incidence2 (version 0.2.2)

incidence: Compute the incidence of events

Description

Compute the incidence of events

Usage

incidence(
  x,
  date_index,
  groups = NULL,
  interval = 1L,
  first_date = NULL,
  last_date = NULL,
  na_as_group = TRUE,
  standard = TRUE,
  count = NULL
)

Arguments

x

A tibble or a data frame (see Note) representing a linelist.

date_index

The time index of the given data. This should be the name, with or without quotation, corresponding to a date column in x of the class: integer, numeric, Date, POSIXct, POSIXlt, and character. (See Note about numeric and character formats)

groups

An optional vector giving the names of the groups of observations for which incidence should be grouped. This can be given with or without quotation.`

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).

first_date, last_date

optional first/last dates to be used. 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].

na_as_group

A logical value indicating if missing group values (NA) should treated as a separate category (TRUE) or removed from consideration (FALSE).

standard

(Only applicable where date_index references a Date object) 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).

count

The count variable of the given data. If NULL (default) the data is taken to be a linelist of individual observations.

Value

An incidence2 object. This is a subclass of tibble that represents and aggregated count of observations grouped according to the specified interval and, optionally, the given groups. By default it will contain the following columns:

• bin_date: The dates marking the left side of the bins used for counting events. When standard = TRUE and the interval represents weeks, months, quarters, or years, the first date will represent the first standard date (See Interval specification, below).

• -groups-: If specified, column(s) containing the categories of the given groups.

• count: The aggregated observation count.

If a "week" interval is specified then the object may also contain additional columns:

• weeks: Dates in week format (YYYY-Www), where YYYY corresponds to the year of the given week and ww represents the numeric week of the year. This will be a produced from the function aweek::date2week(). Note that these will have a special "week_start" attribute indicating which day of the ISO week the week starts on (see Weeks, below).

Examples

# NOT RUN {
if (requireNamespace("outbreaks", quietly = TRUE)) {
  withAutoprint({
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist


    # daily incidence
    dat %>%
      incidence(date_of_onset)

    # weekly incidence
    dat %>%
      incidence(date_of_onset, interval = "week", standard = FALSE)

    # starting on a Monday
    dat %>%
      incidence(date_of_onset, interval = "isoweek")

    # starting on a Sunday
    dat %>%
      incidence(date_of_onset, interval = "epiweek")

    # starting on a Saturday
    dat %>%
      incidence(date_of_onset, interval = "saturday epiweek")

    # group by gender
    dat %>%
      incidence(date_of_onset, interval = 7, groups = gender)

    # group by gender and hospital
    dat %>%
      incidence(date_of_onset,
                interval = "2 weeks",
                groups = c(gender, hospital))
  })
}

# use of first_date
dat <- data.frame(dates = Sys.Date() + sample(-3:10, 10, replace = TRUE))
dat %>% incidence(dates,
                  interval = "week",
                  first_date = Sys.Date() + 1)
# }