Reorganize documentation

R/assert.R

@@ -33,7 +33,7 @@ validate <- function(expr) {
 #'
 #'  `needs()` is an alias for `assert_package()`.
 #' @return Invisibly returns `NULL`.
-#' @family validation methods
+#' @family checking methods
 #' @author N. Frerebeau
 #' @export
 assert_package <- function(x, ask = TRUE) {
@@ -80,7 +80,7 @@ needs <- assert_package
 #' @return
 #'  Throws an error, if any, and returns `x` invisibly otherwise.
 #' @author N. Frerebeau
-#' @family validation methods
+#' @family checking methods
 #' @export
 assert_length <- function(x, expected, empty = FALSE) {
   arg <- deparse(substitute(x))
@@ -150,7 +150,7 @@ assert_dimensions <- function(x, expected) {
 #' @return
 #'  Throws an error, if any, and returns `x` invisibly otherwise.
 #' @author N. Frerebeau
-#' @family validation methods
+#' @family checking methods
 #' @export
 assert_names <- function(x, expected = NULL) {
   arg <- deparse(substitute(x))
@@ -199,22 +199,15 @@ assert_colnames <- function(x, expected = NULL) {
 }
 
 # NA/NaN/Inf/duplicates ========================================================
-#' Check Data
+#' Check Missing Values
 #'
-#' * `assert_missing()` and `assert_infinite()` check if an object contains any
-#' missing (`NA`, `NaN`) or infinite (`Inf`) value.
-#' * `assert_unique()` checks if an object contains duplicated elements.
+#' Checks if an object contains any missing (`NA`, `NaN`) values.
 #' @param x An object to be checked.
 #' @return
 #'  Throws an error, if any, and returns `x` invisibly otherwise.
 #' @author N. Frerebeau
-#' @family validation methods
-#' @name assert_data
-#' @rdname assert_data
-NULL
-
+#' @family checking methods
 #' @export
-#' @rdname assert_data
 assert_missing <- function(x) {
   arg <- deparse(substitute(x))
   n <- sum(is.na(x))
@@ -226,8 +219,15 @@ assert_missing <- function(x) {
   invisible(x)
 }
 
+#' Check Infinite Values
+#'
+#' Checks if an object contains any infinite (`Inf`) values.
+#' @param x An object to be checked.
+#' @return
+#'  Throws an error, if any, and returns `x` invisibly otherwise.
+#' @author N. Frerebeau
+#' @family checking methods
 #' @export
-#' @rdname assert_data
 assert_infinite <- function(x) {
   arg <- deparse(substitute(x))
   n <- sum(is.infinite(x))
@@ -239,8 +239,15 @@ assert_infinite <- function(x) {
   invisible(x)
 }
 
+#' Check Duplicates
+#'
+#' Checks if an object contains duplicated elements.
+#' @param x An object to be checked.
+#' @return
+#'  Throws an error, if any, and returns `x` invisibly otherwise.
+#' @author N. Frerebeau
+#' @family checking methods
 #' @export
-#' @rdname assert_data
 assert_unique <- function(x) {
   arg <- deparse(substitute(x))
   if (has_duplicates(x)) {
@@ -333,7 +340,7 @@ assert_function <- function(x) {
 #' @return
 #'  Throws an error, if any, and returns `x` invisibly otherwise.
 #' @author N. Frerebeau
-#' @family validation methods
+#' @family checking methods
 #' @name assert_numeric
 #' @rdname assert_numeric
 NULL
@@ -404,7 +411,7 @@ assert_even <- function(x, na.rm = FALSE, ...) {
 #' @return
 #'  Throws an error, if any, and returns `x` invisibly otherwise.
 #' @author N. Frerebeau
-#' @family validation methods
+#' @family checking methods
 #' @export
 assert_constant <- function(x, ...) {
   arg <- deparse(substitute(x))
@@ -444,7 +451,7 @@ assert_increasing <- function(x, ...) {
 #' @return
 #'  Throws an error, if any, and returns `x` invisibly otherwise.
 #' @author N. Frerebeau
-#' @family validation methods
+#' @family checking methods
 #' @export
 assert_lower <- function(x, y, ...) {
   arg_x <- deparse(substitute(x))
@@ -474,7 +481,7 @@ assert_greater <- function(x, y, ...) {
 #' @param x A [`matrix`] to be checked.
 #' @return Throw an error, if any, and returns `x` invisibly otherwise.
 #' @author N. Frerebeau
-#' @family validation methods
+#' @family checking methods
 #' @export
 assert_square <- function(x) {
   arg <- deparse(substitute(x))
@@ -503,7 +510,7 @@ assert_symmetric <- function(x) {
 # @param expected An appropriate expected value.
 # @return Throw an error, if any.
 # @author N. Frerebeau
-# @family validation methods
+# @family checking methods
 # @keywords internal
 # @export
 # assert_dag <- function(x) {

README.Rmd

@@ -23,9 +23,9 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
 [![Dependencies](https://tinyverse.netlify.app/badge/arkhe)](https://cran.r-project.org/package=arkhe)
 
 [![r-universe](https://tesselle.r-universe.dev/badges/arkhe)](https://tesselle.r-universe.dev/arkhe){.pkgdown-devel}
-[![CRAN Version](http://www.r-pkg.org/badges/version/arkhe)](https://cran.r-project.org/package=arkhe){.pkgdown-release}
+[![CRAN Version](https://www.r-pkg.org/badges/version/arkhe)](https://cran.r-project.org/package=arkhe){.pkgdown-release}
 [![CRAN checks](https://badges.cranchecks.info/worst/arkhe.svg)](https://cran.r-project.org/web/checks/check_results_arkhe.html){.pkgdown-release}
-[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/arkhe)](https://cran.r-project.org/package=arkhe){.pkgdown-release}
+[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/arkhe)](https://cran.r-project.org/package=arkhe){.pkgdown-release}
 
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 
@@ -92,4 +92,5 @@ replace_NA(X, value = 0)
 ```
 
 ## Contributing
+
 Please note that the **arkhe** project is released with a [Contributor Code of Conduct](https://www.tesselle.org/conduct.html). By contributing to this project, you agree to abide by its terms.

README.md

@@ -16,15 +16,16 @@ src="https://tesselle.r-universe.dev/badges/arkhe"
 alt="r-universe" /></a>
 <a href="https://cran.r-project.org/package=arkhe"
 class="pkgdown-release"><img
-src="http://www.r-pkg.org/badges/version/arkhe"
+src="https://www.r-pkg.org/badges/version/arkhe"
 alt="CRAN Version" /></a>
 <a href="https://cran.r-project.org/web/checks/check_results_arkhe.html"
 class="pkgdown-release"><img
 src="https://badges.cranchecks.info/worst/arkhe.svg"
 alt="CRAN checks" /></a>
 <a href="https://cran.r-project.org/package=arkhe"
 class="pkgdown-release"><img
-src="http://cranlogs.r-pkg.org/badges/arkhe" alt="CRAN Downloads" /></a>
+src="https://cranlogs.r-pkg.org/badges/arkhe"
+alt="CRAN Downloads" /></a>
 
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
@@ -48,7 +49,7 @@ To cite arkhe in publications use:
 Frerebeau N (2024). *arkhe: Tools for Cleaning Rectangular Data*.
 Université Bordeaux Montaigne, Pessac, France.
 <doi:10.5281/zenodo.3526659> <https://doi.org/10.5281/zenodo.3526659>, R
-package version 1.7.0, <https://packages.tesselle.org/arkhe/>.
+package version 1.7.0.9000, <https://packages.tesselle.org/arkhe/>.
 
 This package is a part of the tesselle project
 <https://www.tesselle.org>.
@@ -83,48 +84,48 @@ k <- sample(1:25, 3, FALSE)
 X[k] <- NA
 X
 #>      [,1] [,2] [,3] [,4] [,5]
-#> [1,]    7    8    9    1   NA
-#> [2,]    8    9    7    2    3
-#> [3,]    8   NA    2   10    2
-#> [4,]    4    7    7    5    3
-#> [5,]    4    7   NA    6    1
+#> [1,]    1    7   10    2    6
+#> [2,]    9    7    7    3    5
+#> [3,]    6   NA    8   10    5
+#> [4,]    1   10    8    2   NA
+#> [5,]   NA    1    4    9    8
 
 ## Count missing values in rows
 count(X, f = is.na, margin = 1)
-#> [1] 1 0 1 0 1
+#> [1] 0 0 1 1 1
 ## Count non-missing values in columns
 count(X, f = is.na, margin = 2, negate = TRUE)
-#> [1] 5 4 4 5 4
+#> [1] 4 4 5 5 4
 
 ## Find row with NA
 detect(X, f = is.na, margin = 1)
-#> [1]  TRUE FALSE  TRUE FALSE  TRUE
+#> [1] FALSE FALSE  TRUE  TRUE  TRUE
 ## Find column without any NA
 detect(X, f = is.na, margin = 2, negate = TRUE, all = TRUE)
-#> [1]  TRUE FALSE FALSE  TRUE FALSE
+#> [1] FALSE FALSE  TRUE  TRUE FALSE
 
 ## Remove row with any NA
 discard(X, f = is.na, margin = 1, all = FALSE)
 #>      [,1] [,2] [,3] [,4] [,5]
-#> [1,]    8    9    7    2    3
-#> [2,]    4    7    7    5    3
+#> [1,]    1    7   10    2    6
+#> [2,]    9    7    7    3    5
 ## Remove column with any NA
 discard(X, f = is.na, margin = 2, all = FALSE)
 #>      [,1] [,2]
-#> [1,]    7    1
-#> [2,]    8    2
+#> [1,]   10    2
+#> [2,]    7    3
 #> [3,]    8   10
-#> [4,]    4    5
-#> [5,]    4    6
+#> [4,]    8    2
+#> [5,]    4    9
 
 ## Replace NA with zeros
 replace_NA(X, value = 0)
 #>      [,1] [,2] [,3] [,4] [,5]
-#> [1,]    7    8    9    1    0
-#> [2,]    8    9    7    2    3
-#> [3,]    8    0    2   10    2
-#> [4,]    4    7    7    5    3
-#> [5,]    4    7    0    6    1
+#> [1,]    1    7   10    2    6
+#> [2,]    9    7    7    3    5
+#> [3,]    6    0    8   10    5
+#> [4,]    1   10    8    2    0
+#> [5,]    0    1    4    9    8
 ```
 
 ## Contributing