epiprocess

This package introduces a common data structure for epidemiological data sets measured over space and time, and offers associated utilities to perform basic signal processing tasks. See the getting started guide and vignettes for examples.

Installation

To install (unless you're making changes to the package, use the stable version):

# Stable version
pak::pkg_install("cmu-delphi/epiprocess@main")

# Dev version
pak::pkg_install("cmu-delphi/epiprocess@dev")

epi_df: snapshot of a data set

The first main data structure in the epiprocess package is called epi_df. This is simply a tibble with a couple of required columns, geo_value and time_value. It can have any other number of columns, which can be seen as measured variables, which we also call signal variables. In brief, an epi_df object represents a snapshot of a data set that contains the most up-to-date values of the signals variables, as of a given time.

By convention, functions in the epiprocess package that operate on epi_df objects begin with epi. For example:

• epi_slide(), for iteratively applying a custom computation to a variable in an epi_df object over sliding windows in time;
• epi_cor(), for computing lagged correlations between variables in an epi_df object, (allowing for grouping by geo value, time value, or any other variables).

Functions in the package that operate directly on given variables do not begin with epi. For example:

• growth_rate(), for estimating the growth rate of a given signal at given time values, using various methodologies;
• detect_outlr(), for detecting outliers in a given signal over time, using either built-in or custom methodologies.

epi_archive: full version history of a data set

The second main data structure in the package is called epi_archive. This is a special class (R6 format) wrapped around a data table that stores the archive (version history) of some signal variables of interest.

By convention, functions in the epiprocess package that operate on epi_archive objects begin with epix (the "x" is meant to remind you of "archive"). These are just wrapper functions around the public methods for the epi_archive R6 class. For example:

• epix_as_of(), for generating a snapshot in epi_df format from the data archive, which represents the most up-to-date values of the signal variables, as of the specified version;
• epix_fill_through_version(), for filling in some fake version data following simple rules, for use when downstream methods expect an archive that is more up-to-date (e.g., if it is a forecasting deadline date and one of our data sources cannot be accessed to provide the latest versions of its data)
• epix_merge(), for merging two data archives with each other, with support for various approaches to handling when one of the archives is more up-to-date version-wise than the other;
• epix_slide(), for sliding a custom computation to a data archive over local windows in time, much like epi_slide for an epi_df object, but with one key difference: the sliding computation at any given reference time t is performed only on the data that would have been available as of t.