Replace los with days

Replace lengths of stay with days

Author: jlubken

settings.cfg

@@ -1,13 +1,13 @@
 --current-hospitalized 14
 --doubling-time 4.0
---hospitalized-los 7
+--hospitalized-days 7
 --hospitalized-rate 0.025
---icu-los 9
+--icu-days 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-days 10
 --ventilated-rate 0.005

src/penn_chime/cli.py

@@ -9,7 +9,7 @@
 from pandas import DataFrame
 
 from .constants import CHANGE_DATE
-from .parameters import Parameters, RateLos
+from .parameters import Parameters, RateDays
 from .models import SimSirModel as Model
 
 
@@ -74,7 +74,7 @@ def parse_args():
             "Doubling time before social distancing (days)",
             True,
         ),
-        ("--hospitalized-los", int, 0, None, "Hospitalized Length of Stay (days)", True),
+        ("--hospitalized-days", int, 0, None, "Average Hospital Length of Stay (days)", True),
         (
             "--hospitalized-rate",
             float,
@@ -83,7 +83,7 @@ def parse_args():
             "Hospitalized Rate: 0.00001 - 1.0",
             True,
         ),
-        ("--icu-los", int, 0, None, "ICU Length of Stay (days)", True),
+        ("--icu-days", int, 0, None, "Average Days in ICU", True),
         ("--icu-rate", float, 0.0, 1.0, "ICU Rate: 0.0 - 1.0", True),
         (
             "--market_share",
@@ -104,10 +104,14 @@ def parse_args():
             True,
         ),
         ("--population", int, 1, None, "Regional Population >= 1", True),
-        ("--ventilated-los", int, 0, None, "Ventilated Length of Stay (days)", True),
+        ("--ventilated-days", int, 0, None, "Average Days on Ventilator", True),
         ("--ventilated-rate", float, 0.0, 1.0, "Ventilated Rate: 0.0 - 1.0", True),
     ):
-        parser.add_argument(arg, type=validator(arg, cast, min_value, max_value, required))
+        parser.add_argument(
+            arg,
+            type=validator(arg, cast, min_value, max_value, required),
+            help=help,
+        )
     return parser.parse_args()
 
 
@@ -125,9 +129,9 @@ def main():
         relative_contact_rate=a.relative_contact_rate,
         population=a.population,
 
-        hospitalized=RateLos(a.hospitalized_rate, a.hospitalized_los),
-        icu=RateLos(a.icu_rate, a.icu_los),
-        ventilated=RateLos(a.ventilated_rate, a.ventilated_los),
+        hospitalized=RateDays(a.hospitalized_rate, a.hospitalized_days),
+        icu=RateDays(a.icu_rate, a.icu_days),
+        ventilated=RateDays(a.ventilated_rate, a.ventilated_days),
     )
 
     m = Model(p)

src/penn_chime/models.py

@@ -35,8 +35,8 @@ def __init__(self, p: Parameters):
             for key, d in p.dispositions.items()
         }
 
-        self.lengths_of_stay = {
-            key: d.length_of_stay
+        self.days = {
+            key: d.days
             for key, d in p.dispositions.items()
         }
 
@@ -170,7 +170,7 @@ def run_projection(self, p):
         )
         self.dispositions_df = build_dispositions_df(self.raw_df, self.rates, p.market_share, p.current_date)
         self.admits_df = build_admits_df(self.dispositions_df)
-        self.census_df = build_census_df(self.admits_df, self.lengths_of_stay)
+        self.census_df = build_census_df(self.admits_df, self.days)
         self.current_infected = self.raw_df.infected.loc[self.i_day]
 
     def get_loss(self) -> float:

src/penn_chime/parameters.py

@@ -11,7 +11,7 @@
 
 # (0.02, 7) is 2%, 7 days
 # be sure to multiply by 100 when using as a default to the percent widgets!
-RateLos = namedtuple("RateLos", ("rate", "length_of_stay"))
+RateDays = namedtuple("RateDays", ("rate", "days"))
 
 
 class Regions:
@@ -32,10 +32,10 @@ def __init__(
         self,
         *,
         current_hospitalized: int,
-        hospitalized: RateLos,
-        icu: RateLos,
+        hospitalized: RateDays,
+        icu: RateDays,
         relative_contact_rate: float,
-        ventilated: RateLos,
+        ventilated: RateDays,
         current_date: date = date.today(),
         date_first_hospitalized: Optional[date] = None,
         doubling_time: Optional[float] = None,

src/penn_chime/presentation.py

@@ -16,7 +16,7 @@
 )
 
 from .utils import dataframe_to_base64
-from .parameters import Parameters, RateLos
+from .parameters import Parameters, RateDays
 from .models import SimSirModel as Model
 
 hide_menu_style = """
@@ -196,27 +196,27 @@ def display_sidebar(st, d: Parameters) -> Parameters:
         "Ventilated %(total infections)",
         value=d.ventilated.rate,
     )
-    hospitalized_los_input = NumberInput(
+    hospitalized_days_input = NumberInput(
         st_obj,
-        "Hospital Length of Stay",
+        "Average Hospital Length of Stay (days)",
         min_value=0,
-        value=d.hospitalized.length_of_stay,
+        value=d.hospitalized.days,
         step=1,
         format="%i",
     )
-    icu_los_input = NumberInput(
+    icu_days_input = NumberInput(
         st_obj,
-        "ICU Length of Stay",
+        "Average Days in ICU",
         min_value=0,
-        value=d.icu.length_of_stay,
+        value=d.icu.days,
         step=1,
         format="%i",
     )
-    ventilated_los_input = NumberInput(
+    ventilated_days_input = NumberInput(
         st_obj,
-        "Vent Length of Stay",
+        "Average Days on Ventilator",
         min_value=0,
-        value=d.ventilated.length_of_stay,
+        value=d.ventilated.days,
         step=1,
         format="%i",
     )
@@ -267,13 +267,13 @@ def display_sidebar(st, d: Parameters) -> Parameters:
     relative_contact_rate = relative_contact_pct_input()
 
     st.sidebar.markdown("### Severity Parameters [ℹ]({docs_url}/what-is-chime/parameters)".format(docs_url=DOCS_URL))
-    infectious_days = infectious_days_input()
     hospitalized_rate = hospitalized_pct_input()
     icu_rate = icu_pct_input()
     ventilated_rate = ventilated_pct_input()
-    hospitalized_los = hospitalized_los_input()
-    icu_los = icu_los_input()
-    ventilated_los = ventilated_los_input()
+    infectious_days = infectious_days_input()
+    hospitalized_days = hospitalized_days_input()
+    icu_days = icu_days_input()
+    ventilated_days = ventilated_days_input()
 
     st.sidebar.markdown("### Display Parameters [ℹ]({docs_url}/what-is-chime/parameters)".format(docs_url=DOCS_URL))
     n_days = n_days_input()
@@ -285,11 +285,10 @@ def display_sidebar(st, d: Parameters) -> Parameters:
 
     return Parameters(
         current_hospitalized=current_hospitalized,
-        hospitalized=RateLos(hospitalized_rate, hospitalized_los),
-        icu=RateLos(icu_rate, icu_los),
-        #known_infected=known_infected,
+        hospitalized=RateDays(hospitalized_rate, hospitalized_days),
+        icu=RateDays(icu_rate, icu_days),
         relative_contact_rate=relative_contact_rate,
-        ventilated=RateLos(ventilated_rate, ventilated_los),
+        ventilated=RateDays(ventilated_rate, ventilated_days),
 
         current_date=current_date,
         date_first_hospitalized=date_first_hospitalized,

src/penn_chime/settings.py

@@ -2,7 +2,7 @@
 
 from datetime import date
 
-from .parameters import Parameters, Regions, RateLos
+from .parameters import Parameters, Regions, RateDays
 
 DEFAULTS = Parameters(
     region=Regions(
@@ -15,11 +15,11 @@
     current_hospitalized=32,
     date_first_hospitalized=date(2020,3,7),
     doubling_time=4.0,
-    hospitalized=RateLos(0.025, 7),
-    icu=RateLos(0.0075, 9),
+    hospitalized=RateDays(0.025, 7),
+    icu=RateDays(0.0075, 9),
     infectious_days=14,
     market_share=0.15,
     n_days=60,
     relative_contact_rate=0.3,
-    ventilated=RateLos(0.005, 10),
+    ventilated=RateDays(0.005, 10),
 )

tests/by_date_first_hospitalized/settings.cfg

@@ -1,13 +1,13 @@
 --current-hospitalized 14
 --date-first-hospitalized 2020-03-07
---hospitalized-los 7
+--hospitalized-days 7
 --hospitalized-rate 0.025
---icu-los 9
+--icu-days 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-days 10
 --ventilated-rate 0.005

tests/by_doubling_time/settings.cfg

@@ -1,13 +1,13 @@
 --current-hospitalized 14
 --doubling-time 4.0
---hospitalized-los 7
+--hospitalized-days 7
 --hospitalized-rate 0.025
---icu-los 9
+--icu-days 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-days 10
 --ventilated-rate 0.005

tests/test_app.py

@@ -22,7 +22,7 @@
 )
 from src.penn_chime.parameters import (
     Parameters,
-    RateLos,
+    RateDays,
     Regions,
 )
 from src.penn_chime.presentation import display_header
@@ -45,9 +45,9 @@
     n_days=60,
     market_share=0.15,
     relative_contact_rate=0.3,
-    hospitalized=RateLos(0.025, 7),
-    icu=RateLos(0.0075, 9),
-    ventilated=RateLos(0.005, 10),
+    hospitalized=RateDays(0.025, 7),
+    icu=RateDays(0.0075, 9),
+    ventilated=RateDays(0.005, 10),
 )
 
 PARAM = Parameters(
@@ -56,9 +56,9 @@
     market_share=0.05,
     relative_contact_rate=0.15,
     population=500000,
-    hospitalized=RateLos(0.05, 7),
-    icu=RateLos(0.02, 9),
-    ventilated=RateLos(0.01, 10),
+    hospitalized=RateDays(0.05, 7),
+    icu=RateDays(0.02, 9),
+    ventilated=RateDays(0.01, 10),
     n_days=60,
 )
 
@@ -68,9 +68,9 @@
     market_share=0.05,
     relative_contact_rate=0.7,
     population=500000,
-    hospitalized=RateLos(0.05, 7),
-    icu=RateLos(0.02, 9),
-    ventilated=RateLos(0.01, 10),
+    hospitalized=RateDays(0.05, 7),
+    icu=RateDays(0.02, 9),
+    ventilated=RateDays(0.01, 10),
     n_days=60,
 )