Changes_for_v1_1_1

Changes for v1.1.1 with model changes.

Author: jlubken

e2e/cypress/integration/tests/steppers.spec.js

@@ -6,7 +6,7 @@ context('Increment steppers', () => {
   });
 
   it('Increment regional population', () => {
-    cy.contains('Hospitalized Admissions peaks at 301');
+    cy.contains('Hospitalized Admissions peaks at 300');
 
     cy.get('input.st-al').eq(0)
       .should('has.value', '3600000');
@@ -16,11 +16,11 @@ context('Increment steppers', () => {
     cy.get('input.st-al').eq(0)
       .should('has.value', '3600001');
 
-    cy.contains('Hospitalized Admissions peaks at 301');
+    cy.contains('Hospitalized Admissions peaks at 300');
   });
 
   it('Increment hospital market share', () => {
-    cy.contains('Hospitalized Admissions peaks at 301');
+    cy.contains('Hospitalized Admissions peaks at 300');
 
     cy.get('input.st-al').eq(1)
       .should('has.value', '15');
@@ -30,11 +30,11 @@ context('Increment steppers', () => {
     cy.get('input.st-al').eq(1)
       .should('has.value', '15.1');
 
-    cy.contains('Hospitalized Admissions peaks at 303');
+    cy.contains('Hospitalized Admissions peaks at 302');
   });
 
   it('Increment doubling time', () => {
-    cy.contains('Hospitalized Admissions peaks at 301');
+    cy.contains('Hospitalized Admissions peaks at 300');
 
     cy.get('input.st-al').eq(3)
       .should('has.value', '4');
@@ -44,6 +44,6 @@ context('Increment steppers', () => {
     cy.get('input.st-al').eq(3)
       .should('has.value', '4.25');
 
-    cy.contains('Hospitalized Admissions peaks at 273');
+    cy.contains('Hospitalized Admissions peaks at 272');
   });
 });

setup.py

@@ -1,6 +1,6 @@
 """Setup file for chime
 """
-__version__ = "1.1.0"
+__version__ = "1.1.1"
 __author__ = "Predictive Healthcare @ Penn Medicine"
 
 from os import path

src/app.py

@@ -40,7 +40,7 @@
 
 st.subheader("New Admissions")
 st.markdown("Projected number of **daily** COVID-19 admissions. \n\n _NOTE: Now including estimates of prior admissions for comparison._")
-admits_chart = build_admits_chart(alt=alt, admits_df=m.admits_df, max_y_axis=p.max_y_axis)
+admits_chart = build_admits_chart(alt=alt, admits_floor_df=m.admits_floor_df, max_y_axis=p.max_y_axis)
 st.altair_chart(admits_chart, use_container_width=True)
 st.markdown(build_descriptions(chart=admits_chart, labels=p.labels, suffix=" Admissions"))
 display_download_link(
@@ -54,15 +54,15 @@
     if not st.checkbox("Show Daily Counts"):
         admits_modulo = 7
     table_df = build_table(
-        df=m.admits_df,
+        df=m.admits_floor_df,
         labels=p.labels,
         modulo=admits_modulo)
     st.table(table_df)
 
 
 st.subheader("Admitted Patients (Census)")
 st.markdown("Projected **census** of COVID-19 patients, accounting for arrivals and discharges \n\n _NOTE: Now including estimates of prior census for comparison._")
-census_chart = build_census_chart(alt=alt, census_df=m.census_df, max_y_axis=p.max_y_axis)
+census_chart = build_census_chart(alt=alt, census_floor_df=m.census_floor_df, max_y_axis=p.max_y_axis)
 st.altair_chart(census_chart, use_container_width=True)
 st.markdown(build_descriptions(chart=census_chart, labels=p.labels, suffix=" Census"))
 display_download_link(
@@ -76,15 +76,15 @@
     if not st.checkbox("Show Daily Census Counts"):
         census_modulo = 7
     table_df = build_table(
-        df=m.census_df,
+        df=m.census_floor_df,
         labels=p.labels,
         modulo=census_modulo)
     st.table(table_df)
 
 
 st.subheader("Susceptible, Infected, and Recovered")
 st.markdown("The number of susceptible, infected, and recovered individuals in the hospital catchment region at any given moment")
-sim_sir_w_date_chart = build_sim_sir_w_date_chart(alt=alt, sim_sir_w_date_df=m.sim_sir_w_date_df)
+sim_sir_w_date_chart = build_sim_sir_w_date_chart(alt=alt, sim_sir_w_date_floor_df=m.sim_sir_w_date_floor_df)
 st.altair_chart(sim_sir_w_date_chart, use_container_width=True)
 display_download_link(
     st,
@@ -94,7 +94,7 @@
 
 if st.checkbox("Show SIR Simulation in tabular form"):
     table_df = build_table(
-        df=m.sim_sir_w_date_df,
+        df=m.sim_sir_w_date_floor_df,
         labels=p.labels)
     st.table(table_df)
 

src/penn_chime/charts.py

@@ -14,19 +14,14 @@
 def build_admits_chart(
     *,
     alt,
-    admits_df: pd.DataFrame,
+    admits_floor_df: pd.DataFrame,
     max_y_axis: Optional[int] = None,
 ) -> Chart:
     """Build admits chart."""
     y_scale = alt.Scale()
     if max_y_axis is not None:
         y_scale.domain = (0, max_y_axis)
 
-    ceil_df = admits_df.copy()
-    ceil_df.hospitalized = np.ceil(ceil_df.hospitalized)
-    ceil_df.icu = np.ceil(ceil_df.icu)
-    ceil_df.ventilated = np.ceil(ceil_df.ventilated)
-
     x = dict(shorthand="date:T", title="Date", axis=alt.Axis(format=(DATE_FORMAT)))
     y = dict(shorthand="value:Q", title="Daily admissions", scale=y_scale)
     color = "key:N"
@@ -45,14 +40,14 @@ def build_admits_chart(
         .transform_filter(alt.datum.day == 0)
         .mark_rule(color="black", opacity=0.35, size=2)
     )
-    return alt.layer(points, bar, data=ceil_df)
+    return alt.layer(points, bar, data=admits_floor_df)
 
 
 
 def build_census_chart(
     *,
     alt,
-    census_df: pd.DataFrame,
+    census_floor_df: pd.DataFrame,
     max_y_axis: Optional[int] = None,
 ) -> Chart:
     """Build census chart."""
@@ -78,13 +73,13 @@ def build_census_chart(
         .transform_filter(alt.datum.day == 0)
         .mark_rule(color="black", opacity=0.35, size=2)
     )
-    return alt.layer(points, bar, data=census_df)
+    return alt.layer(points, bar, data=census_floor_df)
 
 
 def build_sim_sir_w_date_chart(
     *,
     alt,
-    sim_sir_w_date_df: pd.DataFrame,
+    sim_sir_w_date_floor_df: pd.DataFrame,
     max_y_axis: Optional[int] = None,
 ) -> Chart:
     """Build sim sir w date chart."""
@@ -110,7 +105,7 @@ def build_sim_sir_w_date_chart(
         .transform_filter(alt.datum.day == 0)
         .mark_rule(color="black", opacity=0.35, size=2)
     )
-    return alt.layer(points, bar, data=sim_sir_w_date_df)
+    return alt.layer(points, bar, data=sim_sir_w_date_floor_df)
 
 
 def build_descriptions(
@@ -162,5 +157,6 @@ def build_table(
     modulo: int = 1,
 ) -> pd.DataFrame:
     table_df = df[np.mod(df.day, modulo) == 0].copy()
+    table_df.date = table_df.date.dt.strftime(DATE_FORMAT)
     table_df.rename(labels)
     return table_df

src/penn_chime/constants.py

@@ -7,7 +7,7 @@
 longer match current results, indicating when users should
 re-run their reports
 """
-CHANGE_DATE = date(year=2020, month=3, day=30)
+CHANGE_DATE = date(year=2020, month=4, day=1)
 
 DATE_FORMAT = "%b, %d"  # see https://strftime.org
 DOCS_URL = "https://code-for-philly.gitbook.io/chime"

src/penn_chime/models.py

@@ -9,7 +9,7 @@
 from datetime import date, datetime, timedelta
 from logging import INFO, basicConfig, getLogger
 from sys import stdout
-from typing import Dict, Generator, Tuple, Optional
+from typing import Dict, Generator, Tuple, Sequence,Optional
 
 import numpy as np
 import pandas as pd
@@ -40,6 +40,8 @@ def __init__(self, p: Parameters):
             for key, d in p.dispositions.items()
         }
 
+        self.keys = ("susceptible", "infected", "recovered")
+
         # Note: this should not be an integer.
         # We're appoximating infected from what we do know.
         # TODO market_share > 0, hosp_rate > 0
@@ -153,7 +155,11 @@ def __init__(self, p: Parameters):
             self.beta_t * susceptible - gamma + 1)
         self.doubling_time_t = doubling_time_t
 
-        self.sim_sir_w_date_df = build_sim_sir_w_date_df(self.raw_df, p.current_date)
+        self.sim_sir_w_date_df = build_sim_sir_w_date_df(self.raw_df, p.current_date, self.keys)
+
+        self.sim_sir_w_date_floor_df = build_floor_df(self.sim_sir_w_date_df, self.keys)
+        self.admits_floor_df = build_floor_df(self.admits_df, p.dispositions.keys())
+        self.census_floor_df = build_floor_df(self.census_df, p.dispositions.keys())
 
         self.daily_growth_rate = get_growth_rate(p.doubling_time)
         self.daily_growth_rate_t = get_growth_rate(self.doubling_time_t)
@@ -252,7 +258,8 @@ def gen_sir(
 
 
 def sim_sir_df(
-    s: float, i: float, r: float, gamma: float, i_day: int, *args
+    s: float, i: float, r: float,
+    gamma: float, i_day: int, *args
 ) -> pd.DataFrame:
     """Simulate the SIR model forward in time."""
     return pd.DataFrame(
@@ -264,14 +271,28 @@ def sim_sir_df(
 def build_sim_sir_w_date_df(
     raw_df: pd.DataFrame,
     current_date: datetime,
+    keys: Sequence[str],
 ) -> pd.DataFrame:
     day = raw_df.day
     return pd.DataFrame({
         "day": day,
         "date": day.astype('timedelta64[D]') + np.datetime64(current_date),
-        "susceptible": raw_df.susceptible,
-        "infected": raw_df.infected,
-        "recovered": raw_df.recovered,
+        **{
+            key: raw_df[key]
+            for key in keys
+        }
+    })
+
+
+def build_floor_df(df, keys):
+    """Build floor sim sir w date."""
+    return pd.DataFrame({
+        "day": df.day,
+        "date": df.date,
+        **{
+            key: np.floor(df[key])
+            for key in keys
+        }
     })
 
 
@@ -314,7 +335,7 @@ def build_census_df(
             key: (
                 admits_df[key].cumsum()
                 - admits_df[key].cumsum().shift(los).fillna(0)
-            ).apply(np.ceil)
+            )
             for key, los in lengths_of_stay.items()
         }
     })

src/penn_chime/presentation.py

@@ -279,7 +279,9 @@ def display_sidebar(st, d: Parameters) -> Parameters:
 
     # Build in desired order
     st.sidebar.markdown(
-        """**CHIME [v1.1.0](https://github.com/CodeForPhilly/chime/releases/tag/v1.1.0) (2020/03/30)**"""
+        """**CHIME [v1.1.1](https://github.com/CodeForPhilly/chime/releases/tag/v1.1.1) ({change_date})**""".format(
+            change_date=CHANGE_DATE
+        )
     )
 
     st.sidebar.markdown(

tests/conftest.py

@@ -8,7 +8,7 @@
     Disposition,
     Regions,
 )
-from src.penn_chime.models import SimSirModel
+from src.penn_chime.models import SimSirModel, build_floor_df
 
 
 class MockStreamlit:
@@ -107,8 +107,18 @@ def admits_df():
     )
 
 
+@pytest.fixture
+def admits_floor_df(param, admits_df):
+    return build_floor_df(admits_df, param.dispositions.keys())
+
+
 @pytest.fixture
 def census_df():
     return pd.read_csv(
         "tests/by_doubling_time/2020-03-28_projected_census.csv", parse_dates=["date"]
     )
+
+@pytest.fixture
+def census_floor_df(param, census_df):
+    return build_floor_df(census_df, param.dispositions.keys())
+

tests/penn_chime/test_charts.py

@@ -13,18 +13,21 @@
 # TODO add test for asterisk
 
 
-def test_admits_chart(admits_df):
-    chart = build_admits_chart(alt=alt, admits_df=admits_df)
+DISPOSITION_KEYS = ("hospitalized", "icu", "ventilated")
+
+
+def test_admits_chart(admits_floor_df):
+    chart = build_admits_chart(alt=alt, admits_floor_df=admits_floor_df)
     assert isinstance(chart, (alt.Chart, alt.LayerChart))
-    assert round(chart.data.iloc[40].icu, 0) == 39
+    assert round(chart.data.iloc[40].icu, 0) == 38
 
     # test fx call with no params
     with pytest.raises(TypeError):
         build_admits_chart()
 
 
-def test_build_descriptions(admits_df, param):
-    chart = build_admits_chart(alt=alt, admits_df=admits_df)
+def test_build_descriptions(admits_floor_df, param):
+    chart = build_admits_chart(alt=alt, admits_floor_df=admits_floor_df)
     description = build_descriptions(chart=chart, labels=param.labels)
 
     hosp, icu, vent = description.split("\n\n")  # break out the description into lines
@@ -33,16 +36,16 @@ def test_build_descriptions(admits_df, param):
     assert str(ceil(max_hosp)) in hosp
 
 
-def test_no_asterisk(admits_df, param):
+def test_no_asterisk(admits_floor_df, param):
     param.n_days = 600
 
-    chart = build_admits_chart(alt=alt, admits_df=admits_df)
+    chart = build_admits_chart(alt=alt, admits_floor_df=admits_floor_df)
     description = build_descriptions(chart=chart, labels=param.labels)
     assert "*" not in description
 
 
-def test_census(census_df, param):
-    chart = build_census_chart(alt=alt, census_df=census_df)
+def test_census(census_floor_df, param):
+    chart = build_census_chart(alt=alt, census_floor_df=census_floor_df)
     description = build_descriptions(chart=chart, labels=param.labels)
 
     assert str(ceil(chart.data["ventilated"].max())) in description
@@ -53,12 +56,12 @@ def test_census(census_df, param):
     )
 
 
-def test_census_chart(census_df):
-    chart = build_census_chart(alt=alt, census_df=census_df)
+def test_census_chart(census_floor_df):
+    chart = build_census_chart(alt=alt, census_floor_df=census_floor_df)
     assert isinstance(chart, (alt.Chart, alt.LayerChart))
     assert chart.data.iloc[1].hospitalized == 3
     assert chart.data.iloc[49].ventilated == 365
 
     # test fx call with no params
     with pytest.raises(TypeError):
-        build_census_chart()
+        build_census_chart()