diff --git a/src/penn_chime/charts.py b/src/penn_chime/charts.py
index fb239356..c29bd5bc 100644
--- a/src/penn_chime/charts.py
+++ b/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),
diff --git a/src/penn_chime/models.py b/src/penn_chime/models.py
index a578ad32..62219b1c 100644
--- a/src/penn_chime/models.py
+++ b/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:
@@ -86,7 +85,6 @@ def build_admissions_df(p) -> pd.DataFrame:
projection = pd.DataFrame.from_dict(data_dict)
# New cases
projection_admits = projection.iloc[:-1, :] - projection.shift(1)
- projection_admits[projection_admits < 0] = 0
projection_admits["day"] = range(projection_admits.shape[0])
return projection_admits
@@ -117,7 +115,7 @@ 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")}
)
diff --git a/src/penn_chime/parameters.py b/src/penn_chime/parameters.py
index 38438d77..37b3a4c2 100644
--- a/src/penn_chime/parameters.py
+++ b/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
diff --git a/src/penn_chime/presentation.py b/src/penn_chime/presentation.py
index 4d7c8aa4..4b37660f 100644
--- a/src/penn_chime/presentation.py
+++ b/src/penn_chime/presentation.py
@@ -44,6 +44,7 @@ def display_header(st, p):
""",
unsafe_allow_html=True,
)
+ st.markdown("""**IMPORTANT NOTICE**: Admissions and Census calculations were previously **undercounting**. Please update your reports. See more about this issue [here](https://github.com/CodeForPhilly/chime/pull/190).""")
st.markdown(
"""*This tool was developed by the [Predictive Healthcare team](http://predictivehealthcare.pennmedicine.org/) at
Penn Medicine. For questions on how to use this tool see the [User docs](https://code-for-philly.gitbook.io/chime/). For questions and comments please see our
diff --git a/tests/test_app.py b/tests/test_app.py
index fc51e6ad..73df291e 100644
--- a/tests/test_app.py
+++ b/tests/test_app.py
@@ -6,7 +6,7 @@
import altair as alt # type: ignore
from src.penn_chime.charts import new_admissions_chart, admitted_patients_chart
-from src.penn_chime.models import sir, sim_sir
+from src.penn_chime.models import sir, sim_sir, build_admissions_df
from src.penn_chime.parameters import Parameters
from src.penn_chime.presentation import display_header
from src.penn_chime.settings import DEFAULTS
@@ -228,8 +228,14 @@ def test_parameters():
assert round(param.infected_v[1], 0) == 43735
assert round(param.recovered_v[30], 0) == 224048
assert [d[0] for d in param.dispositions] == [100.0, 40.0, 20.0]
- assert [round(d[-1], 0) for d in param.dispositions] == [115.0, 46.0, 23.0]
+ assert [round(d[-1], 0) for d in param.dispositions] == [1182.0, 473.0, 236.0]
# change n_days, make sure it cascades
param.n_days = 2
assert len(param.susceptible_v) == len(param.infected_v) == len(param.recovered_v) == param.n_days + 1 == 3
+
+ # test that admissions are being properly calculated (thanks @PhilMiller)
+ admissions = build_admissions_df(param)
+ cumulative_admissions = admissions.cumsum()
+ diff = cumulative_admissions["Hospitalized"][1:-1] - (0.05*0.05 * (param.infected_v[1:-1] + param.recovered_v[1:-1]) - 100)
+ assert (diff.abs() < 0.1).all()