reconhub/incidence: incidence version 1.5.0

This release of incidence contains a couple of bug fixes, new accessor functions for incidence elements, and a new plotting parameter that highlights individual cases for small epicurves. Below are a couple of highlights:

Individual cases in epicurves

You can now use the option show_cases = TRUE to show individual cases on the epicurve:

library("incidence")
library("outbreaks") 
require("ggplot2")

onset <- ebola_sim$linelist$date_of_onset
sex <- ebola_sim$linelist$gender
inc.week.gender <- incidence(onset, interval = 7, groups = sex)

## show individual cases at the beginning of the epidemic
inc.week.8 <- subset(inc.week.gender, to = "2014-06-01")

plot(inc.week.8, show_cases = TRUE, border = "black")

Accessing and fixing group names

If you use a grouping factor that contains mistakes (i.e. a typo in a location column), you can correct those mistakes by using group_names():

library("incidence")
set.seed(2018-11-01)
dat <- rpois(200, 10)
grp <- sample(c("Shire", "Mordor", "Isengard", "Eisengard"), 
              200,
              replace = TRUE,
              prob = c(1, 1, 1, 0.05))
i   <- incidence(dat, group = grp)
plot(i, show_cases = TRUE)

Clearly "Eisengard" is supposed to be "Isengard" in this case. To correct it, we just have to correct the group names and re-assign them:

# fix Eisengard to Isengard
print(gnames <- group_names(i))
#> [1] "Eisengard" "Isengard"  "Mordor"    "Shire"
gnames[gnames == "Eisengard"] <- "Isengard"
print(gnames)
#> [1] "Isengard" "Isengard" "Mordor"   "Shire"
i.fix <- group_names(i, gnames)
plot(i.fix, show_cases = TRUE)

^{Created on 2018-11-01 by the [reprex package](https://reprex.tidyverse.org) (v0.2.1)}

Full Changeset for incidence 1.5.0 NEW FUNCTIONS

• group_names() allows the user to retrieve and set the group names.
• get_timespan() returns the $timespan element.
• get_n() returns the $n element.
• dim(), nrow(), and ncol() are now available for incidence objects, returning the dimensions of the number of bins and the number of groups.

NEW FEATURES

• A new argument to plot() called show_cases has been added to draw borders around individual cases for EPIET-style curves. See https://github.com/reconhub/incidence/pull/72 for details.

DOCUMENTATION UPDATES

• An example of EPIET-style bars for small data sets has been added to the plot customisation vignette by @jakobschumacher. See https://github.com/reconhub/incidence/pull/68 for details.
• The incidence class vignette has been updated to use the available accessors.

BUG FIX

• estimate_peak() no longer fails with integer dates
• incidence() no longer fails when providing both group information and a first_date or last_date parameter that is inside the bounds of the observed dates. Thanks to @mfaber for reporting this bug. See https://github.com/reconhub/incidence/issues/70 for details.

MISC

• code has been spread out into a more logical file structure where the internal_checks.R file has been split into the relative components.
• A message is now printed if missing observations are present when creating the incidence object.