fix addiotional CRAN comments

fix docs

fix more check comments

some more fixes

fix docs

more fixes

more fixes

add comma

.Rbuildignore

@@ -17,4 +17,4 @@ cran-comments.md
 ^doc$
 ^Meta$
 ^vignettes/web$
-TODO.md
+TODO.md

DESCRIPTION

@@ -19,7 +19,7 @@ Description: Analyze repertory grids, a qualitative-quantitative
 Version: 0.1.15
 Date: 2024-02-18
 Encoding: UTF-8
-URL: https://github.com/markheckmann/OpenRepGrid, http://markheckmann.github.io/OpenRepGrid/
+URL: https://github.com/markheckmann/OpenRepGrid
 Imports:
     methods,
     graphics,

NAMESPACE

@@ -45,13 +45,11 @@ export(alignByLoadings)
 export(apply_pb)
 export(as.gridlist)
 export(bertin)
-export(bertinBase)
 export(bertinCluster)
 export(bind)
 export(bindConstructs)
 export(biplot2d)
 export(biplot3d)
-export(biplot3dBase2)
 export(biplotDraw)
 export(biplotEsa2d)
 export(biplotEsa3d)

R/bertin.r

@@ -222,29 +222,29 @@ bertin2PlusLegend <- function(x, ratings = TRUE, top = unit(40, "mm"),
 #       -splitString has a bug, breaks too late
 #       -trimming of elements and constructs
 #
-#' Workhorse for the biplot printing.
-#'
-#' Prints a bertin to the output
-#' device. It uses the R base graphics system and
-#' this is very fast. This is useful for working with grids. Not so much for
-#' producing high-quality output.
-#'
-#' @param x         `repgrid` object.
-#' @param ratings   Vector. rating scores are printed in the cells
-#' @param margins   Vector of length three (default `margins=c(0,1,1)`).
-#'                  1st element denotes the left, 2nd the upper and 3rd the
-#'                  right margin in npc coordinates (i.e. 0 to zero).
-#' @param trim      Vector (default `trim=c(F,F)`).If a number the string
-#'                  is trimmed to the given number of characters. If set
-#'                  to TRUE the labels are trimmed to the available space
-#' @param add       Logical. Whether to add bertin to existent plot (default is
-#'                  `FALSE`). If `TRUE, plot.new()` will not be called
-#'                  `par(new=TRUE)`.
-#' @return `NULL` just for printing.
-#'
-#' @export
-#' @keywords internal
-#'
+# Workhorse for the biplot printing.
+#
+# Prints a bertin to the output
+# device. It uses the R base graphics system and
+# this is very fast. This is useful for working with grids. Not so much for
+# producing high-quality output.
+#
+# @param x         `repgrid` object.
+# @param ratings   Vector. rating scores are printed in the cells
+# @param margins   Vector of length three (default `margins=c(0,1,1)`).
+#                  1st element denotes the left, 2nd the upper and 3rd the
+#                  right margin in npc coordinates (i.e. 0 to zero).
+# @param trim      Vector (default `trim=c(F,F)`).If a number the string
+#                  is trimmed to the given number of characters. If set
+#                  to TRUE the labels are trimmed to the available space
+# @param add       Logical. Whether to add bertin to existent plot (default is
+#                  `FALSE`). If `TRUE, plot.new()` will not be called
+#                  `par(new=TRUE)`.
+# @return `NULL` just for printing.
+#
+# @export
+# @keywords internal
+#
 bertinBase <- function(nrow, ncol, labels = "", labels.elements = "",
                        labels.left = "", labels.right = "",
                        col.text = NA, cex.text = .6, cex.elements = .7,

R/calc.r

@@ -190,7 +190,7 @@ calcAngles <- function(x, dim = c(1, 2), clockwise = TRUE) {
 #'
 #' Reorder indexes for constructs and elements are calculated using the coordinates of the given dimensions.
 #'
-#' @param x`repgrid` object that has been submitted to [calcBiplotCoords()].
+#' @param x A `repgrid` object that has been submitted to [calcBiplotCoords()].
 #' @param dim Dimensions used to calculate angles for reordering grid.
 #' @param clockwise Logical. Positive angles are clockwise with x axis as basis.
 #' @return  A list containing the indexes to reorder the grid. The first list element for the constructs, the second
@@ -631,14 +631,14 @@ print.rmsCor <- function(x, digits = 2, ...) {
 #' variable is set as dependent and independent.
 #' The direction of dependency needs to be specified.
 #'
-#' @param x           `repgrid` object
+#' @param x           `repgrid` object.
 #' @param dependent   A string denoting the direction of dependency in the output
 #'                    table (as d is asymmetrical). Possible values are `"columns"`
 #'                    (the default) for setting the columns as dependent, `"rows"`
 #'                    for setting the rows as the dependent variable and
 #'                    `"symmetric"` for the
 #'                    symmetrical Somers' d measure (the mean of the two directional
-#'                    values for code{"columns"} and `"rows"`).
+#'                    values for `"columns"` and `"rows"`).
 #' @param trim        The number of characters a construct is trimmed to (default is
 #'                    `30`). If `NA` no trimming occurs. Trimming
 #'                    simply saves space when displaying correlation of constructs

R/dev-functions.r

@@ -106,7 +106,7 @@ randomGrids <- function(rep = 3, nc = 10, ne = 15, nwc = 8, nwe = 5,
 #' All Slater distances are returned as a vector. The values can be used e.g. to assess the
 #' distributions standard deviation.
 #'
-#' @param rep       Number of grids to be produced (default is `3`).
+#' @param reps      Number of grids to be produced (default is `3`).
 #' @param nc        Number of constructs (default 10).
 #' @param ne        Number of elements (default 15).
 #' @param range     Minimal and maximal scale value (default `c(1, 5)`).
@@ -129,7 +129,7 @@ randomGrids <- function(rep = 3, nc = 10, ne = 15, nwc = 8, nwe = 5,
 #' hist(vals, breaks = 50)
 #' }
 #'
-quasiDistributionDistanceSlater <- function(rep, nc, ne, range, prob = NULL, progress = TRUE) {
+quasiDistributionDistanceSlater <- function(reps, nc, ne, range, prob = NULL, progress = TRUE) {
   quasis <- randomGrids(rep, nc = nc, ne = ne, range = range, prob = prob, options = 0)
   if (progress) { # whether to show progress bar
     lapply_fun <- lapply_pb
@@ -176,19 +176,18 @@ permuteConstructs <- function(x, progress = TRUE) {
 }
 
 
+#' Permute rows, columns or whole grid matrix.
+#'
 #' Generate one or many permutations of the grid by shuffling
 #' the rows, the columns or the whole grid matrix.
 #'
-#' @title         Permute rows, columns or whole grid matrix.
-#' @param x       `repgrid` object.
-#' @param along   What to permute. `along=1` (default) will permute the rows
-#'                `along=2` the columns, `along=3` the whole matrix.
-#' @param n       The number of permutations to produce.
-#' @return  A `repgrid` object if `n=1` or a list of
-#'                `repgrid` objects if `n>1`.
+#' @param x A `repgrid` object.
+#' @param along What to permute. `along=1` (default) will permute the rows
+#'  `along=2` the columns, `along=3` the whole matrix.
+#' @param n The number of permutations to produce.
+#' @returns  A `repgrid` object if `n = 1` or a list of `repgrid` objects if `n > 1`.
 #' @export
-#' @keywords       internal
-#'
+#' @keywords internal
 #' @examples \dontrun{
 #'
 #' # permute grid
@@ -227,10 +226,3 @@ permuteGrid <- function(x, along = 1, n = 1) {
   }
   res
 }
-
-
-
-### TODO ###
-# Permutation test
-
-# Slater writes:

R/import.r

@@ -24,8 +24,7 @@
 #' Convert the returned object from an import function into a `repgrid`
 #' object. Works for all importXInternal functions (except scivesco).
 #'
-#' @param x   object returned from an import function.
-#' @return  `repgrid` object.
+#' @param import List with relevant entries.
 #' @keywords internal
 #' @export
 #'
@@ -499,7 +498,7 @@ importGridstat <- function(file, dir = NULL, min = NULL, max = NULL) {
 #'                (default `NULL`).
 #' @note          Note that the GRIDCOR data sets the minimum ratings scale range to 1.
 #'                The maximum value can differ and is defined in the data file.
-#' @references <https://www.ub.edu/terdep/gridcor.html>
+#' @references <https://repertorygrid.net/en/>
 #'
 #' @export
 #' @keywords internal
@@ -598,7 +597,7 @@ importGridcorInternal <- function(file, dir = NULL) {
 #' @export
 #' @references  Feixas, G., & Cornejo, J. M. (2002). GRIDCOR: Correspondence Analysis
 #' for Grid Data (version 4.0). Barcelona: Centro de Terapia Cognitiva.
-#' Retrieved from <https://www.ub.edu/terdep/pag/index.html>.
+#' Retrieved from <https://repertorygrid.net/en/>.
 #'
 #' @seealso [importGridcor()],
 #'                [importGridstat()],
@@ -1016,8 +1015,7 @@ importScivescoInternal <- function(file, dir = NULL) {
 #' Convert the returned object from the sci:vesco import function into a `repgrid`
 #' object.
 #'
-#' @param x   object returned from an import function.
-#' @return  `repgrid` object.
+#' @param import List with relevant entries.
 #' @keywords internal
 #' @export
 convertScivescoImportObjectToRepGridObject <- function(import) {

R/measures.r

@@ -101,7 +101,7 @@ print_square_matrix <- function(x, names = NA, trim = NA,
 #'  * `total_elements` Total number of matches across elements.
 #'  * `constructs`: Matrix with no. of matches for constructs.
 #'  * `elements`: Matrix with no. of matches for elements.
-#' 
+#'
 #' @keywords internal
 #' @export
 #' @example inst/examples/example-matches.R
@@ -359,7 +359,7 @@ indexPvaff <- function(x, method = 1) {
 #
 # @param x         Object of class indexPvaff.
 # @param digits    Numeric. Number of digits to round to (default is
-#                  \code{2}).
+#                  `2`).
 # @param ...       Not evaluated.
 # @export
 # @method          print indexPvaff
@@ -619,7 +619,7 @@ print.indexDilemmatic <- function(x, output = "SD", ...) {
 #' Implementation as in the Gridcor program and explained on the correspoding help pages: "\ldots the sum of the
 #' squared values of the correlations of each construct with the rest of the constructs, averaged by the total number
 #' of constructs minus one. This process is repeated with each element, and the overall Intensity is calculated by
-#' averaging the intensity scores of constructs and elements." <https://www.ub.edu/terdep/pag/man11.html>. Currently
+#' averaging the intensity scores of constructs and elements." (Gridcor manual). Currently
 #' the total is calculated as the unweighted average of all single scores (for elements and construct).
 #'
 #' @title Intensity index
@@ -1183,23 +1183,23 @@ indexConflict1 <- function(x) {
 #'
 #' Description of the balance / imbalance assessment:
 #'
-#' 1. Order correlations of the triad by absolute magnitude, so that \eqn{ r_{max} > r_{mdn} > r_{min} }{r_max > r_mdn > r_min}.
-#' 2. Apply Fisher's Z-transformation and division by 3 to yield values between 1 and -1  (\eqn{ Z_{max} > Z_{mdn} > Z_{min} }{Z_max > Z_mdn > Z_min}).
+#' 1. Order correlations of the triad by absolute magnitude, so that \eqn{ r_{max} > r_{mdn} > r_{min}}, \eqn{r_{max} > r_{mdn} > r_{min}}.
+#' 2. Apply Fisher's Z-transformation and division by 3 to yield values between 1 and -1  (\eqn{ Z_{max} > Z_{mdn} > Z_{min}, Z_{max} > Z_{mdn} > Z_{min}}).
 #' 3. Check whether the triad is balanced by assessing if the following relation holds:
 #'
-#'    - If \eqn{ Z_{max} Z_{mdn} > 0 }{ Z_max x Z_mdn > 0},
-#'                the triad is balanced if \eqn{ Z_{max} Z_{mdn} - Z_{min} <= crit }
-#'                { Z_max x Z_mdn - Z_min <= crit }.
-#'    - If \eqn{ Z_{max} Z_{mdn} < 0 }{ Z_max x Z_mdn < 0},
-#'                the triad is balanced if \eqn{ Z_{min}  - Z_{max} Z_{mdn} <= crit }
-#'                { Z_min - Z_max x Z_mdn <= crit }.
+#'    - If \eqn{Z_{max} Z_{mdn} > 0, Z_{max} x Z_{mdn} > 0},
+#'      the triad is balanced if \eqn{Z_{max} Z_{mdn} - Z_{min} <= crit},
+#'      \eqn{Z_{max} x Z_{mdn} - Z_{min} <= crit}.
+#'    - If \eqn{Z_{max} Z_{mdn} < 0,  Z_{max} x Z_{mdn} < 0},
+#'      the triad is balanced if \eqn{Z_{min} - Z_{max} Z_{mdn} <= crit},
+#'      \eqn{Z_{min} - Z_{max} x Z_{mdn} <= crit}.
 #'
 #' @section Personal remarks (MH): I am a bit suspicious about step 2 from above. To devide by 3 appears pretty arbitrary.
 #'        The r for a z-values of 3 is 0.9950548 and not 1.
 #'        The r for 4 is 0.9993293. Hence, why not a value of 4, 5, or 6?
 #'        Denoting the value to devide by with `a`, the relation for the
-#'        first case translates into \eqn{ a  Z_{max}  Z_{mdn} <= \frac{crit}{a} + Z_{min} }
-#'        { a x Z_max x Z_mdn =< crit/a + Z_min}. This shows that a bigger value of `a`
+#'        first case translates into \eqn{a  Z_{max}  Z_{mdn} <= \frac{crit}{a} + Z_{min}},
+#'        \eqn{a x Z_{max} x Z_{mdn} =< crit/a + Z_{min}}. This shows that a bigger value of `a`
 #'        will make it more improbable that the relation will hold.
 #'
 #' @param x A `repgrid` object.
@@ -1752,37 +1752,37 @@ indexDilemmaShowCorrelationDistribution <- function(x, e1, e2) {
 
 # internal workhorse for indexDilemma
 #
-# @param x               \code{repgrid} object.
+# @param x               `repgrid` object.
 # @param self            Numeric. Index of self element.
 # @param ideal           Numeric. Index of ideal self element.
 # @param diff.mode       Numeric. Method adopted to classify construct pairs into congruent
-#                        and discrepant. With \code{diff.mode=1}, the minimal and maximal
-#                        score difference criterion is applied. With \code{diff.mode=0} the Mid-point
-#                        rating criterion is applied. Default is \code{diff.mode=1}.
+#                        and discrepant. With `diff.mode=1`, the minimal and maximal
+#                        score difference criterion is applied. With `diff.mode=0` the Mid-point
+#                        rating criterion is applied. Default is `diff.mode=1`.
 
-# @param diff.congruent  Is used if \code{diff.mode=1}. Maximal difference between
+# @param diff.congruent  Is used if `diff.mode=1`. Maximal difference between
 #                        element ratings to define construct as congruent (default
-#                        \code{diff.congruent=1}). Note that the value
+#                        `diff.congruent=1`). Note that the value
 #                        needs to be adjusted by the user according to the rating scale
 #                        used.
-# @param diff.discrepant Is used if \code{diff.mode=1}. Minimal difference between
+# @param diff.discrepant Is used if `diff.mode=1`. Minimal difference between
 #                        element ratings to define construct as discrepant (default
-#                        \code{diff.discrepant=4}). Note that the value
+#                        `diff.discrepant=4`). Note that the value
 #                        needs to be adjusted by the user according to the rating scale
 #                        used.
 # @param diff.poles      Not yet implemented.
 # @param r.min           Minimal correlation to determine implications between
 #                        constructs ([0, 1]).
 # @param exclude         Whether to exclude the elements self and ideal self
 #                        during the calculation of the inter-construct correlations.
-#                        (default is \code{FALSE}).
+#                        (default is `FALSE`).
 # @param index           Whether to print index numbers in front of each construct
-#                        (default is \code{TRUE}).
+#                        (default is `TRUE`).
 # @param trim            The number of characters a construct (element) is trimmed to (default is
-#                        \code{20}). If \code{NA} no trimming is done. Trimming
+#                        `20`). If `NA` no trimming is done. Trimming
 #                        simply saves space when displaying the output.
 # @param digits          Numeric. Number of digits to round to (default is
-#                        \code{2}).
+#                        `2`).
 # @export
 # @keywords internal
 # @return     A list with four elements containing different steps of the

R/openrepgrid.r

@@ -15,7 +15,7 @@
 #'   - Contributors: Richard C. Bell, Alejandro García Gutiérrez (@j4n7), Diego Vitali (@artoo-git), José Antonio
 #' González Del Puerto (@MindCartographer), Jonathan D. Raskin
 #'
-#'   - How to contribute: You can [contribute in various ways](http://docu.openrepgrid.org/contribute.html).
+#'   - How to contribute: You can [contribute in various ways](https://docs.openrepgrid.org/CONTRIBUTING.html).
 #' The `OpenRepGrid` code is hosted on [GitHub](https://github.com/markheckmann/OpenRepGrid), where you can issue bug
 #' reports or feature requests. You may email your request to the package maintainer.
 #'

R/perturbate.R

@@ -6,11 +6,12 @@
 #' Randomly subtract or add an amount to a proportion of the grid ratings. This
 #' emulates randomness during the rating process, producing a grid which might
 #' also have resulted.
+#'
 #' @param x A `repgrid` object.
 #' @param n Number of perturbated grid to generate.
 #' @param prop The proportion of ratings to be perturbated.
 #' @param amount The amount set of possible perturbations. Will depend on scale
-#'   range. Usually {-1, 1} are reasonable settings
+#'   range. Usually `{-1, 1}` are reasonable settings.
 #' @param prob Probability for each amount to occur.
 #' @export
 #' @example inst/examples/example-perturbate.R

R/repgrid-output.r

@@ -517,7 +517,7 @@ df_out <- function(df, # data frame
 
 # Show method for repgrid
 #
-# @param object a \code{repgrid} object
+# @param object a `repgrid` object
 # @docType methods
 # @usage \S4method{show}{repgrid}(object)
 # @include repgrid.r

R/repgrid-plots.r

@@ -99,7 +99,7 @@ mapCoordinatesToValue <- function(z, val.range = c(.5, 1)) {
 #' the mapped values are transformed into hex color values.
 #'
 #' @param  z          numeric vector.
-#' @param  color      vector of length two giving color values `c("white", "black")`.
+#' @param  colors     vector of length two giving color values `c("white", "black")`.
 #' @param  val.range  numeric vector of lengths two (default `c(.2, .8)`).
 #' @return numeric vector
 #' @keywords internal
@@ -179,17 +179,17 @@ calcCoordsBorders <- function(x, y, xmax = 1, ymax = 1, cx = 0, cy = 0) {
 #
 # TODO: supply x.ext in mm and convert to usr coords
 #
-# @param  xy        \code{dataframe} with x and y coords.
+# @param  xy        `dataframe` with x and y coords.
 # @param  labels    vector of strings.
-# @param  cex       vector of cex values (default is \code{.7}).
+# @param  cex       vector of cex values (default is `.7`).
 # @param  x.ext     scalar giving the horizontal margin
 #                   of the rectangle in NDC coordinates
-#                   (default is \code{.02}).
+#                   (default is `.02`).
 # @param  y.ext     scalar giving the vertical margin
 #                   of the rectangle in NDC coordinates
-#                   (default is \code{.02}).
-# @return \code{dataframe} with coordinates for the lower left and
-#         upper right rectangle borders (\code{x0, y0, x1, y1}).
+#                   (default is `.02`).
+# @return `dataframe` with coordinates for the lower left and
+#         upper right rectangle borders (`x0, y0, x1, y1`).
 #
 calcRectanglesCoordsForLabels <- function(xy, labels, cex = .7,
                                           x.ext = .02, y.ext = .02) {