incidence: Compute the incidence of events
In incidence2: Compute, Handle and Plot Incidence of Dated Events

incidence

R Documentation

Compute the incidence of events

Description

incidence() calculates the incidence of different events across specified time periods and groupings.

Usage

incidence(
  x,
  date_index,
  groups = NULL,
  counts = NULL,
  count_names_to = "count_variable",
  count_values_to = "count",
  date_names_to = "date_index",
  rm_na_dates = TRUE,
  interval = NULL,
  offset = NULL,
  complete_dates = FALSE,
  fill = 0L,
  ...
)

Arguments

`x`	A data frame object representing a linelist or pre-aggregated dataset.
`date_index`	`character`. The time index(es) of the given data. This should be the name(s) corresponding to the desired date column(s) in x. A named vector can be used for convenient relabelling of the resultant output. Multiple indices only make sense when `x` is a linelist.
`groups`	`character`. An optional vector giving the names of the groups of observations for which incidence should be grouped. A named vector can be used for convenient relabelling of the resultant output.
`counts`	`character`. The count variables of the given data. If NULL (default) the data is taken to be a linelist of individual observations. A named vector can be used for convenient relabelling of the resultant output.
`count_names_to`	`character`. The column to create which will store the `counts` column names provided that `counts` is not NULL.
`count_values_to`	`character`. The name of the column to store the resultant count values in.
`date_names_to`	`character`. The name of the column to store the date variables in.
`rm_na_dates`	`bool`. Should `NA` dates be removed prior to aggregation?
`interval`	An optional scalar integer or string indicating the (fixed) size of the desired time interval you wish to use for for computing the incidence. Defaults to NULL in which case the date_index columns are left unchanged. Numeric values are coerced to integer and treated as a number of days to group. Text strings can be one of: * day or daily * week(s) or weekly * epiweek(s) * isoweek(s) * month(s) or monthly * yearmonth(s) * quarter(s) or quarterly * yearquarter(s) * year(s) or yearly More details can be found in the "Interval specification" section.
`offset`	Only applicable when `interval` is not NULL. An optional scalar integer or date indicating the value you wish to start counting periods from relative to the Unix Epoch: Default value of NULL corresponds to 0L. For other integer values this is stored scaled by `n` (`offset <- as.integer(offset) %% n`). For date values this is first converted to an integer offset (`offset <- floor(as.numeric(offset))`) and then scaled via `n` as above.
`complete_dates`	`bool`. Should the resulting object have the same range of dates for each grouping. Missing counts will be filled with `0L` unless the `fill` argument is provided (and this value will take precedence). Will attempt to use `function(x) seq(min(x), max(x), by = 1)` on the resultant date_index column to generate a complete sequence of dates. More flexible completion is possible by using the `complete_dates()` function.
`fill`	`numeric`. Only applicable when `complete_dates = TRUE`. The value to replace missing counts caused by completing dates. If unset then will default to `0L`.
`...`	Not currently used.

Details

incidence2 objects are a sub class of data frame with some additional invariants. That is, an incidence2 object must:

have one column representing the date index (this does not need to be a date object but must have an inherent ordering over time);
have one column representing the count variable (i.e. what is being counted) and one variable representing the associated count;
have zero or more columns representing groups;
not have duplicated rows with regards to the date and group variables.

Value

A tibble with subclass incidence2.

Interval specification

Where interval is specified, incidence(), predominantly uses the grates package to generate appropriate date groupings. The grouping used depends on the value of interval. This can be specified as either an integer value or a string corresponding to one of the classes:

integer values: <grates_period> object, grouped by the specified number of days.
day, daily: <Date> objects.
week(s), weekly, isoweek: <grates_isoweek> objects.
epiweek(s): <grates_epiweek> objects.
month(s), monthly, yearmonth: <grates_yearmonth> objects.
quarter(s), quarterly, yearquarter: <grates_yearquarter> objects.
year(s) and yearly: <grates_year> objects.

For "day" or "daily" interval, we provide a thin wrapper around as.Date() that ensures the underlying data are whole numbers and that time zones are respected. Note that additional arguments are not forwarded to as.Date() so for greater flexibility users are advised to modifying your input prior to calling incidence().

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist
    incidence(dat, "date_of_onset")
    incidence(dat, "date_of_onset", groups = c("gender", "hospital"))
}

incidence2 documentation built on Oct. 7, 2024, 1:07 a.m.