Package 'incidence2' reference manual

Title:	Compute, Handle and Plot Incidence of Dated Events
Description:	Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis (<https://www.reconverse.org>).
Authors:	Tim Taylor [aut, cre] , Thibaut Jombart [ctb]
Maintainer:	Tim Taylor <[email protected]>
License:	MIT + file LICENSE
Version:	2.4.0.9000
Built:	2024-09-20 05:57:28 UTC
Source:	https://github.com/reconverse/incidence2

Access various elements of an incidence object

Description

Access various elements of an incidence object

Usage

get_date_index_name(x, ...)

## Default S3 method:
get_date_index_name(x, ...)

## S3 method for class 'incidence2'
get_date_index_name(x, ...)

get_dates_name(x, ...)

get_count_variable_name(x, ...)

## Default S3 method:
get_count_variable_name(x, ...)

## S3 method for class 'incidence2'
get_count_variable_name(x, ...)

get_count_value_name(x, ...)

## Default S3 method:
get_count_value_name(x, ...)

## S3 method for class 'incidence2'
get_count_value_name(x, ...)

get_group_names(x, ...)

## Default S3 method:
get_group_names(x, ...)

## S3 method for class 'incidence2'
get_group_names(x, ...)

get_date_index(x, ...)

## Default S3 method:
get_date_index(x, ...)

## S3 method for class 'incidence2'
get_date_index(x, ...)

get_dates(x, ...)

get_count_variable(x, ...)

## Default S3 method:
get_count_variable(x, ...)

## S3 method for class 'incidence2'
get_count_variable(x, ...)

get_count_value(x, ...)

## Default S3 method:
get_count_value(x, ...)

## S3 method for class 'incidence2'
get_count_value(x, ...)

get_groups(x, ...)

## Default S3 method:
get_groups(x, ...)

## S3 method for class 'incidence2'
get_groups(x, ...)
get_date_index_name(x, ...)

## Default S3 method:
get_date_index_name(x, ...)

## S3 method for class 'incidence2'
get_date_index_name(x, ...)

get_dates_name(x, ...)

get_count_variable_name(x, ...)

## Default S3 method:
get_count_variable_name(x, ...)

## S3 method for class 'incidence2'
get_count_variable_name(x, ...)

get_count_value_name(x, ...)

## Default S3 method:
get_count_value_name(x, ...)

## S3 method for class 'incidence2'
get_count_value_name(x, ...)

get_group_names(x, ...)

## Default S3 method:
get_group_names(x, ...)

## S3 method for class 'incidence2'
get_group_names(x, ...)

get_date_index(x, ...)

## Default S3 method:
get_date_index(x, ...)

## S3 method for class 'incidence2'
get_date_index(x, ...)

get_dates(x, ...)

get_count_variable(x, ...)

## Default S3 method:
get_count_variable(x, ...)

## S3 method for class 'incidence2'
get_count_variable(x, ...)

get_count_value(x, ...)

## Default S3 method:
get_count_value(x, ...)

## S3 method for class 'incidence2'
get_count_value(x, ...)

get_groups(x, ...)

## Default S3 method:
get_groups(x, ...)

## S3 method for class 'incidence2'
get_groups(x, ...)

Arguments

`x`	An R object.
`...`	Not currently used.

Value

get_date_index_name(): The name of the date_index variable of x.
get_dates_name(): Alias for get_date_index_name().
get_count_variable_name(): The name of the count variable of x.
get_count_value_name(): The name of the count value of x.
get_group_names(): The name(s) of the group variable(s) of x.
get_date_index(): The date_index variable of x.
get_dates(): Alias for get_date_index().
get_count_variable(): The count variable of x.
get_count_value(): The count value of x.
get_groups(): List of the group variable(s) of x.

Examples


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


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

Coerce to a tibble

Description

Coerce to a tibble

Usage

## S3 method for class 'incidence2'
as_tibble(x, ..., .rows, .name_repair, rownames)
## S3 method for class 'incidence2'
as_tibble(x, ..., .rows, .name_repair, rownames)

Arguments

`x`	An incidence2 object.
`...`	Unused, for extensibility.
`.rows`	The number of rows, useful to create a 0-column tibble or just as an additional check.
`.name_repair`	Treatment of problematic column names: `"minimal"`: No name repair or checks, beyond basic existence, `"unique"`: Make sure names are unique and not empty, `"check_unique"`: (default value), no name repair, but check they are `unique`, `"universal"`: Make the names `unique` and syntactic a function: apply custom name repair (e.g., `.name_repair = make.names` for names in the style of base R). A purrr-style anonymous function, see `rlang::as_function()` This argument is passed on as `repair` to `vctrs::vec_as_names()`. See there for more details on these terms and the strategies used to enforce them.
`rownames`	How to treat existing row names of a data frame or matrix: `NULL`: remove row names. This is the default. `NA`: keep row names. A string: the name of a new column. Existing rownames are transferred into this column and the `row.names` attribute is deleted. No name repair is applied to the new column name, even if `x` already contains a column of that name. Use `as_tibble(rownames_to_column(...))` to safeguard against this case. Read more in rownames.

Value

A tibble of the original input but with no additional attributes.

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist
    x <- incidence(dat, "date_of_onset")
    as_tibble(x)
}


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist
    x <- incidence(dat, "date_of_onset")
    as_tibble(x)
}

Convert incident object to a data frame

Description

Convert incident object to a data frame

Usage

## S3 method for class 'incidence2'
as.data.frame(x, row.names, optional, ...)
## S3 method for class 'incidence2'
as.data.frame(x, row.names, optional, ...)

Arguments

`x`	incidence2 object.
`row.names`	Not used.
`optional`	Not used.
`...`	Not used.

Examples


dat <- data.frame(
    dates = Sys.Date() + 1:100,
    names = rep(c("Jo", "John"), 5)
)

dat <- incidence(dat, date_index = "dates", groups = "names")
as.data.frame(dat)


dat <- data.frame(
    dates = Sys.Date() + 1:100,
    names = rep(c("Jo", "John"), 5)
)

dat <- incidence(dat, date_index = "dates", groups = "names")
as.data.frame(dat)

Coerce to a data.table

Description

Coerce to a data.table

Usage

## S3 method for class 'incidence2'
as.data.table(x, keep.rownames, ...)
## S3 method for class 'incidence2'
as.data.table(x, keep.rownames, ...)

Arguments

`x`	An incidence2 object.
`keep.rownames`	Not used.
`...`	Passed to other methods.

Value

A data.table of the original input but with no additional attributes.

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist
    x <- incidence(dat, "date_of_onset")
    as.data.table(x)
}


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist
    x <- incidence(dat, "date_of_onset")
    as.data.table(x)
}

Bootstrap incidence time series

Description

This function can be used to bootstrap incidence2 objects. Bootstrapping is done by sampling with replacement the original input dates.

Usage

bootstrap_incidence(x, randomise_groups = FALSE)
bootstrap_incidence(x, randomise_groups = FALSE)

Arguments

x

An incidence2 object.

randomise_groups

bool.

Should groups be randomised as well in the resampling procedure; respective group sizes will be preserved, but this can be used to remove any group-specific temporal dynamics.

If FALSE (default), data are resampled within groups.

Details

As original data are not stored in incidence2 objects, the bootstrapping is achieved by multinomial sampling of date bins weighted by their relative incidence.

Value

An incidence2 object.

Author(s)

Thibaut Jombart, Tim Taylor

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(fluH7N9_china_2013, package = "outbreaks")
    i <- incidence(
        fluH7N9_china_2013,
        date_index = "date_of_onset",
        groups = "gender"
   )
   bootstrap_incidence(i)
}


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(fluH7N9_china_2013, package = "outbreaks")
    i <- incidence(
        fluH7N9_china_2013,
        date_index = "date_of_onset",
        groups = "gender"
   )
   bootstrap_incidence(i)
}

Complete dates for all group combinations

Description

This function ensures that an incidence object has the same range of dates for each grouping. By default missing counts will be filled with 0L.

Usage

complete_dates(x, expand = TRUE, fill = 0L, by = 1L, allow_POSIXct = FALSE)
complete_dates(x, expand = TRUE, fill = 0L, by = 1L, allow_POSIXct = FALSE)

Arguments

`x`	`⁠<incidence2>⁠` object.
`expand`	`logical`. Should a range of dates from the minimum to maximum value of the date index also be created. If `expand` is TRUE (default) then complete_dates will attempt to use `function(x) seq(min(x), max(x), by = 1)` to generate a complete sequence of dates.
`fill`	`numeric`. The value to replace missing counts by. Defaults to `0L`.
`by`	`Defunct`. Ignored.
`allow_POSIXct`	`logical`. Should this function work with POSIXct dates? Defaults to `FALSE`.

Value

An incidence2 object.

Examples


x <- data.frame(
    dates = Sys.Date() + c(1,3,4),
    groups = c("grp1","grp2", "grp1"),
    counts = 1:3
)

i <- incidence(x, date_index = "dates", groups = "groups", counts = "counts")
complete_dates(i)


x <- data.frame(
    dates = Sys.Date() + c(1,3,4),
    groups = c("grp1","grp2", "grp1"),
    counts = 1:3
)

i <- incidence(x, date_index = "dates", groups = "groups", counts = "counts")
complete_dates(i)

Regional data for COVID-19 cases in the UK

Description

A dataset containing the daily time-series of cases, tests, hospitalisations, and deaths for UK.

Usage

covidregionaldataUK
covidregionaldataUK

Format

A data frame with 6370 rows and 26 variables:

date: the date that the counts were reported (YYYY-MM-DD)
region: the region name
region_code: the region code
cases_new: new reported cases for that day
cases_total: total reported cases up to and including that day
deaths_new: new reported deaths for that day
deaths_total: total reported deaths up to and including that day
recovered_new: new reported recoveries for that day
recovered_total: total reported coveries up to and including that day
hosp_new: new reported hospitalisations for that day
hosp_total: total reported hospitalisations up to and including that day (note this is cumulative total of new reported, not total currently in hospital).
tested_new: tests for that day
tested_total: total tests completed up to and including that day

Details

Extracted using the covidregionaldata package on 2021-06-03.

Source

https://CRAN.R-project.org/package=covidregionaldata

Compute cumulative 'incidence'

Description

cumulate() computes the cumulative incidence over time for an incidence2 object.

Usage

cumulate(x)
cumulate(x)

Arguments

`x`	incidence2 object.

Examples


dat <- data.frame(
  dates = as.integer(c(0,1,2,2,3,5,7)),
  groups = factor(c(1, 2, 3, 3, 3, 3, 1))
)

i <- incidence(dat, date_index = "dates", groups = "groups")
cumulate(i)


dat <- data.frame(
  dates = as.integer(c(0,1,2,2,3,5,7)),
  groups = factor(c(1, 2, 3, 3, 3, 3, 1))
)

i <- incidence(dat, date_index = "dates", groups = "groups")
cumulate(i)

Estimate the peak date of an incidence curve

Description

This function can be used to estimate the peak of an epidemic curve using bootstrapped samples of the available data.

Usage

estimate_peak(x, n = 100L, alpha = 0.05, first_only = TRUE, progress = TRUE)
estimate_peak(x, n = 100L, alpha = 0.05, first_only = TRUE, progress = TRUE)

Arguments

`x`	An incidence2 object.
`n`	`integer`. The number of bootstrap datasets to be generated; defaults to 100. `⁠[double]⁠` vectors will be converted via `as.integer(n)`.
`alpha`	`numeric`. The type 1 error chosen for the confidence interval; defaults to 0.05.
`first_only`	`bool`. Should only the first peak (by date) be kept. Defaults to `TRUE`.
`progress`	`bool`. Should a progress bar be displayed (default = TRUE)

Details

Input dates are resampled with replacement to form bootstrapped datasets; the peak is reported for each, resulting in a distribution of peak times. When there are ties for peak incidence, only the first date is reported.

Note that the bootstrapping approach used for estimating the peak time makes the following assumptions:

the total number of event is known (no uncertainty on total incidence)
dates with no events (zero incidence) will never be in bootstrapped datasets
the reporting is assumed to be constant over time, i.e. every case is equally likely to be reported

Value

A data frame with the the following columns:

observed_date: the date of peak incidence of the original dataset.
observed_count: the peak incidence of the original dataset.
estimated: the median peak time of the bootstrap datasets.
lower_ci/upper_ci: the confidence interval based on bootstrap datasets.
bootstrap_peaks: a nested tibble containing the the peak times of the bootstrapped datasets.

Author(s)

Thibaut Jombart and Tim Taylor, with inputs on caveats from Michael Höhle.

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {

  # load data and create incidence
  data(fluH7N9_china_2013, package = "outbreaks")
  i <- incidence(fluH7N9_china_2013, date_index = "date_of_onset")

  # find 95% CI for peak time using bootstrap
  estimate_peak(i)
}


if (requireNamespace("outbreaks", quietly = TRUE)) {

  # load data and create incidence
  data(fluH7N9_china_2013, package = "outbreaks")
  i <- incidence(fluH7N9_china_2013, date_index = "date_of_onset")

  # find 95% CI for peak time using bootstrap
  estimate_peak(i)
}

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,
  ...
)
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"))
}


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"))
}

Compute the incidence of events (tidyselect compatible)

Description

incidence_() calculates the incidence of different events across specified time periods and groupings. It differs from incidence() only in its support for tidy-select semantics in some of its arguments.

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,
  ...
)
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,
  ...
)

Arguments

`x`	A data frame object representing a linelist or pre-aggregated dataset.
`date_index`	tidyselect. 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`	tidyselect. 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`	tidyselect. 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`. 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()`
`...`	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.

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))
}


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))
}

Keep first, last and peak occurences

Description

keep_first() and keep_last() keep the first and last n rows to occur for each grouping when in ascending date order. keep_peaks() keeps the rows with the maximum count value for each group. first_peak() is a convenience wrapper around keep_peaks() with the first_only argument set to TRUE.

Usage

keep_first(x, n, complete_dates = TRUE, ...)

keep_last(x, n, complete_dates = TRUE, ...)

keep_peaks(x, complete_dates = TRUE, first_only = FALSE, ...)

first_peak(x, complete_dates = TRUE, ...)
keep_first(x, n, complete_dates = TRUE, ...)

keep_last(x, n, complete_dates = TRUE, ...)

keep_peaks(x, complete_dates = TRUE, first_only = FALSE, ...)

first_peak(x, complete_dates = TRUE, ...)

Arguments

`x`	incidence2 object.
`n`	`integer`. Number of entries to keep. `double` vectors will be converted via `as.integer(n)`.
`complete_dates`	`bool`. Should `complete_dates()` be called on the data prior to keeping the first entries. Defaults to TRUE.
`...`	Other arguments passed to `complete_dates()`.
`first_only`	`bool`. Should only the first peak (by date) be kept. Defaults to `TRUE`.

Value

incidence2 object with the chosen entries.

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist
    inci <- incidence(dat, "date_of_onset")
    keep_first(inci, 3)
    keep_last(inci, 3)
}


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist
    inci <- incidence(dat, "date_of_onset")
    keep_first(inci, 3)
    keep_last(inci, 3)
}

Create, modify, and delete incidence2 columns

Description

Method for dplyr::mutate that implicitly accounts for the inherent grouping structure of incidence2 objects.

Usage

## S3 method for class 'incidence2'
mutate(
  .data,
  ...,
  .by,
  .keep = c("all", "used", "unused", "none"),
  .before = NULL,
  .after = NULL
)
## S3 method for class 'incidence2'
mutate(
  .data,
  ...,
  .by,
  .keep = c("all", "used", "unused", "none"),
  .before = NULL,
  .after = NULL
)

Arguments

`.data`	An incidence2 object.
`...`	<`data-masking`> Name-value pairs. The name gives the name of the column in the output. The value can be: A vector of length 1, which will be recycled to the correct length. A vector the same length as the current group (or the whole data frame if ungrouped). `NULL`, to remove the column. A data frame or tibble, to create multiple columns in the output.
`.by`	Not used as grouping structure implicit.
`.keep`	Control which columns from `.data` are retained in the output. Grouping columns and columns created by `...` are always kept. `"all"` retains all columns from `.data`. This is the default. `"used"` retains only the columns used in `...` to create new columns. This is useful for checking your work, as it displays inputs and outputs side-by-side. `"unused"` retains only the columns not used in `...` to create new columns. This is useful if you generate new columns, but no longer need the columns used to generate them. `"none"` doesn't retain any extra columns from `.data`. Only the grouping variables and columns created by `...` are kept.
`.before`, `.after`	<`tidy-select`> Optionally, control where new columns should appear (the default is to add to the right hand side). See `relocate()` for more details.

Value

A modified incidence2 object if the necessary invariants are preserved, otherwise a tibble.

Examples


if (requireNamespace("outbreaks", quietly = TRUE) && requireNamespace("ggplot2", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    ebola_sim_clean$linelist |>
        subset(!is.na(hospital)) |>
        incidence_(date_of_onset, hospital, interval = "isoweek") |>
        mutate(ave = data.table::frollmean(count, n = 3L, align = "right")) |>
        plot(border_colour = "white", angle = 45) +
        ggplot2::geom_line(ggplot2::aes(x = date_index, y = ave))
}


if (requireNamespace("outbreaks", quietly = TRUE) && requireNamespace("ggplot2", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    ebola_sim_clean$linelist |>
        subset(!is.na(hospital)) |>
        incidence_(date_of_onset, hospital, interval = "isoweek") |>
        mutate(ave = data.table::frollmean(count, n = 3L, align = "right")) |>
        plot(border_colour = "white", angle = 45) +
        ggplot2::geom_line(ggplot2::aes(x = date_index, y = ave))
}

Nest rows into a list-column of data frames

Description

Method for tidyr::nest that implicitly accounts for the inherent grouping structure of incidence2 objects.

Usage

## S3 method for class 'incidence2'
nest(.data, ..., .by, .key, .names_sep)
## S3 method for class 'incidence2'
nest(.data, ..., .by, .key, .names_sep)

Arguments

`.data`	An incidence2 object.
`...`	Not used.
`.by`	Not used.
`.key`	The name of the resulting nested column. Only applicable when `...` isn't specified, i.e. in the case of `df %>% nest(.by = x)`. If `NULL`, then `"data"` will be used by default.
`.names_sep`	Not used.

Value

A nested tibble with rows corresponding to the count variable and (optionally) group columns of the input object.

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    ebola_sim_clean$linelist |>
        subset(!is.na(hospital)) |>
        incidence_(date_of_onset, hospital, interval = "isoweek") |>
        nest()
}


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    ebola_sim_clean$linelist |>
        subset(!is.na(hospital)) |>
        incidence_(date_of_onset, hospital, interval = "isoweek") |>
        nest()
}

Plot an incidence object

Description

plot() can be used to provide a bar plot of an incidence object. Due to the complexities with automating plotting it is some what experimental in nature and it may be better to use ggplot2 directly.

Usage

## S3 method for class 'incidence2'
plot(
  x,
  y,
  width = 1,
  colour_palette = vibrant,
  border_colour = NA,
  na_colour = "grey",
  alpha = 0.7,
  fill = NULL,
  legend = c("right", "left", "bottom", "top", "none"),
  title = NULL,
  angle = 0,
  size = NULL,
  nrow = NULL,
  n_breaks = 6L,
  show_cases = FALSE,
  ...
)
## S3 method for class 'incidence2'
plot(
  x,
  y,
  width = 1,
  colour_palette = vibrant,
  border_colour = NA,
  na_colour = "grey",
  alpha = 0.7,
  fill = NULL,
  legend = c("right", "left", "bottom", "top", "none"),
  title = NULL,
  angle = 0,
  size = NULL,
  nrow = NULL,
  n_breaks = 6L,
  show_cases = FALSE,
  ...
)

Arguments

`x`	incidence2 object.
`y`	Not used. Required for compatibility with the `plot()` generic.
`width`	`numeric`. Value between 0 and 1 indicating the relative size of the bars to the interval. Default 1.
`colour_palette`	`function`. The color palette to be used for the different count variables. Defaults to `vibrant` (see `?palettes`).
`border_colour`	`character`. The color to be used for the borders of the bars. Use `NA` (default) for invisible borders.
`na_colour`	`character`. The colour to plot `NA` values in graphs. Defaults to `grey`.
`alpha`	`numeric`. The alpha level for color transparency, with 1 being fully opaque and 0 fully transparent Defaults to 0.7.
`fill`	`character`. Which variable to colour plots by. Must be a `group` or `count` variable and will mean that variable is not used for facetting. If NULL no distinction if made for plot colours.
`legend`	`character`. Position of legend in plot. Only applied if `fill` is not NULL. One of "right" (default), "left", "bottom", "top" or "none".
`title`	`character`. Optional title for the graph.
`angle`	`numeric`. Rotation angle for text.
`size`	`numeric`. text size in pts.
`nrow`	`integer`. Number of rows used for facetting if there are group variables present and just one count in the incidence object. Numeric values are coerced to integer via `as.integer()`.
`n_breaks`	`integer`. Approximate number of breaks calculated using `scales::breaks_pretty()`. Numeric values are coerced to integer via `as.integer()`. Default 6L.
`show_cases`	`logical`. if `TRUE`, then each observation will be shown individually in a square format. Normally only used for outbreaks with a small number of cases. Defaults to `FALSE`.
`...`	Not currently used.

Details

Faceting will occur automatically if either grouping variables or multiple counts are present.
If there are multiple count variables, each count will occupy a different row of the resulting plot.
Utilises ggplot2 so this must be installed to use.

Value

A ggplot2::ggplot() object.

Examples


if (requireNamespace("outbreaks", quietly = TRUE) && requireNamespace("ggplot2", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist

    inci <- incidence(dat, date_index = "date_of_onset", groups = "hospital")
    plot(inci, angle = 45)

    inci2 <- regroup(inci)
    plot(inci2)
}


if (requireNamespace("outbreaks", quietly = TRUE) && requireNamespace("ggplot2", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    dat <- ebola_sim_clean$linelist

    inci <- incidence(dat, date_index = "date_of_onset", groups = "hospital")
    plot(inci, angle = 45)

    inci2 <- regroup(inci)
    plot(inci2)
}

Regroup 'incidence' objects

Description

This function regroups an incidence2 object across the specified groups. The resulting incidence2 object will contains counts aggregated over the specified groups.

Usage

regroup(x, groups = NULL)
regroup(x, groups = NULL)

Arguments

x

⁠<incidence2>⁠ object.

groups

character.

The groups to sum over.

If NULL (default) then the function returns the corresponding object with no groupings.

Examples


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


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

Regroup 'incidence' objects (tidyselect compatible)

Description

This function regroups an ⁠<incidence2>⁠ object across the specified groups. The resulting ⁠<incidence2>⁠ object will contains counts summed over the groups present in the input. It differs from regroup() only in support for <tidy-select> semantics in the groups argument.

Usage

regroup_(x, groups = NULL)
regroup_(x, groups = NULL)

Arguments

x

⁠<incidence2>⁠ object.

groups

<tidyselect>

The groups to sum over.

If NULL (default) then the function returns the corresponding object with no groupings.

Examples


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


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

Divide an incidence2 object in to it's implicit groupings

Description

Split divides and incidence2 object in to it's underlying groupings (count variable and optionally groups).

Usage

## S3 method for class 'incidence2'
split(x, f, drop, ...)
## S3 method for class 'incidence2'
split(x, f, drop, ...)

Arguments

`x`	An incidence2 object.
`f`	Not used. Present only for generic compatibility.
`drop`	Not used. Present only for generic compatibility.
`...`	Not used. Present only for generic compatibility.

Value

A list of tibbles contained the split data. This list also has a "key" attribute which is a tibble with rows corresponding to the grouping of each split.

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    ebola_sim_clean$linelist |>
        subset(!is.na(hospital)) |>
        incidence_(date_of_onset, hospital, interval = "isoweek") |>
        split()
}


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    ebola_sim_clean$linelist |>
        subset(!is.na(hospital)) |>
        incidence_(date_of_onset, hospital, interval = "isoweek") |>
        split()
}

Summarise each grouping down to one row

Description

Method for dplyr::summarise that implicitly accounts for the inherent grouping structure of incidence2 objects.

Usage

## S3 method for class 'incidence2'
summarise(.data, ..., .by, .groups)
## S3 method for class 'incidence2'
summarise(.data, ..., .by, .groups)

Arguments

`.data`	An incidence2 object.
`...`	<`data-masking`> Name-value pairs. The name gives the name of the column in the output. The value can be: A vector of length 1, which will be recycled to the correct length. A vector the same length as the current group (or the whole data frame if ungrouped). `NULL`, to remove the column. A data frame or tibble, to create multiple columns in the output.
`.by`	Not used as grouping structure implicit.
`.groups`	Not used.

Value

A tibble.

Examples


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    ebola_sim_clean$linelist |>
        subset(!is.na(hospital)) |>
        incidence_(date_of_onset, hospital, interval = "isoweek") |>
        summarise(model = list(glm(count ~ date_index, family = "poisson")))
}


if (requireNamespace("outbreaks", quietly = TRUE)) {
    data(ebola_sim_clean, package = "outbreaks")
    ebola_sim_clean$linelist |>
        subset(!is.na(hospital)) |>
        incidence_(date_of_onset, hospital, interval = "isoweek") |>
        summarise(model = list(glm(count ~ date_index, family = "poisson")))
}

Summary of an incidence object

Description

Summary of an incidence object

Usage

## S3 method for class 'incidence2'
summary(object, ...)
## S3 method for class 'incidence2'
summary(object, ...)

Arguments

`object`	An incidence2 object.
`...`	Not used.

Value

object (invisibly).

Examples


data(ebola_sim_clean, package = "outbreaks")
dat <- ebola_sim_clean$linelist
inci <- incidence(dat, "date_of_onset", groups = c("gender", "hospital"))
summary(inci)


data(ebola_sim_clean, package = "outbreaks")
dat <- ebola_sim_clean$linelist
inci <- incidence(dat, "date_of_onset", groups = c("gender", "hospital"))
summary(inci)

Color palettes used in incidence

Description

These functions are color palettes used in incidence. The palettes come from https://personal.sron.nl/~pault/#sec:qualitative and exclude grey, which is reserved for missing data.

Usage

vibrant(n)

muted(n)
vibrant(n)

muted(n)

Arguments

`n`	`integer`. Number of colours. `double` vectors will be converted via `as.integer(n)`.

Examples

vibrant(5)
muted(10)

vibrant(5)
muted(10)

`x`	An R object.
`...`	Additional arguments to be passed to or from other methods.

Package 'incidence2'

Help Index

Access various elements of an incidence object

Description

Usage

Arguments

Value

Examples

Coerce to an incidence object

Description

Usage

Arguments

Value

Coerce to a tibble

Description

Usage

Arguments

Value

Examples

Convert incident object to a data frame

Description

Usage

Arguments

See Also

Examples

Coerce to a data.table

Description

Usage

Arguments

Value

See Also

Examples

Bootstrap incidence time series

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Complete dates for all group combinations

Description

Usage

Arguments

Value

Examples

Regional data for COVID-19 cases in the UK

Description

Usage

Format

Details

Source

Compute cumulative 'incidence'

Description

Usage

Arguments

Examples

Estimate the peak date of an incidence curve

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Compute the incidence of events

Description

Usage

Arguments

Details

Value

Interval specification

See Also

Examples

Compute the incidence of events (tidyselect compatible)

Description

Usage

Arguments

Details