Merge develop

Author: jlubken

docs/CONTRIBUTING.md

@@ -30,6 +30,7 @@ As of March 21, help is especially wanted from contributors with experience in K
 - Request review from the relevant maintainer(s).
 - Check your pull request periodically to see if any changes have been requested or any merge conflicts have arisen.
 - If a merge conflict arises, rebase against the latest `develop` branch and force-push the new branch as early as you can. You may need to do this more than once before your changes get merged. Do your best to keep your branch in a mergeable state until it is finished being reviewed and accepted.
+- If your change affects the results calculated or presented, update `change_date` in `src/penn_chime/parameters.py` when the pull request is ready for merge, so users can see when results have last changed
 - Note: Frequent contributors with write access can submit pull requests from a new branch in the `CodeforPhilly/chime` repository.
 
 ## Review & Release

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

@@ -4,7 +4,6 @@
 import streamlit as st  # type: ignore
 
 from penn_chime.presentation import (
-    # additional_projections_chart,
     display_header,
     display_sidebar,
     draw_census_table,
@@ -22,6 +21,7 @@
     additional_projections_chart,
     admitted_patients_chart,
     new_admissions_chart,
+    chart_descriptions
 )
 
 # This is somewhat dangerous:
@@ -39,36 +39,38 @@
     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)
 
-# PRESENTATION
-# Two more combination variable initialization / input element creation
-as_date = st.checkbox(label="Present result as dates instead of days", value=False)
-
 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, as_date=as_date),
+    new_admissions_chart(alt, m.admits_df, parameters=p),
     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, m.admits_df, as_date=as_date)
+    draw_projected_admissions_table(st, m.admits_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=m.census_df, parameters=p)
 st.altair_chart(
-    admitted_patients_chart(alt=alt, census=m.census_df, parameters=p, as_date=as_date),
+    admitted_patients_chart(alt=alt, census=m.census_df, parameters=p),
     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, m.census_df, as_date=as_date)
+    draw_census_table(st, m.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, model=m, parameters=p, as_date=as_date
+        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, as_date=as_date)
+        draw_raw_sir_simulation_table(st, model=m, parameters=p)
 write_definitions(st)
 write_footer(st)

src/cli.py

@@ -12,7 +12,6 @@
 from penn_chime.models import SimSirModel
 from penn_chime.utils import RateLos
 
-
 class FromFile(Action):
     """From File."""
 

src/penn_chime/charts.py

@@ -1,17 +1,21 @@
+
+from math import ceil
+import datetime
+
 from altair import Chart  # type: ignore
 import pandas as pd  # type: ignore
-import numpy as np  # type: ignore
 
 from .parameters import Parameters
 from .utils import add_date_column
 
 
 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()
 
@@ -45,12 +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"}
@@ -84,10 +89,20 @@ 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, model, parameters
 ) -> Chart:
-    dat = pd.DataFrame({"Infected": i, "Recovered": r})
+
+    # TODO use subselect of df_raw instead of creating a new df
+    raw_df = model.raw_df
+    dat = pd.DataFrame({
+        "infected": raw_df.infected,
+        "recovered": raw_df.recovered
+    })
     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"}
@@ -112,3 +127,43 @@ def additional_projections_chart(
         )
         .interactive()
     )
+
+
+def chart_descriptions(chart: Chart, suffix: str = ""):
+    """
+
+    :param chart: Chart: The alt chart to be used in finding max points
+    :param suffix: str: The assumption is that the charts have similar column names.
+                   The census chart adds " Census" to the column names.
+                   Make sure to include a space or underscore as appropriate
+    :return: str: Returns a multi-line string description of the results
+    """
+    messages = []
+
+    cols = ["hospitalized", "icu", "ventilated"]
+    asterisk = False
+    day = "date" if "date" in chart.data.columns else "day"
+
+    for col in cols:
+        if chart.data[col].idxmax() + 1 == len(chart.data):
+            asterisk = True
+
+        on = chart.data[day][chart.data[col].idxmax()]
+        if day == "date":
+            on = datetime.datetime.strftime(on, "%b %d")  # todo: bring this to an optional arg / i18n
+        else:
+            on += 1  # 0 index issue
+
+        messages.append(
+            "{}{} peaks at {:,} on day {}{}".format(
+                col,
+                suffix,
+                ceil(chart.data[col].max()),
+                on,
+                "*" if asterisk else "",
+            )
+        )
+
+    if asterisk:
+        messages.append("_* The max is at the upper bound of the data, and therefore may not be the actual max_")
+    return "\n\n".join(messages)

src/penn_chime/defaults.py

@@ -32,22 +32,27 @@ def __init__(
         icu: RateLos,
         ventilated: RateLos,
 
-        recovery_days: int = 14,
+        as_date: bool = False,
         market_share: float = 1.0,
+        max_y_axis: int = None,
         n_days: int = 60,
+        recovery_days: int = 14,
     ):
         self.region = region
         self.current_hospitalized = current_hospitalized
         self.known_infected = known_infected
         self.doubling_time = doubling_time
-        self.market_share = market_share
-        self.n_days = n_days
-        self.recovery_days = recovery_days
         self.relative_contact_rate = relative_contact_rate
 
         self.hospitalized = hospitalized
         self.icu = icu
         self.ventilated = ventilated
 
+        self.as_date = as_date
+        self.market_share = market_share
+        self.max_y_axis = max_y_axis
+        self.n_days = n_days
+        self.recovery_days = recovery_days
+
     def __repr__(self) -> str:
         return f"Constants(susceptible_default: {self.region.susceptible}, known_infected: {self.known_infected})"

src/penn_chime/models.py

@@ -1,4 +1,9 @@
-"""Models."""
+"""Models.
+
+Changes affecting results or their presentation should also update
+parameters.py `change_date`, so users can see when results have last
+changed
+"""
 
 from __future__ import annotations
 
@@ -31,10 +36,7 @@ def __init__(self, p: Parameters) -> SimSirModel:
         self.intrinsic_growth_rate = intrinsic_growth_rate = \
             (2.0 ** (1.0 / p.doubling_time) - 1.0) if p.doubling_time > 0.0 else 0.0
 
-        # TODO make this configurable, or more nuanced
-        self.recovery_days = recovery_days = 14.0
-
-        self.gamma = gamma = 1.0 / recovery_days
+        self.gamma = gamma = 1.0 / p.recovery_days
 
         # Contact rate, beta
         self.beta = beta = (

src/penn_chime/parameters.py

@@ -1,4 +1,8 @@
-"""Parameters."""
+"""Parameters.
+
+Changes affecting results or their presentation should also update
+`change_date`, so users can see when results have last changed
+"""
 
 from .utils import RateLos
 
@@ -19,33 +23,38 @@ def __init__(
         icu: RateLos,
         ventilated: RateLos,
 
+        as_date: bool = False,
         market_share: float = 1.0,
         max_y_axis: int = None,
-        n_days: int = 0,
+        n_days: int = 60,
         recovery_days: int = 14,
     ):
-        """
-        __init__.
-        """
         self.current_hospitalized = current_hospitalized
         self.doubling_time = doubling_time
         self.known_infected = known_infected
         self.relative_contact_rate = relative_contact_rate
         self.susceptible = susceptible
 
+        self.hospitalized = hospitalized
+        self.icu = icu
+        self.ventilated = ventilated
+
+        self.as_date = as_date
         self.market_share = market_share
         self.max_y_axis = max_y_axis
         self.n_days = n_days
         self.recovery_days = recovery_days
 
-        self.hospitalized = hospitalized
-        self.icu = icu
-        self.ventilated = ventilated
-
-        # TODO dataframe
         self.dispositions = {
             "hospitalized": hospitalized,
             "icu": icu,
             "ventilated": ventilated,
         }
 
+    def change_date(self):
+        """
+        This reflects a date from which previously-run reports will no
+        longer match current results, indicating when users should
+        re-run their reports
+        """
+        return "March 23 2020"