Merge pull request #35 from markheckmann/roxygen2md

move to Roxygen using markdown

DESCRIPTION

@@ -16,8 +16,8 @@ Description: Analyze repertory grids, a qualitative-quantitative
     to quantitatively analyze and visualize repertory grid data (e.g. Fransella, Bell, & Bannister, 
     2004, ISBN: 978-0-470-09080-0). The package is part of the The package is part of the 
     <https://openrepgrid.org/> project.
-Version: 0.1.15
-Date: 2023-12-22
+Version: 0.1.16
+Date: 2023-12-26
 Encoding: UTF-8
 URL: https://github.com/markheckmann/OpenRepGrid
 Imports:
@@ -75,3 +75,4 @@ NeedsCompilation: no
 Suggests: 
     testthat (>= 2.1.0),
     covr
+Roxygen: list(markdown = TRUE)

R/data-openrepgrid.r

@@ -17,12 +17,12 @@
 #' @aliases bell2010
 #' @docType data
 #' @references  Bell, R. C. (2010).	A note on aligning constructs.
-#'              \emph{Personal Construct Theory and Practice}, 7, 43-48.
+#'              *Personal Construct Theory and Practice*, 7, 43-48.
 #'
 #'              Haritos, A., Gindidis, A., Doan, C., & Bell, R. C. (2004). 
 #'                The effect of element role titles on construct structure 
-#'                and content. \emph{Journal of constructivist 
-#'                psychology, 17}(3), 221-236.
+#'                and content. *Journal of constructivist 
+#'                psychology, 17*(3), 221-236.
 #'
 #' @keywords data
 #'
@@ -69,14 +69,14 @@ NULL
 #' @name data-bellmcgorry1992
 #' @aliases bellmcgorry1992
 #' @docType data
-#' @references  Bell, R. C. (1977). \emph{Using SPSS to 
-#'                Analyse Repertory Grid Data}. Technical Report, 
+#' @references  Bell, R. C. (1977). *Using SPSS to 
+#'                Analyse Repertory Grid Data*. Technical Report, 
 #'                University of Melbourne.
 #' 
 #'              Bell, R. C., & McGorry, P. (1992). The analysis of repertory 
 #'                grids used to monitor the perceptions of recovering psychotic 
-#'                patients. In A. Thomson & P. Cummins (Eds.), \emph{European Perspectives 
-#'                in Personal Construct Psychology} (p. 137-150). 
+#'                patients. In A. Thomson & P. Cummins (Eds.), *European Perspectives 
+#'                in Personal Construct Psychology* (p. 137-150). 
 #'                Lincoln, UK: European Personal Construct Association.
 #'
 #' @keywords data
@@ -134,8 +134,8 @@ NULL
 #' @references    Boeker, H. (1996). The reconstruction of the self in 
 #'                the psychotherapy of chronic schizophrenia: a case study 
 #'                with the Repertory Grid Technique. In: Scheer, J. W., 
-#'                Catina, A. (Eds.): \emph{Empirical Constructivism in Europe - 
-#'                The Personal Construct Approach} (p. 160-167).
+#'                Catina, A. (Eds.): *Empirical Constructivism in Europe - 
+#'                The Personal Construct Approach* (p. 160-167).
 #'                Giessen: Psychosozial-Verlag. 
 #'                
 #' @keywords data
@@ -236,7 +236,7 @@ NULL
 #' @docType data
 #' @references  Feixas, G., & Saul, L. A. (2004). The Multi-Center Dilemma Project: 
 #'              an investigation on the role of cognitive conflicts in health. 
-#'              \emph{The Spanish Journal of Psychology, 7}(1), 69-78.
+#'              *The Spanish Journal of Psychology, 7*(1), 69-78.
 #'
 #' @keywords data
 #'
@@ -303,7 +303,7 @@ NULL
 #' completed repertory grids prior to the group, immediately after the 
 #' group and at 3- and 6-month follow-up." (Leach et al. 2001, p. 230).\cr \cr
 #' 
-#' \code{leach2001a} is the pre-therapy, \code{leach2001b}
+#' `leach2001a` is the pre-therapy, `leach2001b`
 #' is the post-therapy therapy dataset. The construct and elements are 
 #' identical.
 #'
@@ -313,10 +313,10 @@ NULL
 #' @aliases leach2001a leach2001b
 #' @docType data
 #'
-#' @references      Leach, C., Freshwater, K., Aldridge, J., & 
+#' @references   Leach, C., Freshwater, K., Aldridge, J., & 
 #'                  Sunderland, J. (2001). Analysis of repertory grids 
-#'                  in clinical practice. \emph{The British Journal 
-#'                  of Clinical Psychology, 40}, 225-248.
+#'                  in clinical practice. *The British Journal 
+#'                  of Clinical Psychology, 40*, 225-248.
 #'
 #' @keywords data
 #'
@@ -404,8 +404,8 @@ NULL
 #' @docType data
 #' @references  Mackay, N. (1992). Identification, reflection, 
 #'              and correlation: Problems in the bases of repertory 
-#'              grid measures. \emph{International Journal of Personal
-#'              Construct Psychology, 5}(1), 57-75. 
+#'              grid measures. *International Journal of Personal
+#'              Construct Psychology, 5*(1), 57-75. 
 #'
 #' @keywords data
 #'
@@ -491,8 +491,8 @@ NULL
 #' @name data-slater1977a
 #' @aliases slater1977a
 #' @docType data
-#' @references  Slater, P. (1977). \emph{The measurement of intrapersonal space 
-#'              by grid technique}. London: Wiley.
+#' @references  Slater, P. (1977). *The measurement of intrapersonal space 
+#'              by grid technique*. London: Wiley.
 #'
 #' @keywords data
 #'
@@ -548,12 +548,12 @@ NULL
 #' @name data-slater1977b
 #' @aliases slater1977b
 #' @docType data
-#' @references  Slater, P. (1977). \emph{The measurement of intrapersonal space 
-#'              by grid technique}. London: Wiley.
+#' @references  Slater, P. (1977). *The measurement of intrapersonal space 
+#'              by grid technique*. London: Wiley.
 #'
 #'              Watson, J. P. (1970). The relationship between a self-mutilating 
-#'              patient and her doctor. \emph{Psychotherapy and Psychosomatics,
-#'              18}(1), 67-73.
+#'              patient and her doctor. *Psychotherapy and Psychosomatics,
+#'              18*(1), 67-73.
 #'
 #' @keywords data
 #'

R/dev-functions.r

@@ -16,13 +16,13 @@
 #' @param ne        Number of elements (default 15).
 #' @param nwc       Number of random words per construct.
 #' @param nwe       Number of random words per element.
-#' @param range     Minimal and maximal scale value (default \code{c(1, 5)}).
+#' @param range     Minimal and maximal scale value (default `c(1, 5)`).
 #' @param prob      The probability of each rating value to occur. 
-#'                  If \code{NULL} (default) the distribution is uniform.
+#'                  If `NULL` (default) the distribution is uniform.
 #' @param options   Use random sentences as constructs and elements (1) or 
 #'                  not (0). If not, the elements and constructs are given 
 #'                  default names and are numbered.
-#' @return \code{repgrid} object.
+#' @return `repgrid` object.
 #'
 #' @export
 #' @examples \dontrun{
@@ -61,20 +61,20 @@ randomGrid <- function(nc=10, ne=15, nwc=8, nwe=5, range=c(1,5), prob=NULL, opti
 #'
 #' This feature is useful for research purposes like
 #' exploring distributions of indexes etc. The function is a
-#' simple wrapper around \code{\link{randomGrid}}.
+#' simple wrapper around [randomGrid()].
 #' 
-#' @param rep       Number of grids to be produced (default is \code{3}).
+#' @param rep       Number of grids to be produced (default is `3`).
 #' @param nc        Number of constructs (default 10).
 #' @param ne        Number of elements (default 15).
 #' @param nwc       Number of random words per construct.
 #' @param nwe       Number of random words per element.
-#' @param range     Minimal and maximal scale value (default \code{c(1, 5)}).
+#' @param range     Minimal and maximal scale value (default `c(1, 5)`).
 #' @param prob      The probability of each rating value to occur. 
-#'                  If \code{NULL} (default) the distribution is uniform.
+#'                  If `NULL` (default) the distribution is uniform.
 #' @param options   Use random sentences as constructs and elements (1) or 
 #'                  not (0). If not, the elements and constructs are given 
 #'                  default names and are numbered.
-#' @return          A list of \code{repgrid} objects.
+#' @return    A list of `repgrid` objects.
 #'
 #' @export
 #' @examples \dontrun{
@@ -102,20 +102,20 @@ 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 \code{3}).
+#' @param rep       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 \code{c(1, 5)}).
+#' @param range     Minimal and maximal scale value (default `c(1, 5)`).
 #' @param prob      The probability of each rating value to occur. 
-#'                  If \code{NULL} (default) the distribution is uniform.
+#'                  If `NULL` (default) the distribution is uniform.
 #' @param progress  Whether to show a progress bar.
 #'  
-#' @return          A vector containing Slater distance values.
+#' @return    A vector containing Slater distance values.
 #' @keywords        internal
 #' @export
-#' @seealso \code{\link{randomGrids}};  
-#'          \code{\link{distanceSlater}}; 
-#'          \code{\link{distanceHartmann}}.
+#' @seealso [randomGrids()];  
+#'          [distanceSlater()]; 
+#'          [distanceHartmann()].
 #'
 #' @examples \dontrun{
 #'  
@@ -142,10 +142,10 @@ quasiDistributionDistanceSlater <- function(rep, nc, ne, range, prob=NULL, progr
 
 #' Generate a list with all possible construct reflections of a grid.
 #' 
-#' @param x           \code{repgrid} object.
-#' @param progress    Whether to show a progress bar (default is \code{TRUE}).
+#' @param x           `repgrid` object.
+#' @param progress    Whether to show a progress bar (default is `TRUE`).
 #'                    This may be sensible for a larger number of elements.
-#' @return            A list of \code{repgrid} objects with all possible permutations
+#' @return  A list of `repgrid` objects with all possible permutations
 #'                    of the grid.
 #'
 #' @export
@@ -175,12 +175,12 @@ permuteConstructs <- function(x, progress=TRUE){
 #' the rows, the columns or the whole grid matrix.
 #'
 #' @title         Permute rows, columns or whole grid matrix.
-#' @param x       \code{repgrid} object.
-#' @param along   What to permute. \code{along=1} (default) will permute the rows
-#'                \code{along=2} the columns, \code{along=3} the whole 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 \code{repgrid} object if \code{n=1} or a list of 
-#'                \code{repgrid} objects if \code{n>1}.
+#' @return  A `repgrid` object if `n=1` or a list of 
+#'                `repgrid` objects if `n>1`.
 #' @export      
 #' @keywords       internal
 #'