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config.yml
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config.yml
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## This config file will not generate a makefile as currently configured.
## We want to show all of the options available, even though some are not appropriately general for this scope
## In particular, importation and the associated FolderDraw seeding method only work for sets of US states.
## The comments in this file explain how to modify it based on your use case
## Items that must be changed for the process to work are designated by < >.
## Some items in the config can be removed, and we have tried to note these with comments as well.
this_file_is_unedited: TRUE # This config file does not work as presented. There are a few additional files
name: minimal
start_date: 2020-01-31
end_date: 2020-05-31
nsimulations: 15
dt: 0.25
## dynfilter_path: data/filter.txt ## this method of filtering is not currently working
spatial_setup:
census_year: 2010
base_path: data
modeled_states: # To model a region that is not a state, remove modeled_states and the importation: block
- <Your State Postal Code> # e.g., MD You can provide as many of these as you like, but more counties means slower runs
setup_name: minimal
geodata: geodata.csv
mobility: mobility.txt
popnodes: population
nodenames: geoid
include_in_report: include_in_report
shapefile: <shapefile.shp> # We haven't created fake shapefiles yet. Stay tuned.
shapefile_name: <shapefile.shp> # This should be the same as above. We are working to merge the two
importation: ## You can seed the SEIR model directly instead of using importation. To do so, comment out this block
census_api_key: <your census api key> # For use with the tidycensus package
travel_dispersion: 3
maximum_destinations: Inf
dest_type : state
dest_country : USA
aggregate_to: airport
cache_work: TRUE
update_case_data: TRUE
draw_travel_from_distribution: FALSE
print_progress: FALSE
travelers_threshold: 10000
airport_cluster_distance: 80
param_list:
incub_mean_log: log(5.89)
incub_sd_log: log(1.74)
inf_period_nohosp_mean: 15
inf_period_nohosp_sd: 5
inf_period_hosp_mean_log: 1.23
inf_period_hosp_sd_log: 0.79
p_report_source: [0.05, 0.25]
shift_incid_days: -10
delta: 1
seeding: ## If removing the importation, comment out this seeding block
method: FolderDraw
folder_path: importation/minimal/
# seeding: ## If removing importation, uncomment this seeding block
# method: PoissonDistributed
# lambda_file: data/minimal/seeding.csv
seir:
parameters:
sigma: 1 / 5.2
gamma:
distribution: uniform
low: 1 / 6
high: 1 / 2.6
R0s:
distribution: uniform
low: 2
high: 3
interventions:
scenarios:
- None
- Scenario1
settings:
None:
template: ReduceR0
period_start_date: 2020-04-01
period_end_date: 2020-05-15
value:
distribution: fixed
value: 0
Wuhan:
template: ReduceR0
period_start_date: 2020-04-01
period_end_date: 2020-05-15
value:
distribution: uniform
low: .14
high: .33
KansasCity:
template: ReduceR0
period_start_date: 2020-04-01
period_end_date: 2020-05-15
value:
distribution: uniform
low: .04
high: .23
Scenario1:
template: Stacked
scenarios:
- Wuhan
- None
Scenario2:
template: Stacked
scenarios:
- Wuhan
hospitalization:
paths:
output_path: hospitalization
parameters:
time_hosp: [1.23, 0.79]
time_disch: [log(11.5), log(1.22)]
time_death: [log(11.25), log(1.15)]
time_ICU: [log(8.25), log(2.2)]
time_ICUdur: [log(16), log(2.96)]
time_vent: [log(10.5), log((10.5-8)/1.35)]
p_death: [.0025, .005, .01]
p_death_names: ["low","med","high"]
p_death_rate: 0.1
p_ICU: 0.32
p_vent: 0.15
## Report generation is still in it's infancy.
## The parameters in this block are only used in our draft state_report rmarkdown template
## This section can be removed if you are not using that template.
## Many of the parameters in this section may be broken, as that report has been under a lot of development recently.
report:
data_settings:
pop_year: 2010
plot_settings:
plot_intervention: TRUE
parameters_to_display:
sigma:
type: seir
distribution: exp
formal_name: Incubation Period
transform: invert
xlab: Days since symptom onset
gamma:
type: seir
distribution: gamma
formal_name: Duration of Infectiousness
transform: invert
xlab: Days since symptom onset
time_hosp:
type: hospitalization
distribution: lnormal
formal_name: Time to Hospitalization
xlab: Days since symptom onset
xlim: [0,100]
time_disch:
type: hospitalization
distribution: lnormal
formal_name: Time to Discharge
xlab: Days since hospitalization
time_ICU:
type: hospitalization
distribution: lnormal
formal_name: Time to ICU Admission
xlab: Days since hospitalization
xlim: [0,100]
time_ICUdur:
type: hospitalization
distribution: lnormal
formal_name: Time in ICU
xlab: Days since ICU admission
xlim: [0,100]
time_death:
type: hospitalization
distribution: lnormal
formal_name: Time to Death
xlab: Days since hopitalization
time_vent:
type: hospitalization
distribution: lnormal
formal_name: Time to Ventilation
xlab: Days since ICU admission
xlim: [0,100]
formatting:
scenario_labels_short: []
scenario_labels:
- Lockdown followed by Worst Case Uncontrolled Spread
- Lockdown followed by Test and Isolate
- Lockdown followed by Moderate Social Distancing
scenario_colors: ["#D95F02", "#1B9E77", "#7570B3"]
pdeath_labels: ["0.25% IFR", "0.5% IFR", "1% IFR"]
display_dates: ["2020-05-01", "2020-07-01", "2020-09-01"]