cv19rr: S3 methods for the cv19rr class

In ku-awdc/Covid19RR: Estimation of Reproduction Rates for the COVID-19 Pandemic in Denmark based on Publicly Available Data

Description

S3 methods for the cv19rr class

Usage

## S3 method for class 'cv19rr'
print(x, ...)

## S3 method for class 'cv19rr'
plot(x, page = c(1, 2), main = "Kontakttal R", ...)

## S3 method for class 'cv19rr'
autoplot(
  object,
  lag = 7,
  caption_date = Sys.Date(),
  rib_col = "grey85",
  x_by = 5,
  xlim = c("2020-03-24", NA),
  y_marks = waiver(),
  ylim = c(NA, NA),
  ...
)

## S3 method for class 'cv19rr'
as.data.frame(
  x,
  row.names = NULL,
  optional = FALSE,
  lag = 7,
  r2R = function(r) 1 + 4.7 * r,
  ...
)

Arguments

x	An object of class cv19rr
...	Unused arguments provided for compatibility with S3 methods
page	Which page of plots to display (1, 2, 3 or multiple)
main	The plot title
object	An object of class cv19rr
lag	Lag parameter
caption_date	Date to use in the caption
rib_col	Colour for the ribbon
x_by	Increment for the date on the x axis
xlim	Limits of the x axis (date) - if the second element is blank then the caption date is used as the maximum extent of the range
y_marks	Marks to show on the y axis
ylim	Limits for the y axis
row.names	Unused arguments provided for compatibility with S3 methods
optional	Unused arguments provided for compatibility with S3 methods
r2R	function to convert daily growth rates to reproduction number
tests	Number of tests to normalise against

Examples

library("Covid19RR")
dat <- download_data()
mod <- estimate_cv19rr(dat, silent=TRUE)
require("ggplot2")
# Replicate figure 12.1:
autoplot(mod, date = "2020-10-25",
    y_marks = c(0, 0.5, 1, 1.5, 2), ylim = c(0, 2.5))
ggsave("figur 12.1.pdf", height=7, width=11)
# Replicate figure 12.2:
autoplot(mod, caption_date = "2020-10-25", xlim = c("2020-02-23", NA),
    y_marks = c(0, 1, 2), ylim = c(0, 3))
ggsave("figur 12.2.pdf", height=7, width=11)

# To produce graphs from a data frame:
mydf <- as.data.frame(mod)
Covid19RR:::autoplot.cv19rr(mydf)

ku-awdc/Covid19RR documentation built on Feb. 2, 2021, 12:49 p.m.