review documentation 📝

R/addURL.R

@@ -4,9 +4,9 @@
 #'
 #' @param url A URL.
 #' @param text A character string to be searched within.
-#' @param extra Extra A connection object or a character string that stand for a path,
-#' ignored if text is defined.
-#' @param markdown logical. If \code{TRUE}, hyperlinks  marks of Markdown language are sought.
+#' @param extra Extra A connection object or a character string that stand for
+#' a path, ignored if text is defined.
+#' @param markdown logical. If `TRUE`, hyperlinks marks of Markdown language are sought.
 #'
 #' @export
 #'

R/addWebIcon.R

@@ -2,18 +2,15 @@
 #'
 #' Generates a HTML tag to include an icon from an iconic framework.
 #'
-#' @author
-#' Kevin Cazelles
-#'
 #' @param name name of the icon to be added.
-#' @param framework a character use to default is \code{fa} (which stands for Font-Awesome).
-#' @param size default sets to \code{2},
+#' @param framework a character use to default is `fa` (which stands for Font-Awesome).
+#' @param size default sets to `2`,
 #' @export
 #'
 #' @examples
 #' addWebIcon('cc')
 
 addWebIcon <- function(name, framework = "fa", size = 2) {
-    paste0("<i class=\"", framework, " ", framework, "-", name, " ", framework, "-", 
-        size, "x\"></i>")
+  paste0("<i class=\"", framework, " ", framework, "-", name, " ",
+    framework, "-", size, "x\"></i>")
 }

R/adjustString.R

@@ -11,7 +11,7 @@
 #' @param extra character vector, or a vector to be coerced to a character
 #' vector that will be (partially) added to produced a string of
 #' @param before logical. If `TRUE`, then the extra characters are added before
-#' \code{x}
+#' `x`
 #'
 #' @details
 #' This function was originally created to help getting a fixed number of digits
@@ -30,7 +30,7 @@
 
 
 adjustString <- function(x, szchar, extra = 0, before = TRUE) {
-    x %<>% as.character
+    x <- as.character(x)
     szchar %<>% as.numeric %>% floor %>% abs
     extra %<>% as.character %>% strsplit(split = "") %>% extract2(1)
     ##
@@ -39,7 +39,7 @@ adjustString <- function(x, szchar, extra = 0, before = TRUE) {
     ##
     . <- "No note"
     ##
-    if (sum(id1) > 0) {
+    if (sum(id1)) {
         val <- szchar - nchar(x[id1])
         out[id1] <- val %>% as.list %>% lapply(FUN = . %>% rep(extra, length.out = .) %>%
             paste(collapse = "")) %>% unlist

R/aggregateCol.R

@@ -1,25 +1,23 @@
 #' Aggregate columns
 #'
-#' The \code{aggregateCol} function eases the computation of a given function on
-#' a specific subset of columns.
+#' `aggregateCol()` perform summary statistics on a specific subset of columns.
 #'
 #' @author
 #' Kevin Cazelles
 #'
 #' @param data a data frame.
 #' @param grp an integer vector assigning a group to every column of `data`
-#' used to compute operations on a subset of columns. Any integer is a valid group,
-#' `0` indicates that the column must be unchanged, `NA` is used to remove
-#' columns.
+#' used to compute operations on a subset of columns. Any integer is a valid
+#" group, `0` indicates that the column must be unchanged, `NA` removes columns.
 #' @param FUN a function to be applied to all group of columns.
 #' @param names_aggreg column names for aggregated columns.
-#' @param ... further arguments to be passed to \code{FUN}.
+#' @param ... further arguments to be passed to `FUN`.
 #'
 #' @details
 #' An integer vector, whose length is the number of
 #' columns of the input data frame, is used to assign a group to each column
-#' that explicits the subsetting. Furthermore columns can be either kept as is
-#' using \code{0} or discarded by using \code{NA}.
+#' that explicit the subsetting. Furthermore columns can be either kept as is
+#' using `0` or discarded by using `NA`.
 #'
 #' @seealso [stats::aggregate()]
 #'

R/assignClass2df.R

@@ -1,18 +1,17 @@
-#' Assign a class to a set of column of a data frame
+#' Assign a class to columns
 #'
-#' This function is designed to ease the changes of column's class
-#' of a given data frame.
+#' Assign a class to a set of column of a data frame. This function is designed
+#' to ease the changes of column's class of a given data frame.
 #'
 #' @param x a data frame or a R object to be coerced into a data frame.
 #' @param colid the identity of columns for which class are ti be changed.
 #' @param cls a character vector containing the classes' names to be used in the
-#' same order as colid. By default \code{cls} is repeated until its size equals
-#' \code{colid}'s size.
+#' same order as `colid`. By default `cls` is repeated until its size equals
+#' `colid`'s size.
 #'
 #' @return
 #' A data.frame for which columns have the required classes.
 #'
-#' @importFrom magrittr %<>%
 #' @export
 #' @examples
 #' df1 <- matrix(signif(runif(20),4), ncol=2)
@@ -22,14 +21,14 @@
 
 
 assignClass2df <- function(x, colid, cls) {
-    ## 
-    x %<>% as.data.frame
+    ##
+    x <- as.data.frame(x)
     stopifnot(colid %in% 1:ncol(x))
     out <- x
     sz <- length(colid)
     cl <- rep(cls, length.out = sz)
-    ## 
+    ##
     for (i in 1:sz) out[, colid[i]] <- methods::as(x[, colid[i]], cl[i])
-    ## 
-    return(out)
+    ##
+    out
 }

R/assignIds.R

@@ -1,24 +1,23 @@
 #' Assign an id to a list of characters or factors
 #'
-#' This function is done mainly to assign an id to factor or similar character
-#' strings. Regarding factors, \code{as.integer} does such task
-#' but the order obtained could be different.
+#' This function aims to assign an id to factor or similar character
+#' strings. Regarding factors, [as.integer()] does such task but the order
+#' obtained may differ
 #'
 #' @param x an R object to be coerced into character type.
-#' @param alphabetical a logical indicating whether an alphabetical sorting must be applied.
+#' @param alphabetical a logical indicating whether an alphabetical sorting
+#' must be applied.
 #' @return
 #' A vector of Ids.
 #' @importFrom magrittr %>%
-#' @importFrom magrittr %<>%
 #' @export
 #' @examples
 #' assignIds(list(2,'f', 'd', 'f'))
 
-
 assignIds <- function(x, alphabetical = FALSE) {
     tmp <- x %>% as.character %>% unique
     if (alphabetical)
-        tmp %<>% sort
+        tmp <- sort(tmp)
     out <- tmp %>% length %>% integer
     for (i in 1:length(tmp)) out[x == tmp[i]] <- i
     out

R/categorize.R

@@ -3,8 +3,6 @@
 #' Assigns a category to each element of a vector for a given set of threshold
 #' values..
 #'
-#' @author
-#' Kevin Cazelles
 #' @param x A numeric, complex, character or logical vector.
 #' @param categ A set of threshold values used to assign categories.
 #' @param lower A logical, if `TRUE` threshold values (i.e. values within

R/dfTemplate.R

@@ -1,11 +1,9 @@
 #' Create a data frame from scratch or based on one or two data frames.
 #'
-#' This function handles the creation of data frames based on intuitive parameters.
-#' It was originally designed to make row binding easier when columns differs
-#' among data frame by creating data frames with the same columns.
-#'
-#' @author
-#' Kevin Cazelles
+#' This function handles the creation of data frames based on intuitive
+#' parameters. It was originally designed to make row binding easier when
+#' columns differs among data frame by creating data frames with the same
+#' columns.
 #'
 #' @param cols either a number of column or a vector of character used as
 #' columns names of the data frame to be returned.

R/duplicateRow.R

@@ -8,9 +8,8 @@
 #' @param x a data.frame.
 #' @param id.el identity of the elements to be duplicated.
 #' @param times number of times elements are duplicated. Could be a vector of the same length as id.el.
-#' @param append A logical. If \code{TRUE}, duplicated elements will be appended to the dataframe otherwise duplicated elements remain next to their parent. Non-existing columns cannot be duplicated while non-existing rows can and produce \code{NA}.
-#'
-#' @importFrom magrittr %>% %<>%
+#' @param append A logical. If `TRUE`, duplicated elements will be appended to the dataframe otherwise duplicated elements remain next to their parent. Non-existing columns cannot be duplicated while non-existing rows can and produce `NA`.
+#' @importFrom magrittr %>%
 #' @export
 #' @examples
 #' data(iris, package='datasets')
@@ -24,7 +23,7 @@ duplicateRow <- function(x, id.el = 1, times = 1, append = FALSE) {
     if (class(pos) == "character")
         ord <- c(rownames(x), pos) else ord <- c(1:nrow(x), pos)
     if (!append)
-        ord %<>% sort
+        ord <- sort(ord)
 
     x[ord, ]
 }
@@ -37,7 +36,7 @@ duplicateCol <- function(x, id.el = 1, times = 1, append = FALSE) {
     if (class(pos) == "character")
         ord <- c(colnames(x), pos) else ord <- c(1:ncol(x), pos)
     if (!append)
-        ord %<>% sort
+        ord <- sort(ord)
 
     x[, ord]
 }

R/findRef.R

@@ -4,14 +4,14 @@
 #'
 #' @param text A character string to be searched within.
 #' @param con A connection object or a character string that stand for a path,
-#' ignored if \code{text} is used.
-#' @param markdown logical. If \code{TRUE}, citation tags of Markdown langage are sought.
+#' ignored if `text` is used.
+#' @param markdown logical. If `TRUE`, citation tags of Markdown langage are sought.
 #'
 #' @author
 #' Kevin Cazelles
 #'
 #' @return
-#' A dataframe with the citation keys and their frequence.
+#' A data.frame with the citation keys and their frequence.
 #' @export
 #' @examples
 #' test <- findRef(text='First \\cite{Pimm2000}, second \\Citep{May1972}')
@@ -20,22 +20,21 @@
 findRef <- function(text, con, markdown = FALSE) {
     ##---
     if (missing(text)) {
-        if (missing(con)) 
+        if (missing(con))
             stop("Either 'text' or 'con' must be specified.") else {
             lsfile <- readLines(con)
             text <- paste(unlist(lsfile), collapse = "")
         }
     }
     ## ----
-    if (!markdown) 
+    if (!markdown)
         pat <- "[\\].{0,3}[cC]ite.{0,7}\\{[[:alnum:]]+}" else pat <- "@[[:alnum:]]+"
     tbref <- multiMatch(text = text, pattern = pat)
     ## ----
-    if (markdown) 
+    if (markdown)
         tbref <- table(sub("@", "", tbref)) else {
         tbref <- sub("[\\].{0,3}[cC]ite.{0,7}\\{", "", tbref)
         tbref <- table(sub("\\}", "", tbref))
     }
-    tbref <- data.frame(key = names(tbref), freq = as.integer(tbref))
-    tbref
+    data.frame(key = names(tbref), freq = as.integer(tbref))
 }

R/findReplace.R

@@ -6,7 +6,7 @@
 #' @author
 #' Kevin Cazelles
 #'
-#' @param vec a vector where to search for patterns.
+#' @param vec a vector to be searched.
 #' @param vec_pat vector providing the patterns to be searched for.
 #' @param y values to replace matching values.
 #'
@@ -26,7 +26,7 @@
 
 findReplace <- function(vec, vec_pat, y) {
     vec[vec %in% vec_pat] <- y
-    return(vec)
+    vec
 }
 
 
@@ -36,5 +36,5 @@ grepReplace <- function(vec, vec_pat, y) {
     res <- lapply(vec_pat, function(x) grepl(vec, pattern = x))
     res2 <- do.call(cbind, res) %>% apply(1L, sum)
     vec[res2 > 0] <- y
-    return(vec)
+    vec
 }

R/findThem.R

@@ -1,22 +1,21 @@
 #' Find values in a given vector.
 #'
 #' Given a set of values and a vector where the values must be found, the
-#' \code{findThem} function records the matched values and the position in the
+#' `findThem` function records the matched values and the position in the
 #' vector where the values have been searched for.
 #'
 #' @author
 #' Kevin Cazelles
 #' @param what a vector a values to be searched for.
 #' @param where a vector where values will be searched on.
 #' @param todf a logical indicating whether the output object must be a data frame.
-#' @param reportnomatch a logical. If TRUE, values without match are reported in
-#' the data frame with a NA. Only available if \code{todf} is TRUE. Default is
-#' set to FALSE.
+#' @param reportnomatch a logical. If `TRUE`, values without match are reported #' in the data frame with a NA. Only available if `todf` is `TRUE`. Default is
+#' set to `FALSE`.
 #' @return
-#' A list indicating matched positions for each elements of \code{what}. If no
-#' match is found then \code{NA} is returned. If \code{todf} is TRUE
+#' A list indicating matched positions for each elements of `what`. If no
+#' match is found then `NA` is returned. If `todf` is `TRUE`
 #' then a three-columns data frame is returned including values and positions
-#' in both \code{what} and \code{where} vectors.
+#' in both `what` and `where` vectors.
 #' @seealso \code{\link[base]{which}}
 #' @export
 #' @examples
@@ -44,11 +43,7 @@ findThem <- function(what, where, todf = FALSE, reportnomatch = FALSE) {
             out <- data.frame(values = rep(names(tmp), sz), what = rep(1:length(what),
                 sz), where = unlist(tmp))
             rownames(out) <- NULL
-        } else {
-            out <- tmp
-        }
-    } else {
-        out <- NA_integer_
-    }
+        } else out <- tmp
+    } else out <- NA_integer_
     out
 }

R/gaussianShape.R

@@ -1,13 +1,13 @@
-#' Flexible bell-shaped function.
+#' Flexible bell-shaped function
 #'
-#' The \code{gaussianShape} function computes a personalizable Gaussian function.
-#' Default values are the same as in \code{\link[stats]{dnorm}}.
+#' The `gaussianShape()` function computes a personnalisable Gaussian function.
+#' Default values are the same as in [stats::dnorm()].
 #' @author
 #' Kevin Cazelles
 #' @param x a numeric vector.
 #' @param optx x-values at which the maximum is reached.
 #' @param opty extremum value.
-#' @param width the width of the bell.
+#' @param width width of the bell.
 #' @param pow a real number.
 #' @return
 #' A vector containing values standing for categories into which elements of x have fallen.

R/getDigits.R

@@ -11,13 +11,12 @@
 #' @param x a character vector where digits are sought, or an object which can be coerced by `as.character` to a character vector.
 #' @param collapse an optional character string to separate the results (see [base::paste()).
 #'
-#' @importFrom magrittr %>% %<>%
+#' @importFrom magrittr %>%
 #' @export
 #'
 #' @return
 #' A list of digits.
 #'
-#'
 #' @examples
 #' getDigits('txt012-34')
 

R/keepWords.R

@@ -1,15 +1,17 @@
 #' Keep these words.
 #'
-#' Extract words based on their position in a character string, vectorised over \code{string}.
+#' Extract words based on their position in a character string, vectorised over
+#' `string`.
 #'
 #' @author
 #' Kevin Cazelles
 #'
-#' @param string Input vector. A character vector or list from which words will be extracted.
+#' @param string An input character vector or a list from which words will be
+#' extracted.
 #' @param slc Vector of integer indicating the selected positions of the words to be kept.
-#' @param punct.rm A logical indicating whether punctuation characters should be removed.
-#' @param na.rm A logical indicating whether missing values should be removed.
-#' @param collapse An optional character string used to separate selected words. Not \code{NA_character_}.
+#' @param punct.rm A logical Should punctuation characters be removed?
+#' @param na.rm A logical. Should missing values be removed?
+#' @param collapse An optional character string used to separate selected words.
 #'
 #' @return A vector of the selected words concatenated for each string.
 #' @importFrom magrittr %>%