Merge pull request #204 from nickcanz/expand_max_days_input

Change projection days from a slider to a number input to allow larger max values

Author: quinn-dougherty

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

@@ -8,7 +8,9 @@ context('Actions', () => {
   it('All + elements are clickable', () => {
     cy.get('.step-up').click( { multiple: true } )
 
+    // This gets the "first" input from the sidebar. From clicking step up,
+    // the number of days to project should increase from default 60 to 70.
     cy.get('input.st-al')
-      .should('has.value', '7')
+      .should('has.value', '70')
   })
 })

src/app.py

@@ -4,10 +4,8 @@
 import streamlit as st  # type: ignore
 
 from penn_chime.presentation import (
-    # additional_projections_chart,
     display_header,
     display_sidebar,
-    display_n_days_slider,
     draw_census_table,
     draw_projected_admissions_table,
     draw_raw_sir_simulation_table,
@@ -38,10 +36,6 @@
     notes = "The total size of the susceptible population will be the entire catchment area for Penn Medicine entities (HUP, PAH, PMC, CCH)"
     show_more_info_about_this_tool(st=st, parameters=p, inputs=DEFAULTS, notes=notes)
 
-# PRESENTATION
-# Two more combination variable initialization / input element creation
-as_date = st.checkbox(label="Present result as dates instead of days", value=False)
-display_n_days_slider(st, p, DEFAULTS)
 
 # begin format data
 admissions_df = build_admissions_df(p=p)  # p.n_days, *p.dispositions)
@@ -50,34 +44,34 @@
 
 st.subheader("New Admissions")
 st.markdown("Projected number of **daily** COVID-19 admissions at Penn hospitals")
-new_admit_chart = new_admissions_chart(alt, admissions_df, parameters=p, as_date=as_date)
+new_admit_chart = new_admissions_chart(alt, admissions_df, parameters=p)
 st.altair_chart(
     new_admit_chart, use_container_width=True
 )
 
 st.markdown(chart_descriptions(new_admit_chart))
 
 if st.checkbox("Show Projected Admissions in tabular form"):
-    draw_projected_admissions_table(st, admissions_df, as_date=as_date)
+    draw_projected_admissions_table(st, admissions_df, as_date=p.as_date)
 st.subheader("Admitted Patients (Census)")
 st.markdown(
     "Projected **census** of COVID-19 patients, accounting for arrivals and discharges at Penn hospitals"
 )
-census_chart = admitted_patients_chart(alt=alt, census=census_df, parameters=p, as_date=as_date)
+census_chart = admitted_patients_chart(alt=alt, census=census_df, parameters=p)
 st.altair_chart(
     census_chart, use_container_width=True
 )
 st.markdown(chart_descriptions(census_chart, suffix=" Census"))
 if st.checkbox("Show Projected Census in tabular form"):
-    draw_census_table(st, census_df, as_date=as_date)
+    draw_census_table(st, census_df, as_date=p.as_date)
 st.markdown(
     """**Click the checkbox below to view additional data generated by this simulation**"""
 )
 if st.checkbox("Show Additional Projections"):
     show_additional_projections(
-        st, alt, additional_projections_chart, parameters=p, as_date=as_date
+        st, alt, additional_projections_chart, parameters=p
     )
     if st.checkbox("Show Raw SIR Simulation Data"):
-        draw_raw_sir_simulation_table(st, parameters=p, as_date=as_date)
+        draw_raw_sir_simulation_table(st, parameters=p)
 write_definitions(st)
 write_footer(st)

src/penn_chime/charts.py

@@ -10,11 +10,12 @@
 
 
 def new_admissions_chart(
-    alt, projection_admits: pd.DataFrame, parameters: Parameters, as_date: bool = False,
+    alt, projection_admits: pd.DataFrame, parameters: Parameters
 ) -> Chart:
     """docstring"""
     plot_projection_days = parameters.n_days - 10
     max_y_axis = parameters.max_y_axis
+    as_date = parameters.as_date
 
     y_scale = alt.Scale()
 
@@ -48,12 +49,13 @@ def new_admissions_chart(
 
 
 def admitted_patients_chart(
-    alt, census: pd.DataFrame, parameters: Parameters, as_date: bool = False
+    alt, census: pd.DataFrame, parameters: Parameters
 ) -> Chart:
     """docstring"""
 
     plot_projection_days = parameters.n_days - 10
     max_y_axis = parameters.max_y_axis
+    as_date = parameters.as_date
     if as_date:
         census = add_date_column(census)
         x_kwargs = {"shorthand": "date:T", "title": "Date"}
@@ -87,10 +89,16 @@ def admitted_patients_chart(
 
 
 def additional_projections_chart(
-    alt, i: np.ndarray, r: np.ndarray, as_date: bool = False, max_y_axis: int = None
+    alt, parameters: Parameters
 ) -> Chart:
+    i = parameters.infected_v
+    r = parameters.recovered_v
     dat = pd.DataFrame({"Infected": i, "Recovered": r})
     dat["day"] = dat.index
+
+    as_date = parameters.as_date
+    max_y_axis = parameters.max_y_axis
+
     if as_date:
         dat = add_date_column(dat)
         x_kwargs = {"shorthand": "date:T", "title": "Date"}

src/penn_chime/parameters.py

@@ -27,7 +27,8 @@ def __init__(
         icu: RateLos,
         ventilated: RateLos,
         max_y_axis: int = None,
-        n_days: int = None
+        n_days: int = None,
+        as_date: bool = False
     ):
         self.current_hospitalized = current_hospitalized
         self.doubling_time = doubling_time
@@ -42,6 +43,7 @@ def __init__(
         self.ventilated = ventilated
 
         self.max_y_axis = max_y_axis
+        self.as_date = as_date
 
         self.rates = tuple(each.rate for each in (hospitalized, icu, ventilated))
         self.lengths_of_stay = tuple(

src/penn_chime/presentation.py

@@ -94,6 +94,14 @@ def display_sidebar(st, d: Constants) -> Parameters:
     if d.known_infected < 1:
         raise ValueError("Known cases must be larger than one to enable predictions.")
 
+    n_days = st.sidebar.number_input(
+        "Number of days to project",
+        min_value=30,
+        value=d.n_days,
+        step=10,
+        format="%i",
+    )
+
     current_hospitalized = st.sidebar.number_input(
         "Currently Hospitalized COVID-19 Patients",
         min_value=0,
@@ -205,6 +213,8 @@ def display_sidebar(st, d: Constants) -> Parameters:
         format="%i",
     )
 
+    as_date = st.sidebar.checkbox(label="Present result as dates instead of days", value=False)
+
     max_y_axis_set = st.sidebar.checkbox("Set the Y-axis on graphs to a static value")
     max_y_axis = None
     if max_y_axis_set:
@@ -213,6 +223,7 @@ def display_sidebar(st, d: Constants) -> Parameters:
         )
 
     return Parameters(
+        n_days=n_days,
         current_hospitalized=current_hospitalized,
         doubling_time=doubling_time,
         known_infected=known_infected,
@@ -223,18 +234,7 @@ def display_sidebar(st, d: Constants) -> Parameters:
         icu=RateLos(icu_rate, icu_los),
         ventilated=RateLos(ventilated_rate, ventilated_los),
         max_y_axis=max_y_axis,
-    )
-
-
-def display_n_days_slider(st, p: Parameters, d: Constants):
-    """Display n_days_slider."""
-    p.n_days = st.slider(
-        "Number of days to project",
-        min_value=30,
-        max_value=200,
-        value=d.n_days,
-        step=1,
-        format="%i",
+        as_date=as_date,
     )
 
 
@@ -369,7 +369,7 @@ def write_footer(st):
 
 
 def show_additional_projections(
-    st, alt, charting_func, parameters, as_date: bool = False,
+    st, alt, charting_func, parameters
 ):
     st.subheader(
         "The number of infected and recovered individuals in the hospital catchment region at any given moment"
@@ -378,10 +378,7 @@ def show_additional_projections(
     st.altair_chart(
         charting_func(
             alt,
-            parameters.infected_v,
-            parameters.recovered_v,
-            as_date=as_date,
-            max_y_axis=parameters.max_y_axis,
+            parameters=parameters
         ),
         use_container_width=True,
     )
@@ -423,7 +420,8 @@ def draw_census_table(st, census_df: pd.DataFrame, as_date: bool = False):
     return None
 
 
-def draw_raw_sir_simulation_table(st, parameters, as_date: bool = False):
+def draw_raw_sir_simulation_table(st, parameters):
+    as_date = parameters.as_date
     days = np.arange(0, parameters.n_days + 1)
     data_list = [
         days,

tests/test_app.py

@@ -288,7 +288,8 @@ def test_chart_descriptions():
     # census chart
     census_df = pd.read_csv('tests/census_df.csv')
     census_df = census_df.rename(columns={'hosp': 'Hospitalized', 'icu': 'ICU', 'vent': 'Ventilated'})
-    chart = admitted_patients_chart(alt, census_df, PARAM, as_date=True)
+    PARAM.as_date = True
+    chart = admitted_patients_chart(alt, census_df, PARAM)
     description = chart_descriptions(chart)
 
     assert str(ceil(chart.data['Ventilated'].max())) in description