiveList(self.fuchia_database)
arv_and_tb_treatment = (tb_treatment & active_list)
return arv_and_tb_treatment.get_filtered_patients_dataframe(
limit_date,
start_date=start_date,
include_null_dates=include_null_dates), None
def get_active_list_repartition(self,
limit_date,
start_date,
include_null_dates=None):
active_list = ActiveList(self.fuchia_database)
patients = active_list.get_filtered_patients_dataframe(
limit_date,
start_date=start_date,
include_null_dates=include_null_dates)
visits = active_list.filter_visits_by_category(
limit_date, start_date=None, include_null_dates=include_null_dates)
visits = visits[pd.notnull(visits['arv_received'])]
last_visits = visits.groupby('patient_id')['visit_date'].idxmax()
last_visits = last_visits.loc[patients.index]
# Patient drugs
diff = patients.index.difference(visits.loc[last_visits]['patient_id'])
patients = patients.loc[diff]['arv_drugs']
patients = patients.value_counts()
drugs = visits.loc[last_visits].groupby(
'arv_received')['patient_id'].count()
drugs.loc[patients.index] = drugs + patients
return drugs.sort_values(ascending=False)
def filter_patients_dataframe(self, limit_date, start_date=None,
include_null_dates=False):
active_list = ActiveList(
self.fuchia_database
).get_filtered_patients_dataframe(
limit_date,
start_date=start_date,
include_null_dates=include_null_dates
)
visits_tb = self.fuchia_database.visit_tb_dataframe
c1 = visits_tb['treatment_start'] >= start_date
c2 = visits_tb['treatment_start'] <= limit_date
visits_tb = visits_tb[c1 & c2]
ids = pd.Index(visits_tb['patient_id'].unique())
tb_index = active_list.index.intersection(ids)
return active_list.loc[tb_index], None
def filter_patients_dataframe(self,
limit_date,
start_date=None,
include_null_dates=False):
active_list = ActiveList(
self.fuchia_database).get_filtered_patients_dataframe(
limit_date,
start_date=start_date,
include_null_dates=include_null_dates)
p_limit = limit_date - relativedelta(months=self.retention_duration)
p_start = start_date - relativedelta(months=self.retention_duration)
p_limit = getLastDayOfPeriod(p_limit.month, p_limit.year)
p_start = getFirstDayOfPeriod(p_start.month, p_start.year)
arv_started = ArvStartedDuringPeriod(
self.fuchia_database).get_filtered_patients_dataframe(
p_limit,
start_date=p_start,
include_null_dates=include_null_dates)
intersection = active_list.index.intersection(arv_started.index)
return active_list.loc[intersection], None