Plot function for incidence objects
This function is used to visualise the output of the incidence()
function using the package ggplot2. #'
## S3 method for class 'incidence' plot( x, ..., fit = NULL, stack = is.null(fit), color = "black", border = NA, col_pal = incidence_pal1, alpha = 0.7, xlab = "", ylab = NULL, labels_week = !is.null(x$weeks), labels_iso = !is.null(x$isoweeks), show_cases = FALSE, n_breaks = 6 ) add_incidence_fit(p, x, col_pal = incidence_pal1) ## S3 method for class 'incidence_fit' plot(x, ...) ## S3 method for class 'incidence_fit_list' plot(x, ...) scale_x_incidence(x, n_breaks = 6, labels_week = TRUE, ...) make_breaks(x, n_breaks = 6L, labels_week = TRUE)
x |
An incidence object, generated by the function
|
... |
arguments passed to |
fit |
An 'incidence_fit' object as returned by |
stack |
A logical indicating if bars of multiple groups should be stacked, or displayed side-by-side. |
color |
The color to be used for the filling of the bars; NA for invisible bars; defaults to "black". |
border |
The color to be used for the borders of the bars; NA for invisible borders; defaults to NA. |
col_pal |
The color palette to be used for the groups; defaults to
|
alpha |
The alpha level for color transparency, with 1 being fully opaque and 0 fully transparent; defaults to 0.7. |
xlab |
The label to be used for the x-axis; empty by default. |
ylab |
The label to be used for the y-axis; by default, a label will be generated automatically according to the time interval used in incidence computation. |
labels_week |
a logical value indicating whether labels x axis tick marks are in week format YYYY-Www when plotting weekly incidence; defaults to TRUE. |
labels_iso |
(deprecated) This has been superceded by |
show_cases |
if |
n_breaks |
the ideal number of breaks to be used for the x-axis labeling |
p |
An existing incidence plot. |
plot() will visualise an incidence object using ggplot2
make_breaks() calculates breaks from an incidence object that always
align with the bins and start on the first observed incidence.
scale_x_incidence() produces and appropriate ggplot2 scale based on
an incidence object.
plot() a ggplot2::ggplot() object.
make_breaks() a two-element list. The "breaks" element will contain the
evenly-spaced breaks as either dates or numbers and the "labels" element
will contain either a vector of weeks OR a ggplot2::waiver() object.
scale_x_incidence() a ggplot2 "ScaleContinuous" object.
Thibaut Jombart thibautjombart@gmail.com Zhian N. Kamvar zkamvar@gmail.com
The incidence() function to generate the 'incidence'
objects.
if(require(outbreaks) && require(ggplot2)) { withAutoprint({
onset <- outbreaks::ebola_sim$linelist$date_of_onset
## daily incidence
inc <- incidence(onset)
inc
plot(inc)
## weekly incidence
inc.week <- incidence(onset, interval = 7)
inc.week
plot(inc.week) # default to label x axis tick marks with isoweeks
plot(inc.week, labels_week = FALSE) # label x axis tick marks with dates
plot(inc.week, border = "white") # with visible border
## use group information
sex <- outbreaks::ebola_sim$linelist$gender
inc.week.gender <- incidence(onset, interval = "1 epiweek", groups = sex)
plot(inc.week.gender)
plot(inc.week.gender, labels_week = FALSE)
## show individual cases at the beginning of the epidemic
inc.week.8 <- subset(inc.week.gender, to = "2014-06-01")
p <- plot(inc.week.8, show_cases = TRUE, border = "black")
p
## update the range of the scale
lim <- c(min(get_dates(inc.week.8)) - 7*5,
aweek::week2date("2014-W50", "Sunday"))
lim
p + scale_x_incidence(inc.week.gender, limits = lim)
## customize plot with ggplot2
plot(inc.week.8, show_cases = TRUE, border = "black") +
theme_classic(base_size = 16) +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))
## adding fit
fit <- fit_optim_split(inc.week.gender)$fit
plot(inc.week.gender, fit = fit)
plot(inc.week.gender, fit = fit, labels_week = FALSE)
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