autoplot: Autoplot a 'tsd' object

In aedseo: Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

Autoplot a tsd object

Description

Generates a complete 'ggplot' object suitable for visualizing time series data in a tsd, tsd_onset or tsd_onset_and_burden object.

autoplot(tsd)

• Generates points for each observation and connects them with a line.

autoplot(tsd_onset)

• The first plot generates a line connecting the observations. The transparency of the points reflects if seasonal onset has occurred.

• The second plot presents the growth rate for each observation along with confidence intervals. The transparency of the points indicates whether a growth warning condition is met.

autoplot(tsd_onset_and_burden)

• Generates a line connecting the observations in the current season, along with colored regions representing different burdens levels and a vertical line indicating outbreak start. The y-axis is scaled with ggplot2::scale_y_log10 to give better visualisation of the burden levels.

Usage

autoplot(object, ...)

## S3 method for class 'tsd'
autoplot(
  object,
  line_width = 0.7,
  obs_size = 2,
  text_family = "sans",
  time_interval_step = "5 weeks",
  y_label = "Weekly observations",
  ...
)

## S3 method for class 'tsd_onset'
autoplot(
  object,
  disease_color = "black",
  line_width = 0.7,
  obs_size = 2,
  alpha_warning = 0.2,
  alpha_ribbon = 0.1,
  text_family = "sans",
  legend_position = "bottom",
  time_interval_step = "5 weeks",
  y_label = "Weekly observations",
  ...
)

## S3 method for class 'tsd_onset_and_burden'
autoplot(
  object,
  y_lower_bound = 5,
  factor_to_max = 2,
  disease_color = "royalblue",
  season_start = 21,
  season_end = season_start - 1,
  time_interval_step = "3 weeks",
  y_label = "Weekly observations",
  text_burden_size = 10/2.8,
  fill_alpha = c(0.45, 0.6, 0.75, 0.89, 1),
  text_family = "sans",
  line_color = "black",
  line_type = "solid",
  vline_color = "red",
  vline_linetype = "dashed",
  y_scale_labels = scales::label_comma(big.mark = ".", decimal.mark = ","),
  theme_custom = ggplot2::theme_bw(),
  legend_position = "right",
  ...
)

## S3 method for class 'tsd_growth_warning'
autoplot(
  object,
  k = 5,
  skip_current_season = TRUE,
  line_width = 1,
  text_family = "sans",
  legend_position = "bottom",
  breaks_y_axis = 8,
  ...
)

Arguments

object	A tsd_onset object
...	Additional arguments (not used).
line_width	A numeric specifying the width of line connecting observations.
obs_size	A numeric, specifying the size of observational points.
text_family	A character specifying the font family for the text labels.
time_interval_step	A character vector specifying the time interval and how many time steps are desired on the x-axis, e.g. '10 days', '4 weeks', or '3 months'.
y_label	A character vector specifying the y label text.
disease_color	A character specifying the base color of the disease.
alpha_warning	A numeric specifying the alpha (transparency) for the observations with a seasonal_onset_alarm (first plot) or significantly positive growth rate (second plot).
alpha_ribbon	A numeric specifying the alpha for the confidence intervals of the growth rate.
legend_position	A character specifying the position of the legend on the plot.
y_lower_bound	A numeric specifying the lower bound of the y-axis.
factor_to_max	A numeric specifying the factor to multiply the high burden level for extending the y-axis.
season_start, season_end	Integers giving the start and end weeks of the seasons to stratify the observations by.
text_burden_size	A numeric specifying the size of the text labels.
fill_alpha	A numeric vector specifying the transparency levels for the fill colors of burden levels. Must match the number of levels.
line_color	A character specifying the color of the line connecting observations.
line_type	A character specifying the line type for observation line.
vline_color	A character specifying the color of the vertical outbreak start lines.
vline_linetype	A character specifying the line type for outbreak start lines.
y_scale_labels	A function to format y-axis labels.
theme_custom	A function with a ggplot2 theme, specifying the theme to apply to the plot.
k	An integer specifying the window size used to create the tsd_onset object.
skip_current_season	A logical. Do you want to skip your current season?
breaks_y_axis	A numeric specifying how many breaks to show on the y-axis.

Value

A 'ggplot' object for visualizing the tsd data.

A 'ggplot' object for visualizing the tsd_onset data.

A 'ggplot' object for visualizing the tsd_onset_and_burden data for the current season.

A 'ggplot' object for visualizing the tsd_growth_warning data.

Examples

set.seed(345)
# Create an example `tsd` object
time_series <- generate_seasonal_data()
autoplot(time_series)

# Create an `tsd_onset` object
time_series_with_onset <- seasonal_onset(
  tsd = time_series,
  k = 3,
  level = 0.95,
  family = "quasipoisson"
)
autoplot(time_series_with_onset)

# Define `disease_threshold`
disease_threshold <- 150

# Create a `tsd_onset_and_burden` object
tsd_onset_burden <- combined_seasonal_output(
  tsd = time_series,
  disease_threshold = disease_threshold
)
autoplot(tsd_onset_burden)

# Create an `tsd_onset` object
tsd_onset <- seasonal_onset(
  tsd = time_series,
  k = 5,
  family = "quasipoisson",
  season_start = 21,
  only_current_season = FALSE
)

tsd_growth_warning <- consecutive_growth_warnings(tsd_onset)

autoplot(tsd_growth_warning)

aedseo documentation built on April 12, 2025, 1:35 a.m.