Add difference in recovered to calc of new I

Author: Corey Chivers

src/penn_chime/charts.py

@@ -74,7 +74,7 @@ def admitted_patients_chart(
 
     return (
         alt.Chart(census.head(plot_projection_days))
-        .transform_fold(fold=["Hospitalized Census", "ICU Census", "Ventilated Census"])
+        .transform_fold(fold=["Hospitalized", "ICU", "Ventilated"])
         .mark_line(point=True)
         .encode(
             x=alt.X(**x_kwargs),

src/penn_chime/models.py

@@ -70,11 +70,10 @@ def sim_sir_df(p) -> pd.DataFrame:
 
 
 def get_dispositions(
-    infected: np.ndarray, rates: Tuple[float, ...], market_share: float = 1.0
+    patient_state: np.ndarray, rates: Tuple[float, ...], market_share: float = 1.0
 ) -> Tuple[np.ndarray, ...]:
     """Get dispositions of infected adjusted by rate and market_share."""
-    return (*(infected * rate * market_share for rate in rates),)
-
+    return (*(patient_state * rate * market_share for rate in rates),)
 
 
 def build_admissions_df(p) -> pd.DataFrame:
@@ -117,7 +116,7 @@ def build_census_df(
     census_df = census_df[["day", "Hospitalized", "ICU", "Ventilated"]]
     census_df = census_df.head(n_days)
     census_df = census_df.rename(
-        columns={disposition: f"{disposition} Census"
+        columns={disposition: f"{disposition}"
                  for disposition
                  in ("Hospitalized", "ICU", "Ventilated")}
     )

src/penn_chime/parameters.py

@@ -112,7 +112,13 @@ def n_days(self, n_days: int):
         )
         self.susceptible_v, self.infected_v, self.recovered_v = s_v, i_v, r_v
 
-        self.dispositions = hospitalized_v, icu_v, ventilated_v = \
+        i_hospitalized_v, i_icu_v, i_ventilated_v = \
             get_dispositions(i_v, self.rates, self.market_share)
+        r_hospitalized_v, r_icu_v, r_ventilated_v = \
+            get_dispositions(r_v, self.rates, self.market_share)
+
+        self.dispositions = (i_hospitalized_v+r_hospitalized_v, 
+            i_icu_v+r_icu_v, i_ventilated_v+r_ventilated_v)
+
         self.hospitalized_v, self.icu_v, self.ventilated_v = \
-            hospitalized_v, icu_v, ventilated_v
+            i_hospitalized_v, i_icu_v, i_ventilated_v