Finalized code for public release

config-files/sigspatial-trials/1-3-1.cfg

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+[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
+WEEK = '2019-10-28'  # start date of the week to base data off of, must be a Monday
+NUM_TOPICS = 1  # number of Latent Dirichlet Allocation (LDA) topics
+MAXIMUM_NUMBER_OF_MAPPED_POIS = 100  # the top MAXIMUM_NUMBER_OF_MAPPED_POIS for each topic will appear on the topic to poi map
+RANDOM_SEED = 1  # SETTING THIS TO 0 USES THE SYSTEM CLOCK!! random seed for all random events in this script
+PROPORTION_OF_POPULATION = 0.1  # 0.2 => 20% of the actual population is simulated, a number lower than 1 will cause the curve to "flatten" because all POIs are still simulated
+PROPENSITY_TO_LEAVE = 1  # 0.2 => people are only 20% as likely to leave the house as compared to normal
+
+# agent generation parameters
+SIMULATION_TICKS_PER_HOUR = 4  # integer, number of ticks per simulation "hour"
+ORIGIN_CBG = '510594804023'  # only agents in this CBG will begin with the virus, to include all CBGs use 'random'
+PROPORTION_INITIALLY_INFECTED = 0.25  # 0.05 => 5% of the origin CBG (or the entire population if ORIGIN_CBG == 'random') is initially infected or exposed
+ALPHA = 0  # 0.4 => 40% of the population is quarantined in their house for the duration of the simulation
+
+# runtime parameters
+MAX_DWELL_TIME = 16  # maximum dwell time at any POI (hours)
+NUMBER_OF_DWELL_SAMPLES = 5  # a higher number decreases POI dwell time variation and allows less outliers
+MAXIMUM_INTERACTIONS_PER_TICK = 5  # integer, maximum number of interactions an infected person can have with others per tick
+MINIMUM_INTERVENTION_PROPORTION = 0  # 0.1 => all below interventions begin when 10% of the simulated population is infected
+SYMPTOMATIC_QUARANTINES = False  # if True, quarantines all newly-infected agents upon showing symptoms after the MINIMUM_INTERVENTION_PROPORTION is reached
+HOUSEHOLD_QUARANTINES = False  # if True, all household members will quarantine if an agent in their household also quarantines due to symptoms
+QUARANTINE_DURATION = 10  # number of days a symptomatic-induced quarantine lasts
+CLOSED_POI_TYPES = {}  # closes the following POI types (from SafeGraph Core Places "sub_category") after the MINIMUM_INTERVENTION_PROPORTION is reached
+
+# 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 = 0.07  # (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

config-files/sigspatial-trials/1-3-10.cfg

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+[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
+WEEK = '2019-10-28'  # start date of the week to base data off of, must be a Monday
+NUM_TOPICS = 10  # number of Latent Dirichlet Allocation (LDA) topics
+MAXIMUM_NUMBER_OF_MAPPED_POIS = 100  # the top MAXIMUM_NUMBER_OF_MAPPED_POIS for each topic will appear on the topic to poi map
+RANDOM_SEED = 1  # SETTING THIS TO 0 USES THE SYSTEM CLOCK!! random seed for all random events in this script
+PROPORTION_OF_POPULATION = 0.1  # 0.2 => 20% of the actual population is simulated, a number lower than 1 will cause the curve to "flatten" because all POIs are still simulated
+PROPENSITY_TO_LEAVE = 1  # 0.2 => people are only 20% as likely to leave the house as compared to normal
+
+# agent generation parameters
+SIMULATION_TICKS_PER_HOUR = 4  # integer, number of ticks per simulation "hour"
+ORIGIN_CBG = '510594804023'  # only agents in this CBG will begin with the virus, to include all CBGs use 'random'
+PROPORTION_INITIALLY_INFECTED = 0.25  # 0.05 => 5% of the origin CBG (or the entire population if ORIGIN_CBG == 'random') is initially infected or exposed
+ALPHA = 0  # 0.4 => 40% of the population is quarantined in their house for the duration of the simulation
+
+# runtime parameters
+MAX_DWELL_TIME = 16  # maximum dwell time at any POI (hours)
+NUMBER_OF_DWELL_SAMPLES = 5  # a higher number decreases POI dwell time variation and allows less outliers
+MAXIMUM_INTERACTIONS_PER_TICK = 5  # integer, maximum number of interactions an infected person can have with others per tick
+MINIMUM_INTERVENTION_PROPORTION = 0  # 0.1 => all below interventions begin when 10% of the simulated population is infected
+SYMPTOMATIC_QUARANTINES = False  # if True, quarantines all newly-infected agents upon showing symptoms after the MINIMUM_INTERVENTION_PROPORTION is reached
+HOUSEHOLD_QUARANTINES = False  # if True, all household members will quarantine if an agent in their household also quarantines due to symptoms
+QUARANTINE_DURATION = 10  # number of days a symptomatic-induced quarantine lasts
+CLOSED_POI_TYPES = {}  # closes the following POI types (from SafeGraph Core Places "sub_category") after the MINIMUM_INTERVENTION_PROPORTION is reached
+
+# 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 = 0.07  # (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

config-files/sigspatial-trials/1-3-50.cfg

@@ -0,0 +1,39 @@
+[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
+WEEK = '2019-10-28'  # start date of the week to base data off of, must be a Monday
+NUM_TOPICS = 50  # number of Latent Dirichlet Allocation (LDA) topics
+MAXIMUM_NUMBER_OF_MAPPED_POIS = 100  # the top MAXIMUM_NUMBER_OF_MAPPED_POIS for each topic will appear on the topic to poi map
+RANDOM_SEED = 1  # SETTING THIS TO 0 USES THE SYSTEM CLOCK!! random seed for all random events in this script
+PROPORTION_OF_POPULATION = 0.1  # 0.2 => 20% of the actual population is simulated, a number lower than 1 will cause the curve to "flatten" because all POIs are still simulated
+PROPENSITY_TO_LEAVE = 1  # 0.2 => people are only 20% as likely to leave the house as compared to normal
+
+# agent generation parameters
+SIMULATION_TICKS_PER_HOUR = 4  # integer, number of ticks per simulation "hour"
+ORIGIN_CBG = '510594804023'  # only agents in this CBG will begin with the virus, to include all CBGs use 'random'
+PROPORTION_INITIALLY_INFECTED = 0.25  # 0.05 => 5% of the origin CBG (or the entire population if ORIGIN_CBG == 'random') is initially infected or exposed
+ALPHA = 0  # 0.4 => 40% of the population is quarantined in their house for the duration of the simulation
+
+# runtime parameters
+MAX_DWELL_TIME = 16  # maximum dwell time at any POI (hours)
+NUMBER_OF_DWELL_SAMPLES = 5  # a higher number decreases POI dwell time variation and allows less outliers
+MAXIMUM_INTERACTIONS_PER_TICK = 5  # integer, maximum number of interactions an infected person can have with others per tick
+MINIMUM_INTERVENTION_PROPORTION = 0  # 0.1 => all below interventions begin when 10% of the simulated population is infected
+SYMPTOMATIC_QUARANTINES = False  # if True, quarantines all newly-infected agents upon showing symptoms after the MINIMUM_INTERVENTION_PROPORTION is reached
+HOUSEHOLD_QUARANTINES = False  # if True, all household members will quarantine if an agent in their household also quarantines due to symptoms
+QUARANTINE_DURATION = 10  # number of days a symptomatic-induced quarantine lasts
+CLOSED_POI_TYPES = {}  # closes the following POI types (from SafeGraph Core Places "sub_category") after the MINIMUM_INTERVENTION_PROPORTION is reached
+
+# 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 = 0.07  # (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