Skip to contents

Keep epidist objects in their class

Source: R/epidist_data.R
epidist_data.Rd

Every epidist data object also carries the epidist_data class. The methods documented here re-check an object after it has been modified and drop any epidist class whose requirements the modified object no longer meets, warning about what was dropped and why. An object that still carries an epidist class is therefore a valid object of that class, so functions which accept one do not need to re-check it.

Usage

# S3 method for class 'epidist_data'
x[...]

# S3 method for class 'epidist_data'
x[...] <- value

# S3 method for class 'epidist_data'
x[[...]] <- value

# S3 method for class 'epidist_data'
x$... <- value

# S3 method for class 'epidist_data'
names(x) <- value

# S3 method for class 'epidist_data'
rbind(..., deparse.level = 1)

# S3 method for class 'epidist_data'
dplyr_reconstruct(data, template)

Arguments

x

An object with the epidist_data class.

...

Passed to the underlying method.

value

A replacement value.

deparse.level

Passed to base::rbind().

data, template

Passed to dplyr::dplyr_reconstruct().

Value

The modified object with any epidist class whose requirements it no longer meets removed.

Details

Methods are provided for base subsetting and replacement, and for dplyr::dplyr_reconstruct(), which dplyr verbs such as dplyr::mutate(), dplyr::filter() and dplyr::select() use to restore the class of their input. dplyr::group_by() is an exception, as it builds a grouped tibble rather than restoring the class of its input. See epidist issue 629.

A result with no columns is unclassed without a warning. Such a result is almost always the prototype vctrs takes internally, in dplyr::bind_cols() for example, rather than something the user asked for, and it cannot be told apart from a deliberate empty selection.

See also

Other epidist_data: is_epidist_data()

Examples

linelist_data <- sierra_leone_ebola_data |>
  as_epidist_linelist_data(
    pdate_lwr = "date_of_symptom_onset",
    sdate_lwr = "date_of_sample_tested"
  )
#> ℹ No primary event upper bound provided, using the primary event lower bound + 1 day as the assumed upper bound.
#> ℹ No secondary event upper bound provided, using the secondary event lower bound + 1 day as the assumed upper bound.
#> ℹ No observation time column provided, using 2015-09-14 as the observation date (the maximum of the secondary event upper bound).

# Subsetting rows keeps the class
class(linelist_data[1:10, ])
#> [1] "epidist_linelist_data" "epidist_data"          "tbl_df"               
#> [4] "tbl"                   "data.frame"           

# Dropping a required column drops the class
class(dplyr::select(linelist_data, -"obs_time"))
#> Warning: ! Dropping the <epidist_linelist_data> class because the object no longer meets
#>   its requirements:
#> ✖ Assertion on 'names(data)' failed: Names must include the elements
#>   {'ptime_lwr','ptime_upr','stime_lwr','stime_upr','obs_time'}, but is missing
#>   elements {'obs_time'}.
#> ℹ Use the matching `as_epidist_*()` function to recreate the object.
#> [1] "tbl_df"     "tbl"        "data.frame"