plot.projections {projections} | R Documentation |
Plot projections objects
Description
The plot
method of projections
objects (output by the function
project
) shows quantiles of predicted incidence over time. The
function add_projections
can be used to add a similar plot to an
existing incidence
plot. This latter function is piping friendly (see
examples).
Usage
## S3 method for class 'projections'
plot(x, ylab = NULL, title = NULL, ...)
add_projections(
p,
x,
quantiles = c(0.01, 0.05, 0.1, 0.5),
ribbon = TRUE,
boxplots = FALSE,
palette = quantile_pal,
quantiles_alpha = 1,
linetype = 1,
linesize = 0.5,
ribbon_quantiles = NULL,
ribbon_color = NULL,
ribbon_alpha = 0.3,
boxplots_color = "#47476b",
boxplots_fill = "grey",
boxplots_alpha = 0.8,
outliers = TRUE
)
Arguments
x |
A |
ylab |
An optional label for the y-axis. If missing will default to "predicted incidence" or, if cumulative, "predicted cumulative incidence" |
title |
An optional title. |
... |
Further arguments to be passed to |
p |
A previous incidence plot to which projections should be added. |
quantiles |
A vector of quantiles to plot, automatically completed to be symmetric around the median. |
ribbon |
A logical indicating if a ribbon should be drawn; defaults to
|
boxplots |
A logical indicating if boxplots should be drawn. |
palette |
A color palette to be used for plotting the quantile lines;
defaults to |
quantiles_alpha |
A number used to control the transparency of the quantile lines, from 0 (full transparency) to 1 (full opacity); defaults to 1. |
linetype |
An integer indicating the type of line used for plotting the quantiles; defaults to 1 for a plain line. |
linesize |
An integer indicating the size of line used for plotting the quantiles; defaults to 0.5. |
ribbon_quantiles |
A vector of 2 quantiles to be used to determine the limits of the ribbon; if NULL (default); uses the most extreme quantiles if available; if quantiles are not provided, the daily range will be used. |
ribbon_color |
Any valid color, used for the ribbon. |
ribbon_alpha |
A number used to control the transparency of the ribbon, from 0 (full transparency) to 1 (full opacity); defaults to 0.3. |
boxplots_color |
Any valid color, used for the boxplot. |
boxplots_fill |
Any valid color, used for filling the boxplot. |
boxplots_alpha |
A number used to control the transparency of the boxplots, from 0 (full transparency) to 1 (full opacity); defaults to 0.8. |
outliers |
A logical indicating if outliers should be displayed
alongside the boxplots; defaults to |
Author(s)
Thibaut Jombart thibautjombart@gmail.com
See Also
project
to generate projections
Examples
if (require(outbreaks) &&
require(distcrete) &&
require(incidence) &&
require(magrittr)) {
si <- distcrete("gamma",
interval = 1L,
shape = 2.4,
scale = 4.7,
w = 0.5)
i <- incidence(ebola_sim$linelist$date_of_onset)
plot(i)
## add projections after the first 100 days, over 60 days
set.seed(1)
proj <- project(x = i[1:100], R = 1.4, si = si, n_days = 60)
## plotting projections: different options
plot(proj)
plot(proj, quantiles = c(.025, .5)) # 95% CI
plot(proj, ribbon_color = "red", quantiles = FALSE) # range
plot(proj, ribbon_color = "red", quantiles = FALSE,
ribbon_quantiles = c(.025, .5))
plot(proj, boxplots = TRUE, quantiles = FALSE, ribbon = FALSE)
plot(proj, boxplots = TRUE, quantiles = FALSE, outliers = FALSE)
plot(proj, linetype = 3)
## adding them to incidence plot
plot(i) %>% add_projections(proj)
plot(i[1:160]) %>% add_projections(proj)
plot(i[1:160]) %>% add_projections(proj, boxplots = FALSE)
plot(i[1:160]) %>%
add_projections(proj, boxplots_alpha = .3, boxplots_color = "red")
## same, with customised quantiles and colors
quantiles <- c(.001, .01, 0.05, .1, .2, .3, .4, .5)
pal <- colorRampPalette(c("#b3c6ff", "#00e64d", "#cc0066"))
plot(i[1:200]) %>%
add_projections(proj, quantiles, palette = pal)
}