# incidence: Compute incidence of events from a vector of dates. In incidence: Compute, Handle, Plot and Model Incidence of Dated Events

## 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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25``` ```incidence(dates, interval = 1L, ...) ## Default S3 method: incidence(dates, interval = 1L, ...) ## S3 method for class 'Date' incidence(dates, interval = 1L, standard = TRUE, groups = NULL, na_as_group = TRUE, first_date = NULL, last_date = NULL, ...) ## S3 method for class 'integer' incidence(dates, interval = 1L, groups = NULL, na_as_group = TRUE, first_date = NULL, last_date = NULL, ...) ## S3 method for class 'numeric' incidence(dates, interval = 1L, groups = NULL, na_as_group = TRUE, first_date = NULL, last_date = NULL, ...) ## S3 method for class 'POSIXt' incidence(dates, interval = 1L, standard = TRUE, groups = NULL, na_as_group = TRUE, first_date = NULL, last_date = NULL, ...) ## S3 method for class '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.

## Details

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

## 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.

## Note

If `interval` is a valid character (e.g. "week" or "month"), then the bin will start at the beginning of the interval just before the first observation by default. For example, if the first case was recorded on Wednesday, 2018-05-09:

• "week" : first day of the ISOweek (i.e. Monday, 2018-05-07)

• "month" : first day of the month (i.e. 2018-05-01)

• "quarter" : first day of the quarter (i.e. 2018-04-01)

• "year" : first day of the calendar year (i.e. 2018-01-01)

These default intervals can be overridden in two ways:

1. Specify `standard = FALSE`, which sets the interval to begin at the first observed case.

2. Specify a date in the `first_date` field.

The intervals for "month", "quarter", and "year" will necessarily vary in the number of days they encompass and warnings will be generated when the first date falls outside of a calendar date that is easily represented across the interval.

## Author(s)

Thibaut Jombart, Rich Fitzjohn, Zhian Kamvar

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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31``` ```## 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 })} ```

incidence documentation built on Aug. 25, 2018, 1:03 a.m.