Check the Properties of Common R Objects • checkr

checkr has been superseded by the chk package.

checkr is a light-weight R package of expressive, assertive, pipe-friendly functions to check the properties of common R objects.

In the case of failure the functions, which are designed to be used in scripts and packages, issue informative error messages.

For an overview of the functions see the checkr-naming vignette and for a comparison with similar packages see the assertive-programming vignette.

Demonstration

The following code demonstrates the check_data() function

library(checkr)

# the starwars data frame in the dplyr package fails many of these checks
check_data(dplyr::starwars, values = list(
  height = c(66L, 264L),
  name = "",
  mass = c(20,1358, NA),
  hair_color = c("blond", "brown", "black", NA),
  gender = c("male", "female", "hermaphrodite", "none", NA)), 
    order = TRUE, nrow = c(81, 84), key = "hair_color", error = FALSE)
#> Warning: `check_data()` was deprecated in checkr 0.5.1.
#> ℹ Please use `chk::check_data()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: dplyr::starwars column names must include 'height', 'name', 'mass',
#> 'hair_color' and 'gender' in that order
#> Warning: column height of dplyr::starwars must not include missing values
#> Warning: the values in column mass of dplyr::starwars must lie between 20 and
#> 1358
#> Warning: column hair_color of dplyr::starwars can only include values 'black',
#> 'blond' or 'brown'
#> Warning: column gender of dplyr::starwars can only include values 'female',
#> 'hermaphrodite', 'male' or 'none'
#> Warning: dplyr::starwars must not have more than 84 rows
#> Warning: column 'hair_color' in dplyr::starwars must be a unique key

Syntax

checkr uses objects to check the values of other objects using an elegant and expressive syntax.

Class

To check the class simply pass an object of the desired class.

y <- c(2,1,0,1,NA)
check_vector(y, values = numeric(0))
#> Warning: `check_vector()` was deprecated in checkr 0.5.1.
#> ℹ Please use chk::chk_vector(), chk::check_dim(), chk::chk_unique(),
#>   chk::chk_sorted(), chk::chk_named(), and/or chk::check_values() instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
check_vector(y, values = integer(0))
#> Error: y must be class integer

Missing Values

To check that a vector does not include missing values pass a single non-missing value (of the correct class).

check_vector(y, 1)
#> Error: y must not include missing values

To allow it to include missing values include a missing value.

check_vector(y, c(1, NA))

And to check that it only includes missing values only pass a missing value (of the correct class)

check_vector(y, NA_real_)
#> Error: y must only include missing values

Range

To check the range of a vector pass two non-missing values (as well as the missing value if required).

check_vector(y, c(0, 2, NA))
check_vector(y, c(-1, -10, NA))
#> Error: the values in y must lie between -10 and -1

Specific Values

To check the vector only includes specific values pass three or more non-missing values or set only = TRUE.

check_vector(y, c(0, 1, 2, NA))
check_vector(y, c(1, 1, 2, NA))
#> Error: y can only include values 1 or 2
check_vector(y, c(1, 2, NA), only = TRUE)
#> Error: y can only include values 1 or 2

Naming Objects

By default, the name of an object is determined from the function call.

check_vector(list(x = 1))
#> Error: list(x = 1) must be an atomic vector

This simplifies things but results in less informative error messages when used in a pipe.

library(magrittr)
#> 
#> Attaching package: 'magrittr'
#> The following objects are masked from 'package:testthat':
#> 
#>     equals, is_less_than, not
y %>% check_list()
#> Warning: `check_list()` was deprecated in checkr 0.5.1.
#> ℹ Please use chk::chk_list(), chk::check_dim(), chk::chk_unique(),
#>   chk::chk_named(), and/or chk::check_values() instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Error: . must be a list

The argument x_name can be used to override the name.

y %>% check_list(x_name = "y")
#> Error: y must be a list

Scalars

The four wrapper functions check_lgl(), check_int(), check_dbl() and check_str() check whether an object is an attribute-less non-missing scalar logical (flag), integer, double (number) or character (string). They are really useful for checking the types of arguments in functions

fun <- function(x) { check_lgl(x)}
fun(x = NA)
#> Warning: `check_lgl()` was deprecated in checkr 0.5.1.
#> ℹ Please use `chk::chk_lgl()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Error: x must not include missing values
fun(x = TRUE)
fun(x = 1)
#> Error: x must be class logical

Additional scalar wrappers are check_date() and check_dttm() for scalar Date and POSIXct objects. Alternatively you can roll your own using the more general check_scalar() function.

Installation

To install the latest development version from r-universe.

install.packages("checkr", repos = c("https://poissonconsulting.r-universe.dev", "https://cloud.r-project.org"))

To install the latest development version from GitHub

# install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
pak::pak("poissonconsulting/checkr")

Citation

To cite checkr in publications use:

  Joe Thorley (2018). checkr: An R package for Assertive Programming.
  Journal of Open Source Software, 3(23), 624. URL
  https://doi.org/10.21105/joss.00624

A BibTeX entry for LaTeX users is

  @Article{,
    title = {checkr: {An} {R} package for {Assertive} {Programming}},
    author = {Joe Thorley},
    journal = {Journal of Open Source Software},
    year = {2018},
    volume = {3},
    number = {23},
    pages = {624},
    url = {http://joss.theoj.org/papers/10.21105/joss.00624},
  }

Contribution

Please report any issues.

Pull requests are always welcome.

Code of Conduct

Please note that the checkr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms