Fix issue 255

Fix issue 255

Author: jlubken

date_first_hospitalized.cfg

@@ -0,0 +1,14 @@
+--current-hospitalized 14
+--date-first-hospitalized 2020-03-07
+--hospitalized-los 7
+--hospitalized-rate 0.025
+--icu-los 9
+--icu-rate 0.0075
+--infectious-days 14
+--known-infected 510
+--market_share 0.15
+--n-days 60
+--population 4119405
+--relative-contact-rate 0.3
+--ventilated-los 10
+--ventilated-rate 0.005

doubling_time.cfg

@@ -0,0 +1,14 @@
+--current-hospitalized 14
+--doubling-time 4.0
+--hospitalized-los 7
+--hospitalized-rate 0.025
+--icu-los 9
+--icu-rate 0.0075
+--infectious-days 14
+--known-infected 510
+--market_share 0.15
+--n-days 60
+--population 4119405
+--relative-contact-rate 0.3
+--ventilated-los 10
+--ventilated-rate 0.005

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

@@ -10,7 +10,7 @@ context('Actions', () => {
 
     // This gets the "first" input from the sidebar. From clicking step up,
     // the Regional Population should increase from default 4119405 to 4219405.
-    cy.get('input.st-al')
+    cy.get('input.st-al').eq(1)
       .should('has.value', '4119406')
   })
 });

settings.cfg

@@ -1,13 +1,13 @@
 --current-hospitalized 14
---doubling-time 4.0 
---known-infected 510
---relative-contact-rate 0.3
+--doubling-time 4.0
 --hospitalized-los 7
 --hospitalized-rate 0.025
 --icu-los 9
 --icu-rate 0.0075
+--infectious-days 14
 --market_share 0.15
 --n-days 60
 --population 4119405
+--relative-contact-rate 0.3
 --ventilated-los 10
 --ventilated-rate 0.005

src/app.py

@@ -4,25 +4,22 @@
 import streamlit as st  # type: ignore
 
 from penn_chime.presentation import (
-    build_download_link,
+    display_download_link,
     display_header,
+    display_more_info,
     display_sidebar,
-    draw_census_table,
-    draw_projected_admissions_table,
-    draw_raw_sir_simulation_table,
     hide_menu_style,
-    show_additional_projections,
-    show_more_info_about_this_tool,
     write_definitions,
     write_footer,
 )
 from penn_chime.settings import DEFAULTS
 from penn_chime.models import SimSirModel
 from penn_chime.charts import (
-    additional_projections_chart,
-    admitted_patients_chart,
-    new_admissions_chart,
-    chart_descriptions
+    build_admits_chart,
+    build_census_chart,
+    build_descriptions,
+    build_sim_sir_w_date_chart,
+    build_table,
 )
 
 # This is somewhat dangerous:
@@ -38,71 +35,67 @@
 
 if st.checkbox("Show more info about this tool"):
     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, model=m, parameters=p, defaults=DEFAULTS, notes=notes)
+    display_more_info(st=st, model=m, parameters=p, defaults=DEFAULTS, notes=notes)
 
 st.subheader("New Admissions")
 st.markdown("Projected number of **daily** COVID-19 admissions at Penn hospitals")
-new_admit_chart = new_admissions_chart(alt, m.admits_df, parameters=p)
-st.altair_chart(
-    new_admissions_chart(alt, m.admits_df, parameters=p),
-    use_container_width=True,
+admits_chart = build_admits_chart(alt=alt, admits_df=m.admits_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))
+display_download_link(
+    st,
+    filename=f"{p.current_date}_projected_admits.csv",
+    df=m.admits_df,
 )
 
-st.markdown(chart_descriptions(new_admit_chart, p.labels))
-
 if st.checkbox("Show Projected Admissions in tabular form"):
-    if st.checkbox("Show Daily Counts"):
-        draw_projected_admissions_table(st, m.admits_df, p.labels, 1, as_date=p.as_date)
-    else:
-        admissions_day_range = st.slider(
-            label="Interval of Days",
-            key="admissions_day_range_slider",
-            min_value=1,
-            max_value=10,
-            value=7 
-        )
-        draw_projected_admissions_table(st, m.admits_df, p.labels, admissions_day_range, as_date=p.as_date)
-    build_download_link(st,
-        filename="projected_admissions.csv",
+    admits_modulo = 1
+    if not st.checkbox("Show Daily Counts"):
+        admits_modulo = 7
+    table_df = build_table(
         df=m.admits_df,
-        parameters=p
-    )
+        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 at Penn hospitals"
-)
-census_chart = admitted_patients_chart(alt=alt, census=m.census_df, parameters=p)
-st.altair_chart(
-    admitted_patients_chart(alt=alt, census=m.census_df, parameters=p),
-    use_container_width=True,
+st.markdown("Projected **census** of COVID-19 patients, accounting for arrivals and discharges at Penn hospitals")
+census_chart = build_census_chart(alt=alt, census_df=m.census_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(
+    st,
+    filename=f"{p.current_date}_projected_census.csv",
+    df=m.census_df,
 )
-st.markdown(chart_descriptions(census_chart, p.labels, suffix=" Census"))
+
 if st.checkbox("Show Projected Census in tabular form"):
-    if st.checkbox("Show Daily Census Counts"):
-        draw_census_table(st, m.census_df, p.labels, 1, as_date=p.as_date)
-    else:
-        census_day_range = st.slider(
-            label='Interval of Days',
-            key="census_day_range_slider",
-            min_value=1,
-            max_value=10,
-            value=7 
-        )
-        draw_census_table(st, m.census_df, p.labels, census_day_range, as_date=p.as_date)
-    build_download_link(st,
-        filename="projected_census.csv",
+    census_modulo = 1
+    if not st.checkbox("Show Daily Census Counts"):
+        census_modulo = 7
+    table_df = build_table(
         df=m.census_df,
-        parameters=p
-    )
+        labels=p.labels,
+        modulo=census_modulo)
+    st.table(table_df)
+
 
-st.markdown(
-    """**Click the checkbox below to view additional data generated by this simulation**"""
+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)
+st.altair_chart(sim_sir_w_date_chart, use_container_width=True)
+display_download_link(
+    st,
+    filename=f"{p.current_date}_sim_sir_w_date.csv",
+    df=m.sim_sir_w_date_df,
 )
-if st.checkbox("Show Additional Projections"):
-    show_additional_projections(
-        st, alt, additional_projections_chart, model=m, parameters=p
-    )
-    if st.checkbox("Show Raw SIR Simulation Data"):
-        draw_raw_sir_simulation_table(st, model=m, parameters=p)
+
+if st.checkbox("Show SIR Simulation in tabular form"):
+    table_df = build_table(
+        df=m.sim_sir_w_date_df,
+        labels=p.labels)
+    st.table(table_df)
+
 write_definitions(st)
 write_footer(st)