Package index • epiprocess

`epi_df` basics

Constructors and information for epi_df objects.

as_epi_df() is_epi_df() new_epi_df(): Test for epi_df format

group_epi_df(): Group an epi_df object by default keys

`epi_df` manipulation

Functions operating on epi_df objects.

complete(<epi_df>): "Complete" an epi_df, adding missing rows and/or replacing NAs

epi_slide(): More general form of epi_slide_opt for rolling/running computations

epi_slide_opt() epi_slide_mean() epi_slide_sum(): Calculate rolling or running means, sums, etc., or custom calculations

sum_groups_epi_df(): Aggregate an epi_df object

epi_cor(): Compute correlations between variables in an epi_df object

detect_outlr() detect_outlr_rm() detect_outlr_stl(): Detect outliers

growth_rate(): Estimate growth rate

growth_rate_params(): Optional parameters for growth rate methods

as_tibble(<epi_df>): Convert to tibble

as_tsibble(<epi_df>): Convert to tsibble format

`epi_archive` basics

Constructors and information for epi_archive objects.

as_epi_archive() is_epi_archive() new_epi_archive() validate_epi_archive(): as_epi_archive converts a data frame, data table, or tibble into an epi_archive object.

clone(): Clone an epi_archive object.

group_by(<epi_archive>) group_by(<grouped_epi_archive>) group_by_drop_default(<grouped_epi_archive>) group_vars(<grouped_epi_archive>) groups(<grouped_epi_archive>) ungroup(<grouped_epi_archive>) is_grouped_epi_archive(): group_by and related methods for epi_archive, grouped_epi_archive

`epi_archive` manipulation

Functions operating on epi_archive objects.

epix_as_of(): Generate a snapshot from an epi_archive object

epix_as_of_current(): Get the latest snapshot from an epi_archive object.

epix_slide(): Take each requested (group and) version in an archive, run a computation (e.g., forecast)

revision_analysis() print(<revision_analysis>) revision_summary(): A function to describe revision behavior for an archive.

epix_merge(): Merge two epi_archive objects

filter(<epi_archive>): dplyr::filter for epi_archives

epix_fill_through_version(): Fill epi_archive unobserved history

epix_truncate_versions_after(): Filter an epi_archive object to keep only older versions

set_versions_end(): Set the versions_end attribute of an epi_archive object

Basic analysis and visualization

autoplot(<epi_df>) autoplot(<epi_archive>) plot(<epi_df>) plot(<epi_archive>): Automatically plot an epi_df or epi_archive

print(<epi_archive>): Print information about an epi_archive object

print(<epi_df>) summary(<epi_df>) group_by(<epi_df>) ungroup(<epi_df>) group_modify(<epi_df>) unnest(<epi_df>): Base S3 methods for an epi_df object

revision_analysis() print(<revision_analysis>) revision_summary(): A function to describe revision behavior for an archive.

Example data

cases_deaths_subset: Subset of JHU daily state COVID-19 cases and deaths from 6 states (from epidatasets)

archive_cases_dv_subset: Subset of daily COVID-19 doctor visits and cases from 6 states in archive format (from epidatasets)

covid_incidence_county_subset: Subset of JHU daily COVID-19 cases from counties in Massachusetts and Vermont (from epidatasets)

covid_incidence_outliers: Subset of JHU daily COVID-19 cases from New Jersey and Florida (from epidatasets)

covid_case_death_rates_extended: JHU daily COVID-19 cases and deaths rates from all states (from epidatasets)