Finalized code for public release

README.md

@@ -10,7 +10,7 @@ Codebase for SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and
 
 3. Download the SafeGraph Open Census Data [here](https://www.safegraph.com/open-census-data). Save it to `safegraph-data/safegraph_open_census_data`.
 
-4. Get free access to the remaining SafeGraph data by following [these steps](https://www.safegraph.com/covid-19-data-consortium).
+4. Get free access to the remaining SafeGraph data by following [these steps](https://www.safegraph.com/covid-19-data-consortium). A non-disclosure agreement must be signed as part of the process.
 
 5. Download the SafeGraph Weekly Patterns (v2) data. Save it to `safegraph-data/safegraph_weekly_patterns_v2`.
 
@@ -20,8 +20,12 @@ Codebase for SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and
 
 ## Usage
 
-* `county-parser.py` is used to extract locality data. Run this at least once, and then run `simulation.py`. The results will be located in `results/`.
+* `county-parser.py` is used to extract locality data. Run this at least once, and then run `simulation.py`. To create custom simulation configurations, place new `.cfg` files in `config-files/`. Use `config-files/default-config.cfg` as a template.
 
-* To create custom simulation configurations, place new `.cfg` files in `config-files/`. Use `config-files/default-config.cfg` as a template.
+* `simulation-naive.py` is used to simulate community and household spread in a naive way by weighting POIs equally, ignoring the time of day, and using a constant dwell time. In most cases, the virus will only reach a very small number of agents because agents will not congregate at popular POIs, making this simulation version unrealistic.
 
 * `mobility-stats.py` is used to evaluate mobility data assuming no virus has been introduced. It provides the total number of visitors to each POI within a specified timeframe.
+
+* `sigspatial-trials.txt`, `sigspatial-trial-runner.py`, and any files in a folder that is titled `sigspatial-trials/` were used to generate results for the conference publication. These files will likely not be applicable in other cases.
+
+* All results will be located in `results/`.

config-files/default-config.cfg

@@ -1,5 +1,3 @@
-[Settings]
-
 # preliminary parameters
 LOCALITY = 'Fairfax'  # can be a county, borough, or parish; independent cities (e.g. Baltimore City) are not currently compatible
 STATE_ABBR = 'VA'  # state abbreviation of where the locality is located
@@ -28,12 +26,12 @@ CLOSED_POI_TYPES = {}  # closes the following POI types (from SafeGraph Core Pla
 
 # virus parameters
 # For COVID-19, a close contact is defined as ay individual who was within 6 feet of an infected person for at least 15 minutes starting from 2 days before illness onset (or, for asymptomatic patients, 2 days prior to positive specimen collection) until the time the patient is isolated. (https://www.cdc.gov/coronavirus/2019-ncov/php/contact-tracing/contact-tracing-plan/contact-tracing.html)
-percent_asymptomatic = 0.4  # (recommended: 0.4) https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html
-secondary_attack_rate = 0.05  # (recommended: 0.05) chance of contracting the virus on close contact with someone, DO NOT DIVIDE BY SIMULATION_TICKS_PER_HOUR https://jamanetwork.com/journals/jama/fullarticle/2768396
-asymptomatic_relative_infectiousness = 0.75  # (recommended: 0.75) https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html
-distribution_of_exposure = scipy.stats.gamma(4, 0, 0.75)  # (recommended: 4, 0, 0.75) gamma distribution of the duration (days) between exposure and infectiousness, k=4 μ=3 => midpoint is 2.754 days https://www.nature.com/articles/s41591-020-0962-9
-distribution_of_preclinical = scipy.stats.gamma(4, 0, 0.525)  # (recommended: 4, 0, 0.525) gamma distribution of the duration (days) between infectiousness and symptoms for symptomatic cases, k=4 μ=2.1 => midpoint is 1.928 days https://www.nature.com/articles/s41591-020-0962-9
-distribution_of_clinical = scipy.stats.gamma(4, 0, 0.725)  # (recommended: 4, 0, 0.725) gamma distribution of the duration (days) between symptoms and non-infectiousness (recovery) for symptomatic cases, k=4 μ=2.9 => midpoint is 2.662 days https://www.nature.com/articles/s41591-020-0962-9
-distribution_of_subclinical = scipy.stats.gamma(4, 0, 1.25)  # (recommended: 4, 0, 1.25) gamma distribution of the duration (days) between infectiousness and non-infectiousness (recovery) for asymptomatic cases, k=4 μ=5 => midpoint is 4.590 days https://www.nature.com/articles/s41591-020-0962-9
-total_chance_of_small_household_transmission = 0.204  # (recommended: 0.091) chance of an infected agent spreading the virus to a given household member over the agent's entire period of infection when the household size is six or less https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30471-0/fulltext
-total_chance_of_large_household_transmission = 0.091  # (recommended: 0.204) chance of an infected agent spreading the virus to a given household member over the agent's entire period of infection when the household size is more than six https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30471-0/fulltext
+PERCENT_ASYMPTOMATIC = 0.4  # (recommended: 0.4) https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html
+SECONDARY_ATTACK_RATE = 0.05  # (recommended: 0.05) chance of contracting the virus on close contact with someone, DO NOT DIVIDE BY SIMULATION_TICKS_PER_HOUR https://jamanetwork.com/journals/jama/fullarticle/2768396
+ASYMPTOMATIC_RELATIVE_INFECTIOUSNESS = 0.75  # (recommended: 0.75) https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scenarios.html
+DISTRIBUTION_OF_EXPOSURE = scipy.stats.gamma(4, 0, 0.75)  # (recommended: 4, 0, 0.75) gamma distribution of the duration (days) between exposure and infectiousness, k=4 μ=3 => midpoint is 2.754 days https://www.nature.com/articles/s41591-020-0962-9
+DISTRIBUTION_OF_PRECLINICAL = scipy.stats.gamma(4, 0, 0.525)  # (recommended: 4, 0, 0.525) gamma distribution of the duration (days) between infectiousness and symptoms for symptomatic cases, k=4 μ=2.1 => midpoint is 1.928 days https://www.nature.com/articles/s41591-020-0962-9
+DISTRIBUTION_OF_CLINICAL = scipy.stats.gamma(4, 0, 0.725)  # (recommended: 4, 0, 0.725) gamma distribution of the duration (days) between symptoms and non-infectiousness (recovery) for symptomatic cases, k=4 μ=2.9 => midpoint is 2.662 days https://www.nature.com/articles/s41591-020-0962-9
+DISTRIBUTION_OF_SUBCLINICAL = scipy.stats.gamma(4, 0, 1.25)  # (recommended: 4, 0, 1.25) gamma distribution of the duration (days) between infectiousness and non-infectiousness (recovery) for asymptomatic cases, k=4 μ=5 => midpoint is 4.590 days https://www.nature.com/articles/s41591-020-0962-9
+TOTAL_CHANCE_OF_SMALL_HOUSEHOLD_TRANSMISSION = 0.204  # (recommended: 0.091) chance of an infected agent spreading the virus to a given household member over the agent's entire period of infection when the household size is six or less https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30471-0/fulltext
+TOTAL_CHANCE_OF_LARGE_HOUSEHOLD_TRANSMISSION = 0.091  # (recommended: 0.204) chance of an infected agent spreading the virus to a given household member over the agent's entire period of infection when the household size is more than six https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30471-0/fulltext

docs/cbgs-to-topics-1.html

@@ -1,6 +1,8 @@
 <!DOCTYPE html>
 <head>    
     <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+    <title>SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and Mitigation</title>
+    <link rel="shortcut icon" href="sigspatial.ico">
 
         <script>
             L_NO_TOUCH = false;

docs/cbgs-to-topics-10.html

@@ -1,6 +1,8 @@
 <!DOCTYPE html>
 <head>    
     <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+    <title>SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and Mitigation</title>
+    <link rel="shortcut icon" href="sigspatial.ico">
 
         <script>
             L_NO_TOUCH = false;

docs/cbgs-to-topics-50.html

@@ -1,6 +1,8 @@
 <!DOCTYPE html>
 <head>    
     <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+    <title>SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and Mitigation</title>
+    <link rel="shortcut icon" href="sigspatial.ico">
 
         <script>
             L_NO_TOUCH = false;

docs/index.html

@@ -2,14 +2,15 @@
 <html>
     <head>
         <title>SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and Mitigation</title>
+        <link rel="shortcut icon" href="sigspatial.ico">
         <link href="https://fonts.googleapis.com/css?family=Open+Sans:400,400i,700,700i" rel="stylesheet">
         <link rel="stylesheet" href="stylesheet.css" media="screen" type="text/css">
     </head>
     <body>
         <div class="wrapper">
             <h1>SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and Mitigation</h1>
             <p>Codebase: <a href="https://github.com/jpes707/safegraph-simulation">https://github.com/jpes707/safegraph-simulation</a></p>
-            <p>Topics to POIs heatmaps (top 100 POIs for all trials with 100k agents):</p>
+            <p>Topic POI heatmaps (top 100 POIs for all trials):</p>
             <ul>
                 <li><a href="topics-to-pois-1.html" target="_blank">1 topic</a></li>
                 <li><a href="topics-to-pois-10.html" target="_blank">10 topics</a></li>

docs/topics-to-pois-1.html

@@ -1,6 +1,8 @@
 <!DOCTYPE html>
 <head>    
     <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+    <title>SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and Mitigation</title>
+    <link rel="shortcut icon" href="sigspatial.ico">
 
         <script>
             L_NO_TOUCH = false;

docs/topics-to-pois-10.html

@@ -1,6 +1,8 @@
 <!DOCTYPE html>
 <head>    
     <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+    <title>SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and Mitigation</title>
+    <link rel="shortcut icon" href="sigspatial.ico">
 
         <script>
             L_NO_TOUCH = false;

docs/topics-to-pois-50.html

@@ -1,6 +1,8 @@
 <!DOCTYPE html>
 <head>    
     <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+    <title>SIGSPATIAL ARIC 2020: Foot-Traffic Informed COVID-19 Simulation and Mitigation</title>
+    <link rel="shortcut icon" href="sigspatial.ico">
 
         <script>
             L_NO_TOUCH = false;