checkr has been superseded by the chk package.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.
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
checkr uses objects to check the values of other objects using an elegant and expressive syntax.
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
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
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
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
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
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.
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")
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},
}
Please report any issues.
Pull requests are always welcome.
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
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