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config_nonUS.yml
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config_nonUS.yml
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this_file_is_unedited: TRUE # This config file does not work as presented. There are a few additional files
name: Westeros
start_date: 2020-03-01
end_date: 2020-12-31
nsimulations: 100
dt: 0.25
report_location_name: Westeros
spatial_setup:
census_year: 2020
base_path: data
setup_name: westeros
us_model: FALSE
modeled_states:
- WES
geoid_len: 6
geodata: geodata.csv
mobility: mobility.csv
popnodes: pop
nodenames: geoid
include_in_report: include_in_report
shapefile: geodata/Westeros/Westeros_districts.shp
shapefile_name: geodata/Westeros/Westeros_districts.shp
geoid_params_file: data/geoid-params.csv
# importation:
# census_api_key: <insert-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: 5000
# 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_shape: 0.75
# inf_period_hosp_scale: 5.367
# 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/
#
seeding:
method: PoissonDistributed
lambda_file: data/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:
- Uncontrolled
- PhasedControl
settings:
Uncontrolled:
template: ReduceR0
period_start_date: 2020-03-01
period_end_date: 2020-12-31
value:
distribution: fixed
value: 0
LowSocialDist_ph1:
template: ReduceR0
period_start_date: 2020-03-10
period_end_date: 2020-03-18
value:
distribution: uniform
low: 0.16
high: 0.30
ModSocialDist_ph2:
template: ReduceR0
period_start_date: 2020-03-19
period_end_date: 2020-03-25
value:
distribution: uniform
low: 0.53
high: 0.57
HighControl_ph3:
template: ReduceR0
period_start_date: 2020-03-26
period_end_date: 2020-05-26
value:
distribution: uniform
low: 0.61
high: 0.64
ModControl_ph4:
template: ReduceR0
period_start_date: 2020-05-27
period_end_date: 2020-08-31
value:
distribution: uniform
low: 0.26
high: 0.37
PhasedControl:
template: Stacked
scenarios:
- Uncontrolled
- LowSocialDist_ph1
- ModSocialDist_ph2
- HighControl_ph3
- ModControl_ph4
hospitalization:
paths:
output_path: hospitalization
run_age_adjust: TRUE
parameters:
time_hosp: [log(7), 0.3]
time_disch: [log(11.5), log(1.22)]
time_ICU: [log(3), 0.3]
time_ICUdur: [log(8), 0.2]
time_ventdur: [log(7), 0.2]
time_vent: [log(1), 0.4]
p_death: [.01, .005, .0025]
p_death_names: ["high", "med", "low"]
p_hosp_inf: [0.1, .05, .025]
time_onset_death: [2.84, 0.52]
interventions:
scenarios:
- Uncontrolled
- PhasedControl
settings:
Uncontrolled:
template: ReduceR0
period_start_date: 2020-03-01
period_end_date: 2020-12-31
value:
distribution: fixed
value: 0
LowSocialDist_ph1:
template: ReduceR0
period_start_date: 2020-03-10
period_end_date: 2020-03-18
value:
distribution: uniform
low: 0.16
high: 0.30
ModSocialDist_ph2:
template: ReduceR0
period_start_date: 2020-03-19
period_end_date: 2020-03-25
value:
distribution: uniform
low: 0.53
high: 0.57
HighControl_ph3:
template: ReduceR0
period_start_date: 2020-03-26
period_end_date: 2020-05-26
value:
distribution: uniform
low: 0.61
high: 0.64
ModControl_ph4:
template: ReduceR0
period_start_date: 2020-05-27
period_end_date: 2020-08-31
value:
distribution: uniform
low: 0.26
high: 0.37
PhasedControl:
template: Stacked
scenarios:
- Uncontrolled
- LowSocialDist_ph1
- ModSocialDist_ph2
- HighControl_ph3
- ModControl_ph4
hospitalization:
paths:
output_path: hospitalization
run_age_adjust: TRUE
parameters:
time_hosp: [log(7), 0.3]
time_disch: [log(11.5), log(1.22)]
time_ICU: [log(3), 0.3]
time_ICUdur: [log(8), 0.2]
time_ventdur: [log(7), 0.2]
time_vent: [log(1), 0.4]
p_death: [.01, .005, .0025]
p_death_names: ["high", "med", "low"]
p_hosp_inf: [0.1, .05, .025]
time_onset_death: [2.84, 0.52]
report:
data_settings:
pop_year: 2020
plot_settings:
plot_intervention: FALSE
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: ["Uncontrolled", "PhasedControl"]
scenario_labels:
- Uncontrolled
- Phased Social Distancing and Control
scenario_descriptions: ["Uncontrolled", "Phased social distancing and control measures"]
scenario_colors: ["#43A2CA", "#9933FF"]
pdeath_labels: ["1% IFR", "0.5% IFR", "0.25% IFR"]
display_dates: ["2020-05-01", "2020-06-01", "2020-07-01", "2020-08-01", "2020-09-01","2020-10-01", "2020-11-01","2020-12-01","2020-12-31"]
display_dates2: ["2020-05-01", "2020-07-01", "2020-09-01", "2020-11-01", "2021-12-31"]