COVIDAnalytics · sakshamsoni97 · May 14, 2021 · May 14, 2021 · May 15, 2021 · May 15, 2021
diff --git a/.gitignore b/.gitignore
@@ -8,16 +8,21 @@ __pycache__/
 ._*
 *.pyc
 
+# ipython checkpoints
+.ipynb_checkpoints/
+
 # C extensions
 *.so
 
-
-
 # Mac
 .DS_Store
 
-
-
 # Logging files
 logs/
 *.png
+
+# VS Code
+.vscode/*
+
+# HTML
+*.html
diff --git a/README.md b/README.md
@@ -1,3 +1,63 @@
 # THEMIS: Cost Model for Analyzing Non-Pharmaceutical Interventions
 
 The repository contains code for a framework that attempts to analyze the different sources of costs incurred by the various non-pharmaceutical interventions that have been implemented in the COVID-19 pandemic. 
+
+## 1. Repository Structure
+
+
+Here we briefly describe how the repository is structured for better navigation of the reader.
+
+`THEMIS/`
+1. `cost_functions/` - contains functions and data defining different cost components
+    * `economic_cost/` - contains functions and data for different components of economic cost
+        - `economic_data/` - contains the data for economic costs
+            - `gdp/` - contains the GDP related data
+            - `unemployment/` - contains the unemployment related data
+            - `economic_params` - contains the parameters for economic costs
+        - `long_term_economic_costs.py` (currently empty)
+        - `short_term_economic_costs.py`
+        - `short_term_gdp_costs.py`
+        - `short_term_unemployment_costs.py`
+    * `health_cost/` - contains functions and data for different components of health cost
+        - `health_data/` - contains the data for health costs
+            - `health_params` - contains the parameters for health costs
+        - `death_costs.py`
+        - `hospitalization_costs.py`
+        - `mental_health_costs.py`
+2. `pandemic_functions/` - contains functions and data for simulating the pandemic
+    * `delphi_functions/` - contains functions for running the DELPHI model
+        - `DELPHI_model_policy_scenarios.py` - the DELPHI model
+    * `pandemic_data/` - contains historical data for the cases and deaths as well as DELPHI parameters
+    * `pandemic.py` - encapsulates the pandemic scenario for a region
+    * `pandemic_cost.py` - encapsulates all costs associated with the pandemic
+    * `pandemic_params.py`
+3. `policy_functions/` - functions to define different policies
+    * `policy.py`
+4. `utils/` - miscellaneous tools required in the project
+    * `cost_utils.py`
+    * `visualization_utils.py`
+5. `notebooks/` - this folder contains all the scripts and excel files that are used to process the raw data
+    * `monthly_dominant_policy.ipynb` - gamma values and GDP and Employment impact for different policies in different regions
+    * `visualize_results_final.ipynb` - code to produce the plots
+    * ...
+6. `simulation_results/` - contains the results of the simulations based on which the plots are created
+7. `main.py` - the main script that can be run to compute the results
+8. `LICENSE` - license for this project
+9. `README.md` - brief documentation
+
+## 2. Running the Model
+
+The code was written with **Python 3.8.3**. The model is executed through the main file which takes three arguments
+1. `--region` or `-r` : Region code for the region the simulation will be run. Should be one of "DE", "US-NY", "US-FL", "ES", "BR", "SG"
+2. `--startdate` or `-sd` : (optional, default = "2020-03-01") start date for the simulation as a string in YYYY-MM-DD format
+3. `--length` or `-l` : (optional, default = 3) number of months the simulation will be run for starting from the start date
+\
+Example:
+```
+> python main.py -r "DE" -sd "2020-03-15" -l 3
+```
+
+## 3. Authors
+
+Michael L. Li, Saksham Soni & Baptiste Rossi
+
diff --git a/cost_functions/economic_cost/README.md b/cost_functions/economic_cost/README.md
@@ -1,3 +1 @@
-# THEMIS: Cost Model for Analyzing Non-Pharmaceutical Interventions
-
-The repository contains code for a framework that attempts to analyze the different sources of costs incurred by the various non-pharmaceutical interventions that have been implemented in the COVID-19 pandemic. 
+# Economic Cost Functions for THEMIS
diff --git a/cost_functions/economic_cost/economic_data/economic_params.py b/cost_functions/economic_cost/economic_data/economic_params.py
@@ -1,80 +1,111 @@
 from collections import defaultdict
 
 # For countries with missing data (including Singapore), assuming roughly 1.5 year of GDP per capita
-UNEMPLOYMENT_COST = {"DE": 77510,"US": 100000, "SG": 120000, "BR": 35038 * 1.5}
+UNEMPLOYMENT_COST = {"DE": 77510,"US-NY": 100000, "US-FL": 80000, "SG": 120000, "ES": 66312, "BR": 35038 * 1.5}
 
 def not_implemented():
     raise NotImplementedError
 
 # employment_impact in percentages
-EMPLOYMENT_IMPACT = {}
-EMPLOYMENT_IMPACT["DE"] = defaultdict(not_implemented, { "Lockdown": 2,
-          "Restrict_Mass_Gatherings_and_Schools_and_Others": 1.8,
-          'Restrict_Mass_Gatherings_and_Schools': 1.5,
-          'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 1.2,
-        "Restrict_Mass_Gatherings": 1,
-        "No_Measure": 0})
-
-EMPLOYMENT_IMPACT["US-NY"] = defaultdict(not_implemented, { "Lockdown": 12.3,
-      "Restrict_Mass_Gatherings_and_Schools_and_Others": 10.8,
-      'Restrict_Mass_Gatherings_and_Schools': 9.3,
-      'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 6.1,
-    "Restrict_Mass_Gatherings": 4.8,
-    "No_Measure": 0}) 
-
-EMPLOYMENT_IMPACT["SG"] = defaultdict(not_implemented, { "Lockdown": 1.3,
-      "Restrict_Mass_Gatherings_and_Schools_and_Others": 1.0,
-      'Restrict_Mass_Gatherings_and_Schools': 0.8,
-      'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 0.5,
-    "Restrict_Mass_Gatherings": 0.3,
-    "No_Measure": 0}) 
-
-EMPLOYMENT_IMPACT["BR"] =defaultdict(not_implemented, { "Lockdown": -3.0,
-          "Restrict_Mass_Gatherings_and_Schools_and_Others": -2.7,
-          'Restrict_Mass_Gatherings_and_Schools': -2.5,
-          'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -1.9,
-           "Restrict_Mass_Gatherings": -1.3,
-           "No_Measure": 0})
-
-
-GDP_IMPACT = {}
-
-GDP_IMPACT["DE"] = defaultdict(not_implemented, { "Lockdown": -10,
-          "Restrict_Mass_Gatherings_and_Schools_and_Others": -8,
-          'Restrict_Mass_Gatherings_and_Schools': -6,
-          'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -4,
-           "Restrict_Mass_Gatherings": -3,
-           "No_Measure": 0})
-
-# https://www.bea.gov/taxonomy/term/461
-
-GDP_IMPACT["US-NY"] = defaultdict(not_implemented, { "Lockdown": -12,
-          "Restrict_Mass_Gatherings_and_Schools_and_Others": -10,
-          'Restrict_Mass_Gatherings_and_Schools': -7,
-          'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -5,
-           "Restrict_Mass_Gatherings": -4,
-           "No_Measure": 0})
-
-GDP_IMPACT["SG"] = defaultdict(not_implemented, { "Lockdown": -16,
-          "Restrict_Mass_Gatherings_and_Schools_and_Others": -13,
-          'Restrict_Mass_Gatherings_and_Schools': -10,
-          'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -6,
-           "Restrict_Mass_Gatherings": -4,
-           "No_Measure": 0})
-
-GDP_IMPACT["BR"] = defaultdict(not_implemented, { "Lockdown": -11.1,
-          "Restrict_Mass_Gatherings_and_Schools_and_Others": -8.5,
-          'Restrict_Mass_Gatherings_and_Schools': -6.0,
-          'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -4.7,
-           "Restrict_Mass_Gatherings": -3.5,
-           "No_Measure": 0})
-
+EMPLOYMENT_IMPACT = {
+  'BR': defaultdict(not_implemented, {'No_Measure': 0.0,
+    'Restrict_Mass_Gatherings': 0.4,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 0.7,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': 1.1,
+    'Restrict_Mass_Gatherings_and_Schools': 1.8,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': 2.0,
+    'Lockdown': 2.6}),
+  'DE': defaultdict(not_implemented, {'No_Measure': 0.0,
+    'Restrict_Mass_Gatherings': 0.2,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 0.3,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': 0.5,
+    'Restrict_Mass_Gatherings_and_Schools': 0.8,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': 0.9,
+    'Lockdown': 1.2}),
+  'ES': defaultdict(not_implemented, {'No_Measure': 0.0,
+    'Restrict_Mass_Gatherings': 0.5,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 0.8,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': 1.2,
+    'Restrict_Mass_Gatherings_and_Schools': 1.9,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': 2.1,
+    'Lockdown': 2.8}),
+  'SG': defaultdict(not_implemented, {'No_Measure': 0.0,
+    'Restrict_Mass_Gatherings': 0.2,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 0.3,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': 0.4,
+    'Restrict_Mass_Gatherings_and_Schools': 0.7,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': 0.7,
+    'Lockdown': 1.0}),
+  'US-FL': defaultdict(not_implemented, {'No_Measure': 0.0,
+    'Restrict_Mass_Gatherings': 1.8,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 2.9,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': 4.7,
+    'Restrict_Mass_Gatherings_and_Schools': 7.4,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': 8.2,
+    'Lockdown': 10.8}),
+  'US-NY': defaultdict(not_implemented, {'No_Measure': 0.0,
+    'Restrict_Mass_Gatherings': 1.8,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': 2.9,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': 4.6,
+    'Restrict_Mass_Gatherings_and_Schools': 7.3,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': 8.0,
+    'Lockdown': 10.6})
+}
+
+# GDP impact in percentage of monthly GDP
+GDP_IMPACT = {
+  'BR': defaultdict(not_implemented, {'No_Measure': -0.0,
+    'Restrict_Mass_Gatherings': -0.5,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -0.8,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': -1.2,
+    'Restrict_Mass_Gatherings_and_Schools': -1.9,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': -2.1,
+    'Lockdown': -2.8}),
+  'DE': defaultdict(not_implemented, {'No_Measure': -0.0,
+    'Restrict_Mass_Gatherings': -1.4,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -2.2,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': -3.5,
+    'Restrict_Mass_Gatherings_and_Schools': -5.6,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': -6.2,
+    'Lockdown': -8.1}),
+  'ES': defaultdict(not_implemented, {'No_Measure': -0.0,
+    'Restrict_Mass_Gatherings': -3.5,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -5.7,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': -9.2,
+    'Restrict_Mass_Gatherings_and_Schools': -14.4,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': -16.0,
+    'Lockdown': -21.1}),
+  'SG': defaultdict(not_implemented, {'No_Measure': -0.0,
+    'Restrict_Mass_Gatherings': -4.0,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -6.5,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': -10.5,
+    'Restrict_Mass_Gatherings_and_Schools': -16.5,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': -18.2,
+    'Lockdown': -24.0}),
+  # https://www.bea.gov/taxonomy/term/461
+  'US-FL': defaultdict(not_implemented, {'No_Measure': -0.0,
+    'Restrict_Mass_Gatherings': -1.3,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -2.1,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': -3.5,
+    'Restrict_Mass_Gatherings_and_Schools': -5.4,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': -6.0,
+    'Lockdown': -7.9}),
+  'US-NY': defaultdict(not_implemented, {'No_Measure': -0.0,
+    'Restrict_Mass_Gatherings': -1.4,
+    'Authorize_Schools_but_Restrict_Mass_Gatherings_and_Others': -2.3,
+    'Mass_Gatherings_Authorized_But_Others_Restricted': -3.7,
+    'Restrict_Mass_Gatherings_and_Schools': -5.7,
+    'Restrict_Mass_Gatherings_and_Schools_and_Others': -6.3,
+    'Lockdown': -8.4})
+  }
+
+# For US https://data.bls.gov/pdq/SurveyOutputServlet
+# For ES: World Bank data https://data.worldbank.org/indicator/SL.TLF.TOTL.IN?locations=ES
 # Brazil: https://www.google.com/search?q=brazil+total+labor+force&sxsrf=AOaemvJD58Nn5ymZoi64Re_BOaNYyAGeyA%3A1631390603427&ei=iws9YbapGeahggeHzaLoAg&oq=brazil+total+labor&gs_lcp=Cgdnd3Mtd2l6EAMYADIGCAAQFhAeOgQIIxAnOgQIABBDOgUIABCRAjoECC4QQzoOCC4QgAQQsQMQxwEQowI6BwguELEDEEM6BwgAELEDEEM6CAgAELEDEJECOggIABCABBCxAzoICAAQyQMQkQI6CggAEIAEEIcCEBQ6DQgAEIAEEIcCELEDEBQ6BQgAEIAESgQIQRgAUJJoWM13YKZ_aABwAngAgAHnAYgBmg-SAQYxMC43LjGYAQCgAQHAAQE&sclient=gws-wiz
-TOTAL_LABOR_FORCE = {"DE": 43356000, "US-NY": 9500000, "SG": 3750000, "BR": 107461083}
-
+TOTAL_LABOR_FORCE = {"DE": 43356000, "US-NY": 9500000, "US-FL":10451550, "SG": 3750000, "ES": 22694625, "BR": 107461083}
 
-TOTAL_GDP = {"DE": 3.861e12, "US-NY": 1.77e12, "SG": 4.6909e11, "BR": 7.448e12}
+TOTAL_GDP = {"DE": 3.861e12, "US-NY": 1.77e12, "US-FL": 1.107e12, "SG": 4.6909e11, "ES":1.245e12, "BR": 7.448e12}
 
-COVID_SICK_DAYS = {"DE": 7,"US-NY": 7,"SG": 7, "BR": 7}
+COVID_SICK_DAYS = {"DE": 7,"US-NY": 7,"US-FL": 7,"SG": 7, "ES": 7, "BR": 7}
 
-TOTAL_WORKING_DAYS = {"DE": 254, "US-NY": 261, "SG": 261, "BR": 254}
+TOTAL_WORKING_DAYS = {"DE": 254, "US-NY": 261, "US-FL": 261, "SG": 261, "ES": 252, "BR": 254}
diff --git a/cost_functions/economic_cost/economic_data/gdp/BR.csv b/cost_functions/economic_cost/economic_data/gdp/BR.csv
@@ -1,14 +1,13 @@
-year,month,c,i,g
-2020,1,-12,0,0
-2020,2,-12,0,0
-2020,3,-12,0,0
-2020,4,-66,-21,0
-2020,5,-66,-21,0
-2020,6,-66,-21,0
-2020,7,-41,-19,0
-2020,8,-41,-19,0
-2020,9,-41,-19,0
-2020,10,-17,0,0
-2020,11,-17,0,0
-2020,12,-17,0,0
-2021,1,0,0,0
+year,month,c,i,g,x
+2020,1,-0.8,0,0,-1.2
+2020,2,-0.8,0,0,-1.2
+2020,3,-0.8,0,0,-1.2
+2020,4,-8.5,-3,0,0
+2020,5,-8.5,-3,0,0
+2020,6,-8.5,-3,0,0
+2020,7,-4.6,-2,0,0
+2020,8,-4.6,-2,0,0
+2020,9,-4.6,-2,0,0
+2020,10,-2.7,0,0,-0.2
+2020,11,-2.7,0,0,-0.2
+2020,12,-2.7,0,0,-0.2
diff --git a/cost_functions/economic_cost/economic_data/gdp/DE.csv b/cost_functions/economic_cost/economic_data/gdp/DE.csv
@@ -1,14 +1,13 @@
-year,month,c,i,g
-2020,1,0,0,0
-2020,2,0,0,0
-2020,3,-7.2,-0.3,6
-2020,4,-20.4,-8.5,3.4
-2020,5,-20.4,-8.5,3.4
-2020,6,-20.4,-8.5,3.4
-2020,7,-8.9,-9.5,2.8
-2020,8,-8.9,-9.5,2.8
-2020,9,-8.9,-9.5,2.8
-2020,10,-12.8,-4.2,2.5
-2020,11,-12.8,-4.2,2.5
-2020,12,-12.8,-4.2,2.5
-2021,1,-12.8,-4.2,2.5
+year,month,c,i,g,x
+2020,1,0,0,0,0
+2020,2,0,0,0,0
+2020,3,-3.6,-0.1,0.4,-3.2
+2020,4,-19.1,-3.3,0.2,-8.5
+2020,5,-19.1,-8.5,0.2,-8.5
+2020,6,-19.1,-8.5,0.2,-8.5
+2020,7,-6.8,-4.7,1.8,-0.3
+2020,8,-6.8,-4.7,1.8,-0.3
+2020,9,-6.8,-4.7,1.8,-0.3
+2020,10,-10.2,-2.2,2.1,0
+2020,11,-10.2,-2.2,2.1,0
+2020,12,-10.2,-2.2,2.1,0
diff --git a/cost_functions/economic_cost/economic_data/gdp/ES.csv b/cost_functions/economic_cost/economic_data/gdp/ES.csv
@@ -0,0 +1,13 @@
+year,month,c,i,g,x
+2020,1,0,0,1,0
+2020,2,0,0,1,0
+2020,3,-4.1,-1.0,0.2,-0.2
+2020,4,-13.3,-6.1,0.2,-4.1
+2020,5,-13.3,-6.1,0.2,-4.1
+2020,6,-13.3,-6.1,0.2,-4.1
+2020,7,-4.9,-2.5,0.5,-3.3
+2020,8,-4.9,-2.5,0.5,-3.3
+2020,9,-4.9,-2.5,0.5,-3.3
+2020,10,-6.7,-3,0.9,-1.9
+2020,11,-6.7,-3,0.9,-1.9
+2020,12,-6.7,-3,0.9,-1.9
diff --git a/cost_functions/economic_cost/economic_data/gdp/README.txt b/cost_functions/economic_cost/economic_data/gdp/README.txt
@@ -1,4 +1,4 @@
-For germany, took data from https://data.imf.org/regular.aspx?key=61545852
+For Germany and Spain, took data from https://data.imf.org/regular.aspx?key=61545852
 
 For US states, there are no C/I/G breakdown available on a quarterly level, so we used the whole US C/I/G breakdown from the IMF data source (https://data.imf.org/regular.aspx?key=61545852)
  and https://apps.bea.gov/iTable/iTable.cfm?reqid=19&step=2#reqid=19&step=2&isuri=1&1921=survey, and applied scaling to accommodate for states using https://www.bea.gov/data/gdp/gdp-state. (E.g. If US GDP dropped 20% in Q2, and NY GDP dropped 30%, then we assume every change in NY is 1.5x the US level change. 

diff --git a/cost_functions/economic_cost/economic_data/gdp/SG.csv b/cost_functions/economic_cost/economic_data/gdp/SG.csv
@@ -1,14 +1,13 @@
-year,month,c,i,g
-2020,1,-0.21,0,0
-2020,2,-0.43,0,0
-2020,3,-0.65,0,0
-2020,4,-4.52,-2.8,1.6
-2020,5,-4.52,-2.8,1.6
-2020,6,-4.52,-2.8,1.6
-2020,7,-2.15,-2.4,0.99
-2020,8,-2.15,-2.4,0.99
-2020,9,-2.15,-2.4,0.99
-2020,10,-1.95,-0.57,0.7
-2020,11,-1.95,-0.57,0.7
-2020,12,-1.95,-0.57,0.7
-2021,1,0,0,0
+year,month,c,i,g,x
+2020,1,0,0,0,0
+2020,2,0,0,0,0
+2020,3,-1.1,-0.5,0.1,-0.5
+2020,4,-4.8,-3.6,0.5,0
+2020,5,-4.8,-3.6,0.5,0
+2020,6,-4.8,-3.6,0.5,0
+2020,7,-2.5,-2.7,0.5,0
+2020,8,-2.5,-2.7,0.5,0
+2020,9,-2.5,-2.7,0.5,0
+2020,10,-2.4,-1.2,0.2,0
+2020,11,-2.4,-1.2,0.2,0
+2020,12,-2.4,-1.2,0.2,0
diff --git a/cost_functions/economic_cost/economic_data/gdp/US-FL.csv b/cost_functions/economic_cost/economic_data/gdp/US-FL.csv
@@ -0,0 +1,13 @@
+year,month,c,i,g,x
+2020,1,0,0,0,0
+2020,2,0,0,0,0
+2020,3,0,-0.3,0.4,0
+2020,4,-4.8,-2.4,0.5,0
+2020,5,-4.8,-2.4,0.5,0
+2020,6,-4.8,-2.4,0.5,0
+2020,7,-0.6,-0.4,0.1,-0.2
+2020,8,-0.6,-0.4,0.1,-0.2
+2020,9,-0.6,-0.4,0.1,-0.2
+2020,10,-0.6,0,0.1,-0.8
+2020,11,-0.6,0,0.1,-0.8
+2020,12,-0.6,0,0.1,-0.8