sub_linelist: Subsetting of linelist objects

In epiverse-trace/linelist: Tagging and Validating Epidemiological Data

Subsetting of linelist objects

Description

The ⁠[]⁠ and ⁠[[]]⁠ operators for linelist objects behaves like for regular data.frame or tibble, but check that tagged variables are not lost, and takes the appropriate action if this is the case (warning, error, or ignore, depending on the general option set via lost_tags_action()) .

Usage

## S3 method for class 'linelist'
x[i, j, drop = FALSE]

## S3 replacement method for class 'linelist'
x[i, j] <- value

## S3 replacement method for class 'linelist'
x[[i, j]] <- value

## S3 replacement method for class 'linelist'
x$name <- value

Arguments

x	a linelist object
i	a vector of integer or logical to subset the rows of the linelist
j	a vector of character, integer, or logical to subset the columns of the linelist
drop	a logical indicating if, when a single column is selected, the data.frame class should be dropped to return a simple vector, in which case the linelist class is lost as well; defaults to FALSE
value	the replacement to be used for the entries identified in x
name	a literal character string or a name (possibly backtick quoted). For extraction, this is normally (see under ‘Environments’) partially matched to the names of the object.

Value

If no drop is happening, a linelist. Otherwise an atomic vector.

See Also

• lost_tags_action() to set the behaviour to adopt when tags are lost through subsetting; default is to issue a warning

• get_lost_tags_action() to check the current the behaviour

Examples

if (require(outbreaks) && require(dplyr) && require(magrittr)) {
  ## create a linelist
  x <- measles_hagelloch_1861 %>%
    tibble() %>%
    make_linelist(
      id = "case_ID",
      date_onset = "date_of_prodrome",
      age = "age",
      gender = "gender"
    ) %>%
    mutate(result = if_else(is.na(date_of_death), "survived", "died")) %>%
    set_tags(outcome = "result") %>%
    rename(identifier = case_ID)
  x

  ## dangerous removal of a tagged column setting it to NULL issues a warning
  x[, 1] <- NULL
  x

  x[[2]] <- NULL
  x

  x$age <- NULL
  x
}

epiverse-trace/linelist documentation built on April 26, 2024, 5:35 a.m.