incidence (version 1.5.0)

incidence: Compute incidence of events from a vector of dates.

Description

This function computes incidence based on dates of events provided in various formats. A fixed interval, provided as numbers of days, is used to define time intervals. Counts within an interval always include the first date, after which they are labeled, and exclude the second. For instance, intervals labeled as 0, 3, 6, ... mean that the first bin includes days 0, 1 and 2, the second interval includes 3, 4 and 5 etc.

Usage

incidence(dates, interval = 1L, ...)
# S3 method for default
incidence(dates, interval = 1L, ...)
# S3 method for Date
incidence(dates, interval = 1L, standard = TRUE,
  groups = NULL, na_as_group = TRUE, first_date = NULL,
  last_date = NULL, ...)
# S3 method for integer
incidence(dates, interval = 1L, groups = NULL,
  na_as_group = TRUE, first_date = NULL, last_date = NULL, ...)
# S3 method for numeric
incidence(dates, interval = 1L, groups = NULL,
  na_as_group = TRUE, first_date = NULL, last_date = NULL, ...)
# S3 method for POSIXt
incidence(dates, interval = 1L, standard = TRUE,
  groups = NULL, na_as_group = TRUE, first_date = NULL,
  last_date = NULL, ...)
# S3 method for incidence
print(x, ...)

Arguments

dates

A vector of dates, which can be provided as objects of the class: integer, numeric, Date, POSIXct. Note that decimal numbers will be floored with a warning.

interval

An integer or character indicating the (fixed) size of the time interval used for computing the incidence; defaults to 1 day. This can also be a text string that corresponds to a valid date interval: day, week, month, quarter, or year. See Note.

...

Additional arguments passed to other methods (none are used).

standard

(Only applicable to Date objects) When TRUE (default) and the interval one of "week", "month", "quarter", or "year", then this will cause the bins for the counts to start at the beginning of the interval (See Note). This is overridden by defining a non-NULL first_date.

groups

An optional factor defining groups of observations for which incidence should be computed separately.

na_as_group

A logical value indicating if missing group (NA) should be treated as a separate group.

first_date, last_date

optional first/last dates to be used in the epicurve. When these are NULL (default), the dates from the first/last dates are taken from the observations. If these dates are provided, the observations will be trimmed to the range of [first_date, last_date].

x

An 'incidence' object.

Value

An list with the class incidence, which contains the following items:

• dates: The dates marking the left side of the bins used for counting events. When ISO week-based weekly incidence is computed, the dates are the first days of corresponding isoweeks.

• counts: A matrix of incidence counts, which one column per group (and a single column if no groups were used).

• timespan: The length of the period for which incidence is computed, in days.

• interval: The bin size, in number of days; e.g. 7 indicates weekly incidence.

• n: The total number of cases.

• isoweeks: ISO 8601 week format yyyy-Www, which is returned only when ISO week-based weekly incidence is computed.

Details

For details about the incidence class, see the dedicated vignette: vignette("incidence_class", package = "incidence")

See Also

The main other functions of the package include:

• incidence::plot.incidence(): Plot epicurves from an incidence object.

• incidence::fit(): Fit log-linear model to computed incidence.

• incidence::fit_optim_split(): Find the optimal peak of the epidemic and fits log-linear models on either side of the peak.

• incidence::subset(): Handling of incidence objects.

• incidence::pool(): Sum incidence over groups.

• incidence::as.data.frame.incidence(): Convert an incidence object to a data.frame.

The following vignettes are also available:

• overview: Provides an overview of the package's features.

• customize_plot: Provides some tips on finer plot customization.

• incidence_class: Details the content of the incidence class.

Examples

# NOT RUN {
## toy example
incidence(c(1, 5, 8, 3, 7, 2, 4, 6, 9, 2))
incidence(c(1, 5, 8, 3, 7, 2, 4, 6, 9, 2), 2)

## example using simulated dataset
if(require(outbreaks)) { withAutoprint({
  onset <- ebola_sim$linelist$date_of_onset

  ## daily incidence
  inc <- incidence(onset)
  inc
  plot(inc)

  ## weekly incidence
  inc.week <- incidence(onset, interval = 7, standard = FALSE)
  inc.week
  plot(inc.week)
  plot(inc.week, border = "white") # with visible border
  inc.isoweek <- incidence(onset, interval = 7, standard = TRUE)
  inc.isoweek
  ## use group information
  sex <- ebola_sim$linelist$gender
  inc.week.gender <- incidence(onset, interval = 7,
                               groups = sex, standard = FALSE)
  inc.week.gender
  head(inc.week.gender$counts)
  plot(inc.week.gender)
  inc.isoweek.gender <- incidence(onset, interval = 7,
                                  groups = sex, standard = TRUE)
  inc.isoweek.gender
})}


# }