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Read in the dataset of incident case counts

read_data.Rd

Reads in data from either data API v1 or v2. Data API version is intuited by read_data by the presence of the any_visits_this_day column in the underlying data. Each row of the table corresponds to a single facilities' cases for a reference-date/report-date/disease tuple. We want to aggregate these counts to the level of geographic aggregate/report-date/reference-date/disease. The facility_active_proportion field is used to filter facilities with data outages from the data API v2 (this field is not used for data API v1).

Usage

read_data(
  data_path,
  disease = c("COVID-19", "Influenza", "RSV", "test"),
  geo_value,
  report_date,
  max_reference_date,
  min_reference_date,
  facility_active_proportion = 0.94
)

Arguments

data_path

The path to the local file. This could contain a glob and must be in parquet format.

disease

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

geo_value

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

report_date

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

max_reference_date

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

min_reference_date

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

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.

Value

A dataframe with one or more rows and columns report_date, reference_date, geo_value, confirm

Details

We handle two distinct cases for geographic aggregates:

  1. A single state: Subset to facilities in that state only and aggregate up to the state level 2. The US overall: Aggregate over all facilities without any subsetting

Note that we do not apply exclusions here. The exclusions are applied later, after the aggregations. That means that for the US overall, we aggregate over points that might potentially be excluded at the state level. Our recourse in this case is to exclude the US overall aggregate point.