Revise ceil to floor

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(

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

@@ -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 [v1.1.1](https://github.com/CodeForPhilly/chime/releases/tag/v1.1.1) (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()