plot.incidence.Rd
This function is used to visualise the output of the incidence()
function using the package ggplot2
. #'
# S3 method for 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 incidence_fit plot(x, ...) # S3 method for 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 sidebyside. 
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 xaxis; empty by default. 
ylab  The label to be used for the yaxis; 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 YYYYWww 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labels_iso  (deprecated) This has been superceded by 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 xaxis labeling 
p  An existing incidence plot. 
plot()
a ggplot2::ggplot()
object.
make_breaks()
a twoelement list. The "breaks" element will contain the
evenlyspaced 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.
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.
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 = "20140601") 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("2014W50", "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)$fit plot(inc.week.gender, fit = fit) plot(inc.week.gender, fit = fit, labels_week = FALSE) })}#> > onset < outbreaks::ebola_sim$linelist$date_of_onset #> > inc < incidence(onset) #> > inc #> <incidence object> #> [5888 cases from days 20140407 to 20150430] #> #> $counts: matrix with 389 rows and 1 columns #> $n: 5888 cases in total #> $dates: 389 dates marking the leftside of bins #> $interval: 1 day #> $timespan: 389 days #> $cumulative: FALSE #> #> > plot(inc)#> > inc.week < incidence(onset, interval = 7) #> > inc.week #> <incidence object> #> [5888 cases from days 20140407 to 20150427] #> [5888 cases from ISO weeks 2014W15 to 2015W18] #> #> $counts: matrix with 56 rows and 1 columns #> $n: 5888 cases in total #> $dates: 56 dates marking the leftside of bins #> $interval: 7 days #> $timespan: 386 days #> $cumulative: FALSE #> #> > plot(inc.week)#> > plot(inc.week, labels_week = FALSE)#> > plot(inc.week, border = "white")#> > sex < outbreaks::ebola_sim$linelist$gender #> > inc.week.gender < incidence(onset, interval = "1 epiweek", groups = sex) #> > plot(inc.week.gender)#> > plot(inc.week.gender, labels_week = FALSE)#> > inc.week.8 < subset(inc.week.gender, to = "20140601") #> > p < plot(inc.week.8, show_cases = TRUE, border = "black") #> > p#> > lim < c(min(get_dates(inc.week.8))  7 * 5, aweek::week2date("2014W50", #> + "Sunday")) #> > lim #> [1] "20140302" "20141207" #> > p + scale_x_incidence(inc.week.gender, limits = lim)#>#>#> > plot(inc.week.8, show_cases = TRUE, border = "black") + theme_classic(base_size = 16) + #> + theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))#> > fit < fit_optim_split(inc.week.gender)$fit #> > plot(inc.week.gender, fit = fit)#>#>#>#>#>#>#>#>#> > plot(inc.week.gender, fit = fit, labels_week = FALSE)#>#>#>#>#>#>#>#>