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).
# S3 method for 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 )
x  A 

ylab  An optional label for the yaxis. 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 
project
to generate projections
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) }#>#>#>#>#>#>#>#>#>#>#>#>