Config Class

Represents the complete configuration for the pipeline.

Usage

Config(
  job_id = class_missing,
  task_id = class_missing,
  min_reference_date = class_missing,
  max_reference_date = class_missing,
  report_date = class_missing,
  production_date = class_missing,
  disease = class_missing,
  low_case_count_thresholds = class_missing,
  geo_value = class_missing,
  geo_type = class_missing,
  seed = class_missing,
  horizon = class_missing,
  model = class_missing,
  config_version = class_missing,
  quantile_width = class_missing,
  data = class_missing,
  priors = class_missing,
  parameters = class_missing,
  sampler_opts = class_missing,
  exclusions = class_missing,
  output_container = class_missing,
  facility_active_proportion = class_missing
)

Arguments

job_id

A string specifying the job.

task_id

A string specifying the task.

min_reference_date

A string representing the minimum reference date. Formatted as "YYYY-MM-DD".

max_reference_date

A string representing the maximum reference date. Formatted as "YYYY-MM-DD".

report_date

A string representing the report date. Formatted as "YYYY-MM-DD".

production_date

A string representing the production date. Formatted as "YYYY-MM-DD".

disease

A string specifying the disease being modeled. One of "COVID-19" or "Influenza" or "RSV".

low_case_count_thresholds

A named list of thresholds to use for determining n_low_case_count in diagnostic file Example: list(COVID-19 = 10, Influenza`` = 10, RSV` = 5)

geo_value

An uppercase, two-character string specifying the geographic value, usually a state or "US" for national data.

geo_type

A string specifying the geographic type, usually "state".

seed

An integer for setting the random seed.

horizon

An integer specifying the forecasting horizon.

model

A string specifying the model to be used.

config_version

A numeric value specifying the configuration version.

quantile_width

A vector of numeric values representing the desired quantiles. Passed to tidybayes::median_qi().

data

An instance of Data class containing data configurations.

priors

A list of lists. The first level should contain the key rt with elements mean and sd and the key gp with element alpha_sd.

parameters

An instance of Parameters class containing parameter configurations.

sampler_opts

A list. The Stan sampler options to be passed through EpiNow2. It has required keys: cores, chains, iter_warmup, iter_sampling, max_treedepth, and adapt_delta.

exclusions

An instance of Exclusions class containing exclusion criteria.

output_container

An optional string specifying the output blob storage container.

facility_active_proportion

A numeric value between 0 and 1 specifying the proportion of days during the modeling period that facilities must have reported at least one informative discharge diagnosis (DDI) to be included in the analysis. Default is 0.94 (require active reporting for >=53 of 56 days in the training period). Lower values allow inclusion of facilities with fewer active days.

See also

Other config: Data(), Interval, Parameters(), read_json_into_config()