scale_y_cases_5er: Continuous x-axis and y-axis scale for (case) counts

In ggsurveillance: Tools for Outbreak Investigation/Infectious Disease Surveillance

Continuous x-axis and y-axis scale for (case) counts

Description

A continuous ggplot scale for count data with sane defaults for breaks. It uses base::pretty() to increase the default number of breaks and prefers 5er breaks. Additionally, the first tick (i.e. zero) is aligned to the lower left corner.

Usage

scale_y_cases_5er(
  name = waiver(),
  n = 8,
  min.n = 5,
  u5.bias = 4,
  expand = NULL,
  labels = waiver(),
  limits = NULL,
  oob = scales::censor,
  na.value = NA_real_,
  transform = "identity",
  position = "left",
  sec.axis = waiver(),
  guide = waiver(),
  ...
)

scale_x_cases_5er(
  name = waiver(),
  n = 8,
  min.n = 5,
  u5.bias = 4,
  expand = NULL,
  labels = waiver(),
  limits = NULL,
  oob = scales::censor,
  na.value = NA_real_,
  transform = "identity",
  position = "bottom",
  sec.axis = waiver(),
  guide = waiver(),
  ...
)

Arguments

name	The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.
n	Target number of breaks passed to base::pretty(). Defaults to 8.
min.n	Minimum number of breaks passed to base::pretty(). Defaults to 5.
u5.bias	The "5-bias" parameter passed to base::pretty(); higher values push the breaks more strongly toward multiples of 5. Defaults to 4.
expand	Uses own expansion logic. Use expand = waiver() to restore ggplot defaults or ggplot2::expansion() to modify
labels	One of: NULL for no labels waiver() for the default labels computed by the transformation object A character vector giving labels (must be same length as breaks) An expression vector (must be the same length as breaks). See ?plotmath for details. A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.
limits	One of: NULL to use the default scale range A numeric vector of length two providing limits of the scale. Use NA to refer to the existing minimum or maximum A function that accepts the existing (automatic) limits and returns new limits. Also accepts rlang lambda function notation. Note that setting limits on positional scales will remove data outside of the limits. If the purpose is to zoom, use the limit argument in the coordinate system (see coord_cartesian()).
oob	One of: Function that handles limits outside of the scale limits (out of bounds). Also accepts rlang lambda function notation. The default (scales::censor()) replaces out of bounds values with NA. scales::squish() for squishing out of bounds values into range. scales::squish_infinite() for squishing infinite values into range.
na.value	Missing values will be replaced with this value.
transform	For continuous scales, the name of a transformation object or the object itself. Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time". A transformation object bundles together a transform, its inverse, and methods for generating breaks and labels. Transformation objects are defined in the scales package, and are called ⁠transform_<name>⁠. If transformations require arguments, you can call them from the scales package, e.g. scales::transform_boxcox(p = 2). You can create your own transformation with scales::new_transform().
position	For position scales, The position of the axis. left or right for y axes, top or bottom for x axes.
sec.axis	sec_axis() is used to specify a secondary axis.
guide	A function used to create a guide or its name. See guides() for more information.
...	Additional arguments passed on to base::pretty().

Value

A ggplot2 scale object that can be added to a plot.

See Also

geom_epicurve(), ggplot2::scale_y_continuous(), base::pretty(), theme_mod_remove_minor_grid_y()

Examples

library(ggplot2)

data <- data.frame(date = as.Date("2024-01-01") + 0:30)
ggplot(data, aes(x = date)) +
  geom_epicurve(date_resolution = "week") +
  scale_y_cases_5er() +
  theme_mod_remove_minor_grid_y()

ggsurveillance documentation built on April 12, 2025, 1:09 a.m.