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epi_df basics

Details on epi_df format, and basic functionality.

as_tibble(<epi_df>)
Convert to tibble
as_tsibble(<epi_df>)
Convert to tsibble format
autoplot(<epi_df>)
Automatically plot an epi_df
complete(<epi_df>)
Complete epi_df
as_epi_df() new_epi_df()
epi_df object
group_epi_df()
Group an epi_df object by default keys
is_epi_df()
Test for epi_df format
print(<epi_df>) group_by(<epi_df>) ungroup(<epi_df>) group_modify(<epi_df>) unnest(<epi_df>)
Base S3 methods for an epi_df object
sum_groups_epi_df()
Aggregate an epi_df object
summary(<epi_df>)
Summarize epi_df object
geo_column_names()
potential geo_value columns
time_column_names()
potential time_value columns
version_column_names()
potential version columns

epi_*() functions

Functions that act on epi_df objects.

epi_slide()
Slide a function over variables in an epi_df object
epi_slide_mean()
Optimized slide function for performing rolling averages on an epi_df object
epi_slide_sum()
Optimized slide function for performing rolling sums on an epi_df object
epi_slide_opt()
Optimized slide function for performing common rolling computations on an epi_df object
epi_cor()
Compute correlations between variables in an epi_df object

Vector functions

Functions that act directly on signal variables.

growth_rate()
Estimate growth rate
detect_outlr()
Detect outliers
detect_outlr_rm()
Detect outliers based on a rolling median
detect_outlr_stl()
Detect outliers based on an STL decomposition

epi_archive basics

Details on epi_archive, and basic functionality.

archive_cases_dv_subset
Subset of daily doctor visits and cases in archive format
clone()
Clone an epi_archive object.
new_epi_archive() validate_epi_archive() as_epi_archive()
epi_archive object
epix_slide()
Slide a function over variables in an epi_archive or grouped_epi_archive
epix_truncate_versions_after()
Filter an epi_archive object to keep only older versions
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
print(<epi_archive>)
Print information about an epi_archive object
revision_summary()
A function to describe revision behavior for an archive

epix_*() functions

Functions that act on an epi_archive and/or grouped_epi_archive object.

epix_as_of()
Generate a snapshot from an epi_archive object
epix_fill_through_version()
Fill epi_archive unobserved history
epix_merge()
Merge two epi_archive objects
epix_slide()
Slide a function over variables in an epi_archive or grouped_epi_archive
epix_truncate_versions_after()
Filter an epi_archive object to keep only older versions
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

Example data

archive_cases_dv_subset
Subset of daily doctor visits and cases in archive format
incidence_num_outlier_example
Subset of JHU daily cases from California and Florida
jhu_csse_county_level_subset
Subset of JHU daily cases from counties in Massachusetts and Vermont
jhu_csse_daily_subset
Subset of JHU daily state cases and deaths

Basic automatic plotting

autoplot(<epi_df>)
Automatically plot an epi_df

Advanced internals

compactify
Compactify
epiprocess-package epiprocess
epiprocess: Tools for basic signal processing in epidemiology
max_version_with_row_in()
max(x$version), with error if x has 0 rows
next_after()
Get the next possible value greater than x of the same type
guess_period() experimental
Use max valid period as guess for period of time_values
key_colnames()
Grab any keys associated to an epi_df