Allow the user to prescribe mitigation date

src/penn_chime/models.py

@@ -147,17 +147,29 @@ def __init__(self, p: Parameters):
         self.daily_growth_rate_t = get_growth_rate(self.doubling_time_t)
 
     def run_projection(self, p):
+        if p.mitigation_date is not None:
+            mitigation_day = -(p.current_date - p.mitigation_date).days
+        else:
+            mitigation_day = 0
+
+        total_days = self.i_day + p.n_days
+
+        if mitigation_day < -self.i_day:
+            mitigation_day = -self.i_day
+
+        pre_mitigation_days = self.i_day + mitigation_day
+        post_mitigation_days = total_days - pre_mitigation_days
+
         self.raw_df = sim_sir_df(
             self.susceptible,
             self.infected,
             p.recovered,
             self.gamma,
             -self.i_day,
-            self.beta,
-            self.i_day,
-            self.beta_t,
-            p.n_days
+            self.beta, pre_mitigation_days,
+            self.beta_t, post_mitigation_days
         )
+
         self.dispositions_df = build_dispositions_df(self.raw_df, self.rates, p.market_share, p.current_date)
         self.admits_df = build_admits_df(self.dispositions_df)
         self.census_df = build_census_df(self.admits_df, self.days)

src/penn_chime/parameters.py

@@ -55,6 +55,7 @@ def __init__(
         hospitalized: Disposition,
         icu: Disposition,
         relative_contact_rate: float,
+        mitigation_date: Optional[date] = None,
         ventilated: Disposition,
         current_date: date = date.today(),
         date_first_hospitalized: Optional[date] = None,
@@ -68,7 +69,6 @@ def __init__(
         region: Optional[Regions] = None,
     ):
         self.current_hospitalized = StrictlyPositive(value=current_hospitalized)
-        self.relative_contact_rate = Rate(value=relative_contact_rate)
 
         Rate(value=hospitalized.rate), Rate(value=icu.rate), Rate(value=ventilated.rate)
         StrictlyPositive(value=hospitalized.days), StrictlyPositive(value=icu.days),
@@ -92,6 +92,9 @@ def __init__(
         self.date_first_hospitalized = OptionalDate(value=date_first_hospitalized)
         self.doubling_time = OptionalStrictlyPositive(value=doubling_time)
 
+        self.relative_contact_rate = Rate(value=relative_contact_rate)
+        self.mitigation_date = OptionalDate(value=mitigation_date)
+
         self.infectious_days = StrictlyPositive(value=infectious_days)
         self.market_share = Rate(value=market_share)
         self.max_y_axis = OptionalStrictlyPositive(value=max_y_axis)

src/penn_chime/presentation.py

@@ -11,6 +11,7 @@
     CHANGE_DATE,
     DATE_FORMAT,
     DOCS_URL,
+    EPSILON,
     FLOAT_INPUT_MIN,
     FLOAT_INPUT_STEP,
 )
@@ -204,6 +205,10 @@ def display_sidebar(st, d: Parameters) -> Parameters:
         st_obj, "Date of first hospitalized case - Enter this date to have chime estimate the initial doubling time",
         value=d.date_first_hospitalized,
     )
+    mitigation_date_input = DateInput(
+        st_obj, "Date of social distancing measures effect (may be delayed from implementation)",
+        value=d.mitigation_date
+    )
     relative_contact_pct_input = PercentInput(
         st_obj,
         "Social distancing (% reduction in social contact going forward)",
@@ -309,7 +314,15 @@ def display_sidebar(st, d: Parameters) -> Parameters:
         doubling_time = doubling_time_input()
         date_first_hospitalized = None
 
-    relative_contact_rate = relative_contact_pct_input()
+    if st.sidebar.checkbox(
+        "Social distancing measures have been implemented",
+        value=(d.relative_contact_rate > EPSILON)
+    ):
+        mitigation_date = mitigation_date_input()
+        relative_contact_rate = relative_contact_pct_input()
+    else:
+        mitigation_date = None
+        relative_contact_rate = EPSILON
 
     st.sidebar.markdown(
         "### Severity Parameters [ℹ]({docs_url}/what-is-chime/parameters#severity-parameters)".format(
@@ -343,6 +356,7 @@ def display_sidebar(st, d: Parameters) -> Parameters:
         hospitalized=Disposition(hospitalized_rate, hospitalized_days),
         icu=Disposition(icu_rate, icu_days),
         relative_contact_rate=relative_contact_rate,
+        mitigation_date=mitigation_date,
         ventilated=Disposition(ventilated_rate, ventilated_days),
         current_date=current_date,
         date_first_hospitalized=date_first_hospitalized,

src/penn_chime/settings.py

@@ -16,6 +16,7 @@ def get_defaults():
         infectious_days=14,
         market_share=0.15,
         n_days=100,
+        mitigation_date=date.today(),
         relative_contact_rate=0.3,
         ventilated=Disposition(0.005, 10),
     )

tests/conftest.py

@@ -51,6 +51,7 @@ def DEFAULTS():
         doubling_time=4.0,
         n_days=60,
         market_share=0.15,
+        mitigation_date=datetime(year=2020, month=3, day=28),
         relative_contact_rate=0.3,
         hospitalized=Disposition(0.025, 7),
         icu=Disposition(0.0075, 9),
@@ -65,6 +66,7 @@ def param():
         current_hospitalized=100,
         doubling_time=6.0,
         market_share=0.05,
+        mitigation_date=datetime(year=2020, month=3, day=28),
         relative_contact_rate=0.15,
         population=500000,
         hospitalized=Disposition(0.05, 7),
@@ -81,6 +83,7 @@ def halving_param():
         current_hospitalized=100,
         doubling_time=6.0,
         market_share=0.05,
+        mitigation_date=datetime(year=2020, month=3, day=28),
         relative_contact_rate=0.7,
         population=500000,
         hospitalized=Disposition(0.05, 7),