Plot projections objects — plot.projections • projections2

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 projections object.
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 add_projections.
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 TRUE.
boxplots: A logical indicating if boxplots should be drawn.
palette: A color palette to be used for plotting the quantile lines; defaults to quantile_pal.
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 TRUE.

Author

Thibaut Jombart thibautjombart@gmail.com

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)

}
#> Loading required package: outbreaks
#> Loading required package: magrittr
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the incidence package.
#>   Please report the issue at <https://github.com/reconhub/incidence/issues>.
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.