docs: clean up documentation and docstrings

DESCRIPTION

@@ -74,4 +74,4 @@ URL: https://inseefrlab.github.io/rtauargus,
 BugReports: https://github.com/inseefrlab/rtauargus/issues
 Roxygen: list(markdown = TRUE)
 StagedInstall: no
-Config/roxygen2/version: 8.1.0
+Config/roxygen2/version: 8.1.1

R/analyse_metadata.R

@@ -6,7 +6,7 @@
 #' creating a structured output for further processing.
 #'
 #' @param df_metadata A dataframe containing metadata in wide format.
-#' @param df_eq_indicator A datadframe containing the indicators equations if needed.
+#' @param df_eq_indicator A dataframe containing the indicators equations if needed.
 #' @param verbose Logical. If `TRUE`, returns a detailed list of intermediate results
 #' from each processing step. If `FALSE`, returns only the cluster assignments. Defaults to `FALSE`.
 #'

R/hrc.R

@@ -63,7 +63,7 @@
 #' (nom et emplacement du fichier hrc produit. Si non renseigné, un fichier temporaire.)
 #' @param fill_na fill in any missing values, using an other variable :
 #' \itemize{
-#' \item{`"up"` (default) : hierarchical variable of the level level
+#' \item{`"up"` (default) : hierarchical variable of the level
 #' immediately above}
 #' \item{`"down"` : hierarchical variable of the level immediately
 #' lower}

R/micro_arb.R

@@ -150,7 +150,7 @@ apriori_batch <- function(ntab, hst_names, sep = ',', ignore_err = 0 , exp_triv
 #' protection problems.
 #'
 #' See more details in `vignette("rtauargus")` or in
-#' `vignette("protect_multi_tables)`.
+#' `vignette("protect_multi_tables")`.
 #'
 #' Creates a batch file for microdata, executable by Tau-Argus in
 #' command line. \cr
@@ -196,7 +196,7 @@ apriori_batch <- function(ntab, hst_names, sep = ',', ignore_err = 0 , exp_triv
 #' @section Table identifiers:
 #' If the list `explanatory_vars` has names, these will be
 #' used in the batch to give an identifier to the table, in the form of
-#' of a comment line (`// <TABLE_ID> "..."`). They will be
+#' a comment line (`// <TABLE_ID> "..."`). They will be
 #' reused by the `import` function to name the R format arrays
 #' tables in output.
 #'
@@ -289,7 +289,7 @@ apriori_batch <- function(ntab, hst_names, sep = ',', ignore_err = 0 , exp_triv
 #' renuméroté automatiquement (voir la section 'Syntax').)
 #' @param linked to process the secondary secret jointly on all
 #' tabs. Only one delete command is allowed in this case (applied to all
-#' all tables). \cr
+#' tables). \cr
 #' (pour traiter le secret secondaire conjointement sur toutes les
 #' tabulations. Une seule commande suppress autorisée dans ce cas (appliquée à
 #' tous les tableaux).)

R/micro_asc_rda.R

@@ -67,7 +67,7 @@ write_rda <- function(info_vars) {
 #' protection problems.
 #'
 #' See more details in `vignette("rtauargus")` or in
-#' `vignette("protect_multi_tables)`.
+#' `vignette("protect_multi_tables")`.
 #'
 #' Creates a fixed length text file (asc) and a metadata file
 #' (rda) from microdata and additional information. \cr
@@ -89,11 +89,11 @@ write_rda <- function(info_vars) {
 #' @param holding_var nom de la variable de holding.
 #' (name of the holding variable.) \cr
 #' @param decimals minimum number of decimals to display (see section 'Number of
-#' of decimals').
+#' decimals').
 #' (nombre minimal de décimales à afficher (voir section 'Number of
 #' of decimals').)
 #' @param hrc information about the hierarchical variables (see section
-#' section 'Hierarchical variables'). \cr
+#' 'Hierarchical variables'). \cr
 #' (informations sur les variables hiérarchiques (voir section
 #' 'Hierarchical variables').)
 #' @param hierleadstring character which, repeated n times, indicates that the value is
@@ -120,8 +120,8 @@ write_rda <- function(info_vars) {
 #'
 #' @return
 #' Returns the names of the asc and rda files as a list (invisibly).
-#' invisibly). Empty columns (filled with `NA` or empty strings) are not
-#' strings) will not be exported to the asc file. A
+#' Empty columns (filled with `NA` or empty strings) will not be
+#' exported to the asc file. A
 #' warning message will list the affected columns. \cr
 #' (Renvoie les noms des fichiers asc et rda sous forme de liste (de
 #'   manière invisible). Les colonnes vides (remplies de `NA` ou de chaînes
@@ -136,7 +136,7 @@ write_rda <- function(info_vars) {
 #'
 #' The names of the elements of the vector give the variable concerned, the elements
 #' of the vector give the value of the parameter for Tau-Argus. An unnamed element
-#' element will be the default value, which will be assigned to all
+#' will be the default value, which will be assigned to all
 #' variables that can take this parameter.
 #'
 #' For example :
@@ -173,7 +173,7 @@ write_rda <- function(info_vars) {
 #' hierarchical variables.
 #'
 #' To define a hierarchy based on the positions of characters
-#' (**hierierlevels**), pass a sequence of integers separated by
+#' (**hierlevels**), pass a sequence of integers separated by
 #' spaces.
 #'
 #' *Example :* `c(CODECOM = "2 3 0 0 0")`
@@ -182,7 +182,7 @@ write_rda <- function(info_vars) {
 #' (**hiercodelist**), the function expects the location of this file (and
 #' a possible `hiercodelist` if it differs from the default option of the
 #' package). In this case, you can write explicitly the path to an existing file
-#' file (`c(A38 = "a38.hrc")`), but also make a call to
+#' (`c(A38 = "a38.hrc")`), but also make a call to
 #' `write_hrc()` which will generate an hrc file from microdata.
 #'
 #' *Example :* `c(A38 = write_hrc(microdata, c("A38", "A21", "A10")))`
@@ -238,7 +238,7 @@ write_rda <- function(info_vars) {
 #'
 #' @section Number of decimals:
 #'
-#' The parameter `decimals` indicates the minimum number of decimals to be
+#' The parameter `decimals` indicates the minimum number of decimals to
 #' appear in the output file (whatever the number of decimals
 #' actually present in `microdata`). It applies to all
 #' real variables (double) but not to integer variables (integer). For

R/micro_rtauargus.R

@@ -9,7 +9,7 @@
 #' protection problems.
 #'
 #' See more details in `vignette("rtauargus")` or in
-#' `vignette("protect_multi_tables)`.
+#' `vignette("protect_multi_tables")`.
 #'
 #' Protects tables built from microdata and specifications of the crossings.
 #' The function allows to perform the complete process, namely the creation of
@@ -32,7 +32,7 @@
 #' Intermediate files without a name entered (`asc_filename`...)
 #' will be created in a temporary folder, with randomly generated names.
 #' This mechanism allows the user to abstract from the preparation of
-#' preparation of the data and to maintain the entire chain of
+#' the data and to maintain the entire chain of
 #' processing in R. \cr
 #'
 #' (La fonction exécute séquentiellement les fonctions : \itemize{
@@ -64,7 +64,7 @@
 #' @inheritSection micro_arb Syntax
 #'
 #' @section Microdata already as text files:
-#' To use existing asc and rda files already existing, it is possible to
+#' To use existing asc and rda files, it is possible to
 #' provide, instead of the data.frame, a character vector indicating
 #' the path of these files. The first element of this vector is the asc file,
 #' the second element the rda file. The rda file can be omitted if it has the

R/multitable.R

@@ -11,7 +11,7 @@ journal_add_line <- function(journal,...){
 #' @inheritParams tab_rtauargus
 #' @param list_tables named list of `data.frame` or `data.table` representing the tables to protect
 #' @param list_explanatory_vars named list of character vectors of explanatory
-#' variables of each table mentionned in list_tables. Names of the list are the same as of the list of tables.
+#' variables of each table mentioned in list_tables. Names of the list are the same as of the list of tables.
 #' @param alt_hrc named list for alternative hierarchies (useful for non nested-hierarchies)
 #' @param alt_totcode named list for alternative codes
 #' @param ip_start integer: Interval protection level to apply at first treatment of each table

R/options.R

@@ -92,7 +92,7 @@ df_op.rtauargus <- function(html = FALSE) {
 #' user.*
 #'
 #' On loading the package, all the rtauargus options, that are not already
-#' been set by the user, are set with their default values (see table below).
+#' set by the user, are set with their default values (see table below).
 #' The already defined options keep the values set by the user.
 #'
 #' The options can be set during a session with the following instruction

R/rtauargus_plus.R

@@ -7,23 +7,23 @@
 #'
 #' In interactive mode, Tau-Argus can process up to 10 tabs
 #' simultaneously for the same microdata set. In batch mode, a larger number of
-#' of crossings can be specified. However, doing so
+#' crossings can be specified. However, doing so
 #' can be particularly time consuming, as Tau-Argus takes a lot of time
 #' to read large text files of microdata.
 #'
 #' `rtauargus_plus` helps to improve the speed of execution. The function
 #' splits the list of tabs into groups of size `grp_size` and
 #' makes a call to `micro_rtauargus()` for each group. It writes an
 #' asc file restricted to the only variables actually used within a
-#' of a group.
+#' group.
 #'
 #' The results are then aggregated into a single list, as if Tau-Argus
 #' had been called only once.
 #'
 #' Modifying `grp_size` will not change the result, only the time
 #' execution time. A value around 5 (default) seems to be a good compromise
 #' between reading too large asc files and calling Tau-Argus too often.
-#' Tau-Argus too much. It can be adjusted according to the number of
+#' It can be adjusted according to the number of
 #' common variables within each tab group.
 #
 #' (En mode interactif, Tau-Argus peut traiter jusqu'à 10 tabulations
@@ -52,7 +52,7 @@
 #'
 #' In return for the speed of execution, the crossings must have the
 #' same characteristics (same primary secret rules, same secondary secret method,
-#' same secondary secret, same weighting variable, etc.). The parameters
+#' same weighting variable, etc.). The parameters
 #' `safety_rules`, `supress`, ..., must therefore contain a
 #' unique value.
 #'

R/run_arb.R

@@ -183,14 +183,14 @@ unquote <- function(s) sub("^[\"'](.+)[\"']$", "\\1", s)
 #' therefore requires the software to be accessible from the workstation.
 #'
 #' The location of the TauArgus.exe program is defined globally when the
-#' loading the package. In fact, the argument `tauargus_exe` will not
+#' loading the package. In fact, the argument `tauargus_exe` will
 #' normally not have to be specified (except to override the global option the
 #' time of the execution of the function).
 #'
 #' Checks are made before the actual launching of Tau-Argus:
 #' existence of the software on the computer, of the asc and rda files, of the folders where
 #' write the results, the variables to be used (crossings, response variable) in the
-#' response variable) in the metadata (rda file). \cr
+#' metadata (rda file). \cr
 #'
 #' (Seul l’argument `arb_filename` est obligatoire, car toutes les
 #' informations nécessaires sont présentes dans ce fichier.

R/tab_arb.R

@@ -87,7 +87,7 @@ tab_apriori_batch <- function(hst_names, sep, ignore_err = 0 , exp_triv = 0) {
 #'
 #' @section Syntaxe:
 #'
-#' For tabular data, this function secures only one table at a time#'
+#' For tabular data, this function secures only one table at a time.
 #' Unless specific details, use syntax from Tau-Argus manual \cr
 #' Sauf mention contraire, utiliser la syntaxe mentionnée dans la documentation
 #' de Tau-Argus.
@@ -149,7 +149,7 @@ tab_apriori_batch <- function(hst_names, sep, ignore_err = 0 , exp_triv = 0) {
 #' Chaîne de caractères en syntaxe batch Tau-Argus. Si le secret primaire
 #' a été traité dans un fichier d'apriori : utiliser "MAN(10)")
 #' @param suppress
-#' Algortihm for secondary suppression (Tau-Argus batch syntax), and the
+#' Algorithm for secondary suppression (Tau-Argus batch syntax), and the
 #' parameters for it.\cr
 #' ( Algorithme de gestion du secret secondaire
 #' (syntaxe batch de Tau-Argus), ainsi que les potentiels paramètres associés)
@@ -161,18 +161,18 @@ tab_apriori_batch <- function(hst_names, sep, ignore_err = 0 , exp_triv = 0) {
 #' (Format des fichiers en sortie (codification Tau-Argus).
 #' Valeur par défaut du package : `"2"` (csv for pivot-table).
 #' Pour le format SBS utiliser `"4"`)
-#' @param output_options Additionnal parameter for the output,
+#' @param output_options Additional parameter for the output,
 #' by default : \code{"AS+"} (print Status). To specify no options : `""`.\cr
 #' (Options supplémentaires des fichiers en sortie. Valeur
 #'   par défaut du package : `"AS+"` (affichage du statut). Pour ne
 #'   spécifier aucune option, `""`.)
 #' @param gointeractive Boolean, if TRUE will open a Tau-Argus window and launch
 #' the batch in it (`FALSE` by default). \cr
 #' (Possibilité de lancer le batch depuis le menu de Tau-Argus
-#'  (`FALSE` par défaut).)
+#'  (`FALSE` par défaut).
 #'
 #' @return A list containing two elements :
-#'  the arb file name and the output name (usefull if the name is generated randomly) \cr
+#'  the arb file name and the output name (useful if the name is generated randomly) \cr
 #'  (Une liste de deux éléments : le nom du fichier arb, le nom
 #'   fichiers en sortie (utile pour récupérer les noms générés aléatoirement).)
 #'

R/tab_rda.R

@@ -146,7 +146,7 @@ write_rda_tab <- function(info_vars) {
 #' (Variable indiquant le secret primaire de type booléen:
 #' prend la valeur "TRUE" quand les cellules du tableau doivent être masquées
 #' par le secret primaire, "FALSE" sinon. Permet de créer un fichier d'apriori)
-#' @param secret_var Nae of the boolean variable which specifies the secret, primary or not :
+#' @param secret_var Name of the boolean variable which specifies the secret, primary or not :
 #'  equal to "TRUE" if a cell is concerned by the secret,"FALSE" otherwise.
 #' will  be exported in the apriori file. \cr
 #' (Variable indiquant le secret  de type booléen:
@@ -265,7 +265,7 @@ write_rda_tab <- function(info_vars) {
 #'   `<TOTCODE> "global"` pour toutes les variables catégorielles
 #'   sauf  `size` and `income`} qui se verront affecter
 #'   le total : `<TOTCODE> "total"`
-#'   Par defaut : `<TOTCODE> "Total"`
+#'   Par défaut : `<TOTCODE> "Total"`
 #' }
 #'
 #'
@@ -297,7 +297,7 @@ write_rda_tab <- function(info_vars) {
 #' Les éléments du vecteur en paramètre doivent nommés (avec le nom de la variable),
 #' même s'il n'y a qu'un seul élément.
 #'
-#'*Exemple :*`c(category="category.hrc")`)
+#' *Exemple :* `c(category="category.hrc")`
 #'
 #'
 #' @section Number of decimals:

R/tab_rtauargus.R

@@ -9,7 +9,7 @@
 #'
 #' @param files_name string used to name all the files needed to process.
 #' All files will have the same name, only their extension will be different.
-#' @param dir_name string indicated the path of the directory in which to save
+#' @param dir_name string indicating the path of the directory in which to save
 #' all the files (.rda, .hst, .txt, .arb, .csv) generated by the function.
 #' @param summary_secret If `TRUE`, a statistical summary of the suppression is provided along with the masked data.
 #' @param unif_labels boolean, if explanatory variables have to be standardized

R/writehrc.R

@@ -67,7 +67,7 @@ vect_aro <- Vectorize(arobase, vectorize.args = c("string", "number"))
 #' Si TRUE, inverse l'ordre des colonnes.
 #' @param hier_lead_string character. (Single) character indicating the
 #' hierarchy depth in the .hrc file. By default, the value is set to the current
-#' value mentionned in the package options (i.e. "@" at the package startup).
+#' value mentioned in the package options (i.e. "@" at the package startup).
 #' \cr
 #' Caractère unique repérant le niveau de profondeur dans le .hrc
 #' @param adjust_unique_roots boolean. If TRUE (default) will add fictional roots to the
@@ -83,13 +83,13 @@ vect_aro <- Vectorize(arobase, vectorize.args = c("string", "number"))
 #' character Si adjust_unique_roots est TRUE add_char est l'élément qui sera
 #' utilisé afin de créer des feuilles fictives, il faut être sur que cela
 #' ne crée pas de doublons dans la hiérarchie.La chaine de caractère sera
-#' ajouté au début d'une feuille unique. Par defaut :"ZZZ"
+#' ajouté au début d'une feuille unique. Par défaut : "ZZZ"
 #' @details Creates a .hrc hierarchy file adapted to tau-Argus from a
 #' correspondence table fully describing it. By default, lines are sorted
 #' alphabetically so as to regroup identical levels.
 #'
 #' Ecrit un fichier de hiérarchie .hrc lisible par tau-Argus à
-#' partir d'une table de corrrespondance la décrivant complètement. Par défaut,
+#' partir d'une table de correspondance la décrivant complètement. Par défaut,
 #' les lignes du tableau seront triées afin de regrouper les niveaux de
 #' hiérarchie identiques.
 #'