Create a linelist from a data.frame

This function converts a data.frame or a tibble into a linelist object, where different types of epidemiologically relevant data are tagged. This includes dates of different events (e.g. onset of symptoms, case reporting), information on the patient (e.g. age, gender, location) as well as other information such as the type of case (e.g. confirmed, probable) or the outcome of the disease. The output will seem to be the same data.frame, but linelist-aware packages will then be able to automatically use tagged fields for further data cleaning and analysis.

Usage

make_linelist(x, ..., allow_extra = FALSE)

Arguments

x

a data.frame or a tibble containing case line list data, with cases in rows and variables in columns

...

<dynamic-dots> A series of tags provided as tag_name = "column_name", where tag_name indicates any of the known variables listed in 'Details' and values indicate their name in x; see details for a list of known variable types and their expected content

allow_extra

a logical indicating if additional data tags not currently recognized by linelist should be allowed; if FALSE, unknown tags will trigger an error

Value

The function returns a linelist object.

Details

Known variable types include:

• id: a unique case identifier as numeric or character

• date_onset: date of symptom onset (see below for date formats)

• date_reporting: date of case notification (see below for date formats)

• date_admission: date of hospital admission (see below for date formats)

• date_discharge: date of hospital discharge (see below for date formats)

• date_outcome: date of disease outcome (see below for date formats)

• date_death: date of death (see below for date formats)

• gender: a factor or character indicating the gender of the patient

• age: a numeric indicating the age of the patient, in years

• location: a factor or character indicating the location of the patient

• occupation: a factor or character indicating the professional activity of the patient

• hcw: a logical indicating if the patient is a health care worker

• outcome: a factor or character indicating the outcome of the disease (death or survival)

Dates can be provided in the following formats/types:

• Date objects (e.g. using as.Date on a character with a correct date format); this is the recommended format

• POSIXct/POSIXlt objects (when a finer scale than days is needed)

• numeric values, typically indicating the number of days since the first case

See also

• An overview of the linelist package

• tags_names(): for a list of known tag names

• tags_types(): for the associated accepted types/classes

• tags(): for a list of tagged variables in a linelist

• set_tags(): for modifying tags

• tags_df(): for selecting variables by tags

Examples

if (require(outbreaks)) {

  ## dataset we will convert to linelist
  head(measles_hagelloch_1861)

  ## create linelist
  x <- make_linelist(measles_hagelloch_1861,
    id = "case_ID",
    date_onset = "date_of_prodrome",
    age = "age",
    gender = "gender"
  )

  ## print result - just first few entries
  head(x)

  ## check tags
  tags(x)

  ## Tags can also be passed as a list with the splice operator (!!!)
  my_tags <- list(
    id = "case_ID",
    date_onset = "date_of_prodrome",
    age = "age",
    gender = "gender"
  )
  new_x <- make_linelist(measles_hagelloch_1861, !!!my_tags)

  ## The output is strictly equivalent to the previous one
  identical(x, new_x)
}
#> [1] TRUE