Merge pull request #15 from djgroen/pfacs

Pfacs Beta Version

README.md

@@ -11,6 +11,12 @@ Full documentation can be found at: http://facs.readthedocs.io
 To run a simple simulation of a basic test dataset, type:
 `python3 run.py --location=test --transition_scenario=extend-lockdown --transition_mode=1 --output_dir=.`
 
+To run it in parallel, type (for four core runs):
+`mpirun -np 4 python3 run.py --location=test --transition_scenario=extend-lockdown --transition_mode=1 --output_dir=.`
+
+To do a run of custom length (with -t flag), and with a generically named out.csv output file, type:
+`mpirun -np 1 python3 run.py -t=10 -g --location=test --transition_scenario=extend-lockdown --transition_mode=1 --output_dir=.`
+
 To run a simulation of the Borough of Brent, type:
 `python3 run.py --location=brent --transition_scenario=extend-lockdown --transition_mode=1 --output_dir=.`
 

covid_data/disease_covid19.yml

@@ -34,9 +34,9 @@ hospitalised:
  - [84.5,0.184]
 mortality_period: 8.0 # from day of hospitalisation (ICU)
 recovery_period: 8.0 # from day of hospitalisation (ICU)
-mild_recovery_period: 8.5 # (7-10 days) https://www.ams.edu.sg/view-pdf.aspx?file=media%5c5558_fi_168.pdf&ofile=Period+of+Infectivity+Position+Statement+(final)+23-5-20.pdf
-incubation_period: 3 # https://www.ams.edu.sg/view-pdf.aspx?file=media%5c5558_fi_168.pdf&ofile=Period+of+Infectivity+Position+Statement+(final)+23-5-20.pdf
+mild_recovery_period: 9.0 # (7-10 days) https://www.ams.edu.sg/view-pdf.aspx?file=media%5c5558_fi_168.pdf&ofile=Period+of+Infectivity+Position+Statement+(final)+23-5-20.pdf
+incubation_period: 4 # https://www.ams.edu.sg/view-pdf.aspx?file=media%5c5558_fi_168.pdf&ofile=Period+of+Infectivity+Position+Statement+(final)+23-5-20.pdf
 # 5 days of incubation, infectiousness starts 36 hours before the end of incubation.
 # Clinical course and risk factors for mortality of adult inpatients with Covid-19 in Wuhan, China: a retrospective cohort study
 # Fei Zhou et al. The Lancet vol. 395.
-period_to_hospitalisation: 12.0 #this is period to ICU.
+period_to_hospitalisation: 14.0 #this is period to ICU.

covid_data/measures_uk.yml

@@ -1,30 +1,52 @@
 date_format: "%d/%m/%Y"
 keyworker_fraction: 0.18 # percentage workers that are keyworkers
 
+#Explanation
+dd/mm/yyyy: # date according to date format above
+  case_isolation: True # whether infected people go in quarantine
+  household_isolation: True # whether the rest of the household goes in quarantine when someone has COVID in it.
+  traffic_multiplier: 1.0 # Ratio of expected traffic relative to a non-lockdown situation.
+  work_from_home: 0.0 # Fraction of workers that do not come into office.
+  social_distance: 0.0 # Fraction of persons that comply with a 2m social distancing rule.
+  mask_uptake: 0.0 # Fraction of persons wearing masks outside of the house.
+  mask_uptake_shopping: 0.0 # Fraction of persons wearing masks in shop settings.
+  closure: ["example"] # List of building types that are closed for the public.
+  partial_closure:
+    example: 0.3 # visits to example type facilities are reduced by 30% (e.g. to close schools for non-keyworkers). 
+  track_trace_efficiency: 0.3 # 30% of persons escape the track and trace system. Affects self-isolation compliance.
+
+11/2/2020:
+  case_isolation: True
+  household_isolation: True
+1/3/2020:
+  traffic_multiplier: 0.8
 12/3/2020:
   work_from_home: 0.1
   social_distance: 0.1
-  case_isolation: True
-  household_isolation: True
+  traffic_multiplier: 0.5
 16/3/2020:
   partial_closure: 
     leisure: 0.3
   work_from_home: 0.325 #assumption is that uptake between 11 and 21 Mar is gradual
   social_distance: 0.25 #assumption is that uptake between 11 and 21 Mar is gradual
   mask_uptake: 0.05
+  traffic_multiplier: 0.4
 20/3/2020:
   closure: ["leisure"]
   work_from_home: 0.45 #assumption is that uptake between 11 and 21 Mar is gradual
   social_distance: 0.5 #assumption is that uptake between 11 and 21 Mar is gradual
   mask_uptake: 0.05
+  traffic_multiplier: 0.3
 23/3/2020:
   partial_closure: 
     school: 1.0
     shopping: 0.7 #indicates full school closure, but partial_closure is used to allow keyworkers to be added.
+  closure: ["leisure"]
   social_distance: 0.75
   mask_uptake: 0.05
   mask_uptake_shopping: 0.1
   work_from_home: 1.0
+  traffic_multiplier: 0.25
 22/4/2020:
   partial_closure: 
     school: 1.0
@@ -53,7 +75,8 @@ keyworker_fraction: 0.18 # percentage workers that are keyworkers
   mask_uptake: 0.2
   mask_uptake_shopping: 0.3
   work_from_home: 0.65
-  track_trace_efficacy: 0.8 #Track and trace is assumed to catch 80% of the cases.
+  track_trace_efficacy: 0.5 #Track and trace is assumed to catch 50% of the cases.
+  traffic_multiplier: 0.25
 15/6/2020:
   partial_closure: 
     school: 1.0
@@ -64,7 +87,7 @@ keyworker_fraction: 0.18 # percentage workers that are keyworkers
   mask_uptake_shopping: 0.3
   work_from_home: 0.5
   track_trace_efficacy: 0.5 #Track and trace is assumed to catch 50% of the cases.
-  traffic_multiplier: 0.125
+  traffic_multiplier: 0.3
   masks_on_public_transport: True
 4/7/2020:
   partial_closure: 
@@ -73,47 +96,67 @@ keyworker_fraction: 0.18 # percentage workers that are keyworkers
     leisure: 0.8 
   social_distance: 0.7
   work_from_home: 0.5
-  traffic_multiplier: 0.2
+  track_trace_efficacy: 0.6 # 60% escape.
+  traffic_multiplier: 0.3
 15/7/2020:
   partial_closure: 
     school: 0.8
     leisure: 0.3
   social_distance: 0.7
   work_from_home: 0.5
-  traffic_multiplier: 0.2
+  traffic_multiplier: 0.4
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
-1/9/2020:
+  external_multiplier: 2.0 # some travel possible again.
+22/8/2020:
+  partial_closure: 
+    school: 0.8
+    leisure: 0.3
   social_distance: 0.7
+  work_from_home: 0.5
+  traffic_multiplier: 0.4
+  mask_uptake: 0.2
+  mask_uptake_shopping: 0.8
+  external_multiplier: 4.0 # returns from holidays.
+1/9/2020:
+  social_distance: 0.6
   work_from_home: 0.3
-  traffic_multiplier: 0.25
+  traffic_multiplier: 0.45
+  mask_uptake: 0.2
+  mask_uptake_shopping: 0.8
+8/9/2020:
+  social_distance: 0.6
+  work_from_home: 0.3
+  traffic_multiplier: 0.45
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
 22/9/2020:
-  social_distance: 0.7
-  work_from_home: 0.5
-  traffic_multiplier: 0.25
+  social_distance: 0.6
+  work_from_home: 0.4
+  traffic_multiplier: 0.5
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
 5/11/2020:
   partial_closure: 
     shopping: 0.6
   closure: ["leisure"]
-  social_distance: 0.7
-  work_from_home: 0.7
+  social_distance: 0.6
+  work_from_home: 0.5
   traffic_multiplier: 0.35
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
+  external_multiplier: 2.0 # tighter travel restrictions again.
 2/12/2020:
-  social_distance: 0.7
+  social_distance: 0.6
   work_from_home: 0.5
   traffic_multiplier: 0.5
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
+  external_multiplier: 4.0 # lifting of measures 
 16/12/2020:
   social_distance: 0.6
-  work_from_home: 0.25
-  traffic_multiplier: 0.5
+  work_from_home: 0.6
+  traffic_multiplier: 0.35
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
   track_trace_efficacy: 0.6 
@@ -126,60 +169,80 @@ keyworker_fraction: 0.18 # percentage workers that are keyworkers
   traffic_multiplier: 0.3
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
-  track_trace_efficacy: 0.6 
+  track_trace_efficacy: 0.7 
+23/12/2020: # Christmas bubble
+  partial_closure:
+    leisure: 0.5
+    shopping: 0.1
+  social_distance: 0.3
+  work_from_home: 0.5
+  traffic_multiplier: 0.5
+  mask_uptake: 0.2
+  mask_uptake_shopping: 0.8
+  track_trace_efficacy: 0.7
+27/12/2020: # Christmas bubble ends
+  partial_closure:
+    leisure: 0.5
+    shopping: 0.1
+  social_distance: 0.4
+  work_from_home: 0.7
+  traffic_multiplier: 0.4
+  mask_uptake: 0.2
+  mask_uptake_shopping: 0.8
+  track_trace_efficacy: 0.7
 6/1/2021:
   partial_closure: 
     school: 1.0
     leisure: 1.0
     shopping: 0.8
-  social_distance: 0.7
-  work_from_home: 1.0
+  social_distance: 0.6
+  work_from_home: 0.8
   traffic_multiplier: 0.25
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
-  track_trace_efficacy: 0.4 # assuming track and trace loses efficacy during this surge.
+  track_trace_efficacy: 0.8 # assuming track and trace loses efficacy during this surge.
 8/3/2021:
   partial_closure: 
     leisure: 1.0
     shopping: 0.8
-  social_distance: 0.7
-  work_from_home: 1.0
+  social_distance: 0.6
+  work_from_home: 0.8
   traffic_multiplier: 0.3
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
-  track_trace_efficacy: 0.5 # assuming track and trace loses efficacy during this surge.
+  track_trace_efficacy: 0.8 # assuming track and trace loses efficacy during this surge.
 12/4/2021:
   partial_closure: 
     leisure: 0.5
-  social_distance: 0.7
+  social_distance: 0.6
   work_from_home: 0.5
   traffic_multiplier: 0.55
   mask_uptake: 0.2
   mask_uptake_shopping: 0.8
-  track_trace_efficacy: 0.5 # assuming track and trace loses efficacy during this surge.
+  track_trace_efficacy: 0.8 # assuming track and trace loses efficacy during this surge.
 17/5/2021:
   partial_closure: 
     leisure: 0.2
-  social_distance: 0.6
+  social_distance: 0.5
   work_from_home: 0.5
   traffic_multiplier: 0.55
   mask_uptake: 0.15
   mask_uptake_shopping: 0.8
-  track_trace_efficacy: 0.5 # assuming track and trace loses efficacy during this surge.
+  track_trace_efficacy: 0.8 # assuming track and trace loses efficacy during this surge.
 21/6/2021:
-  social_distance: 0.5
+  social_distance: 0.4
   work_from_home: 0.25
   traffic_multiplier: 0.75
   mask_uptake: 0.1
   mask_uptake_shopping: 0.8
-  track_trace_efficacy: 0.5 # assuming track and trace loses efficacy during this surge.
+  track_trace_efficacy: 0.9 # track and trace largely abandoned.
 19/7/2021:
-  social_distance: 0.1
+  social_distance: 0.3
   work_from_home: 0.2
   traffic_multiplier: 0.9
   mask_uptake: 0.05
   mask_uptake_shopping: 0.5
-  track_trace_efficacy: 0.5 # assuming track and trace loses efficacy during this surge.
+  track_trace_efficacy: 1.0