autoplot-epi: Automatically plot an epi_df or epi_archive

In cmu-delphi/epitools: Tools for basic signal processing in epidemiology

Automatically plot an epi_df or epi_archive

Description

Automatically plot an epi_df or epi_archive

Usage

## S3 method for class 'epi_df'
autoplot(
  object,
  ...,
  .color_by = c("all_keys", "geo_value", "other_keys", ".response", "all", "none"),
  .facet_by = c(".response", "other_keys", "all_keys", "geo_value", "all", "none"),
  .base_color = "#3A448F",
  .facet_filter = NULL,
  .max_facets = deprecated()
)

## S3 method for class 'epi_archive'
autoplot(
  object,
  ...,
  .base_color = "black",
  .versions = NULL,
  .mark_versions = FALSE,
  .facet_filter = NULL
)

## S3 method for class 'epi_df'
plot(x, ...)

## S3 method for class 'epi_archive'
plot(x, ...)

Arguments

object, x	An epi_df or epi_archive
...	<tidy-select> One or more unquoted expressions separated by commas. Variable names can be used as if they were positions in the data frame, so expressions like x:y can be used to select a range of variables.
.color_by	Which variables should determine the color(s) used to plot lines. Options include: all_keys - the default uses the interaction of any key variables including the geo_value geo_value - geo_value only other_keys - any available keys that are not geo_value .response - the numeric variables (same as the y-axis) all - uses the interaction of all keys and numeric variables none - no coloring aesthetic is applied
.facet_by	Similar to .color_by except that the default is to display each numeric variable on a separate facet
.base_color	Lines will be shown with this color if .color_by == "none". For example, with a single numeric variable and faceting by geo_value, all locations would share the same color line.
.facet_filter	Select which facets will be displayed. Especially useful for when there are many geo_value's or keys. This is a <rlang> expression along the lines of dplyr::filter(). However, it must be a single expression combined with the & operator. This contrasts to the typical use case which allows multiple comma-separated expressions which are implicitly combined with &. When multiple variables are selected with ..., their names can be filtered in combination with other factors by using .response_name. See the examples below.
.max_facets
.versions	Select which versions will be displayed. By default, a separate line will be shown with the data as it would have appeared on every day in the archive. This can sometimes become overwhelming. For example, daily data would display a line for what the data would have looked like on every single day. To override this, you can select specific dates, by passing a vector of values here. Alternatively, a sequence can be automatically created by passing a string like "2 weeks" or "month". For time types where the time_value is a date object, any string that is interpretable by base::seq.Date() is allowed. For time_type = "integer", an integer larger than 1 will give a subset of versions.
.mark_versions	Logical. Indicate whether to mark each version with a vertical line. Note that displaying many versions can become busy.

Value

A ggplot2::ggplot object

Examples

# -- Use it on an `epi_df`
autoplot(cases_deaths_subset, cases, death_rate_7d_av)
autoplot(cases_deaths_subset, case_rate_7d_av, .facet_by = "geo_value")
autoplot(cases_deaths_subset, case_rate_7d_av,
  .color_by = "none",
  .facet_by = "geo_value"
)
autoplot(cases_deaths_subset, case_rate_7d_av,
  .color_by = "none",
  .base_color = "red", .facet_by = "geo_value"
)

# .base_color specification won't have any effect due .color_by default
autoplot(cases_deaths_subset, case_rate_7d_av,
  .base_color = "red", .facet_by = "geo_value"
)

# filter to only some facets, must be explicitly combined
autoplot(cases_deaths_subset, cases, death_rate_7d_av,
  .facet_by = "all",
  .facet_filter = (.response_name == "cases" & geo_value %in% c("tx", "pa")) |
    (.response_name == "death_rate_7d_av" &
      geo_value %in% c("ca", "fl", "ga", "ny"))
)
# Just an alias for convenience
plot(cases_deaths_subset, cases, death_rate_7d_av,
  .facet_by = "all",
  .facet_filter = (.response_name == "cases" & geo_value %in% c("tx", "pa")) |
    (.response_name == "death_rate_7d_av" &
      geo_value %in% c("ca", "fl", "ga", "ny"))
)

# -- Use it on an archive

autoplot(archive_cases_dv_subset, percent_cli, .versions = "week")
autoplot(archive_cases_dv_subset_all_states, percent_cli,
  .versions = "week",
  .facet_filter = geo_value %in% c("or", "az", "vt", "ms")
)
autoplot(archive_cases_dv_subset, percent_cli,
  .versions = "month",
  .facet_filter = geo_value == "ca"
)
autoplot(archive_cases_dv_subset_all_states, percent_cli,
  .versions = "1 month",
  .facet_filter = geo_value %in% c("or", "az", "vt", "ms"),
  .mark_versions = TRUE
)
# Just an alias for convenience
plot(archive_cases_dv_subset_all_states, percent_cli,
  .versions = "1 month",
  .facet_filter = geo_value %in% c("or", "az", "vt", "ms"),
  .mark_versions = TRUE
)

cmu-delphi/epitools documentation built on April 17, 2025, 3:33 a.m.