load_data: Assemble a data frame of incident and cumulative cases,...
In reichlab/covidData: Versioned Data for COVID-19

load_data

R Documentation

Assemble a data frame of incident and cumulative cases, deaths or hospitalizations due to COVID-19 as they were available as of one or more past dates.

Description

Assemble a data frame of incident and cumulative cases, deaths or hospitalizations due to COVID-19 as they were available as of one or more past dates.

Usage

load_data(
  issues = NULL,
  as_of = NULL,
  location_code = NULL,
  spatial_resolution = "state",
  temporal_resolution = "weekly",
  measure = "deaths",
  geography = c("US", "global"),
  source = NULL,
  drop_last_date = FALSE
)

Arguments

`issues`	vector of issue dates (i.e. report dates) to use for querying data, either `Date` objects or strings in the format 'yyyy-mm-dd'. Data for the requested measures that were reported or updated exactly on the specified issue date(s) will be returned. If multiple issue dates are provided, the result includes the data for all such issue dates.
`as_of`	character vector of "as of" dates to use for querying truths in format 'yyyy-mm-dd'. For each spatial unit and temporal reporting unit, the last available data with an issue date on or before the given `as_of` date are returned.
`location_code`	character vector of location codes. Default to NULL. For US locations, this should be a list of FIPS code or 'US' For ECDC locations, this should be a list of location name abbreviation.
`spatial_resolution`	character vector specifying spatial unit types to include: one or more of 'county', 'state' and/or 'national'. Default to 'state'. Note that 'county' is not available for hospitalization data. When source is "covidcast", this parameter has to match with location_code, if specified.
`temporal_resolution`	string specifying temporal resolution to include: one of 'daily' or 'weekly'
`measure`	string specifying measure of disease dynamics: one of 'deaths', 'cases', 'hospitalizations', or 'flu hospitalizations'. The first three of these refer to measures of covid intensity. Default to 'deaths'.
`geography`	character, which data to read. Default is "US", other option is "global". Note that "global" is not available for hospitalization data and "covidcast" source.
`source`	string specifying data source. Currently supported sources are "jhu" or "covidcast" for the "deaths" or "cases" measures; "healthdata" or "covidcast" for the "hospitalizations" and "flu hospitalizations" measures. Default to NULL which means "healthdata" for hospitalization data and "jhu" for all other measures.
`drop_last_date`	boolean indicating whether to drop the last 1 day of data for the influenza and COVID hospitalization signals. The last day of data from the HHS data source is unreliable, so it is recommended to set this to `TRUE`. However, the default is `FALSE` so that the function maintains fidelity to the authoritative data source. This argument is ignored if the `measure` is 'deaths' or 'cases'.

Details

Data for a specified issue are only returned if the data were first available on that date, or were updated on that date. A warning is generated for any issue dates for which no data were available.

A query based on an as_of date returns the data for the most recent issue date that is on or before the specified as_of date. A warning is generated for any as_of dates for which no data were available; this only occurs if the as_of date is prior to any data release for the specified measure.

If the user provides values for both issue and as_of, a warning is generated and the argument for issue is ignored.

If multiple issue dates or as_of dates are provided, the result combines the data for all such dates. If no value is provided for either issue or as_of, results for the most recent available as_of date are returned.