Read in disease process parameters from an external file or files

Usage

read_disease_parameters(
  generation_interval_path,
  delay_interval_path,
  right_truncation_path,
  disease,
  as_of_date,
  group,
  report_date
)

Arguments

generation_interval_path, delay_interval_path, right_truncation_path: Path to a local file with the parameter PMF. See read_interval_pmf for details on the file schema. The parameters can be in the same file or a different file.
disease: One of COVID-19 or Influenza
as_of_date: Use the parameters that were used in production on this date. Set for the current date for the most up-to-to date version of the parameters and set to an earlier date to use parameters from an earlier time period.
group: An optional parameter to subset the query to a parameter with a particular two-letter state abbrevation. Right now, the only parameter with state-specific estimates is right_truncation.
report_date: An optional parameter to subset the query to a parameter on or before a particular report_date. Right now, the only parameter with report date-specific estimates is right_truncation. Note that this is similar to, but different from as_of_date. The report_date is used to select the particular value of a time-varying estimate. This estimate may itself be regenerated over time (e.g., as new data becomes available or with a methodological update). We can pull the estimate for date report_date as generated on date as_of_date.

Value

A named list with three PMFs. The list elements are named generation_interval, delay_interval, and right_truncation. If a path to a local file is not provided (NA or NULL), the corresponding parameter estimate will be NA in the returned list.

Details

generation_interval_path is required because the generation interval is a required parameter for $R_t$ estimation. delay_interval_path and right_truncation_path are optional (but strongly suggested).