Update CA documentation, vignettes, and improve package examples

.Rbuildignore

@@ -6,3 +6,9 @@
 ^docs$
 ^pkgdown$
 ^CRAN-SUBMISSION$
+^doc$
+^Meta$
+^examples/temp/
+^tests/temp/
+
+

.gitignore

@@ -7,3 +7,5 @@
 .o
 .so
 .dll
+/doc/
+/Meta/

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.1
-Date: 2024-09-14 10:57:51 UTC
-SHA: eb5656ea33fc519c7f43ebe74b0963825b5943c0
+Version: 2.2
+Date: 2024-11-13 18:00:38 UTC
+SHA: 323e03f56d02eec77b7c9d98aa46ed597b3f3b74

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: biplotEZ
 Title: EZ-to-Use Biplots
-Version: 2.1
+Version: 2.3
 Authors@R: 
     c(person("Sugnet", "Lubbe", , "muvisu@sun.ac.za", role = c("aut", "cre","cph"),
            comment = c(ORCID = "0000-0003-2762-9944")),
@@ -27,7 +27,7 @@ Description: Provides users with an EZ-to-use platform for representing data
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Suggests: 
@@ -40,14 +40,17 @@ Suggests:
     knitr,
     MASS,
     R.devices,
+    RColorBrewer,
     rgl,
-    rmarkdown,
-    testthat (>= 3.0.0)
+    rmarkdown
 Imports: 
     graphics,
     grDevices,
     plotrix,
+    Rcpp,
     splines,
     stats,
     withr
 NeedsCompilation: yes
+LinkingTo: 
+    Rcpp

NAMESPACE

@@ -3,6 +3,7 @@
 S3method(AoD,biplot)
 S3method(CA,biplot)
 S3method(CVA,biplot)
+S3method(CatPCA,biplot)
 S3method(PCA,biplot)
 S3method(PCO,biplot)
 S3method(classification,biplot)
@@ -12,15 +13,14 @@ S3method(regress,biplot)
 S3method(summary,biplot)
 export(AoD)
 export(CA)
-export(CATPCA)
 export(CLPs)
 export(CLRs)
 export(CVA)
+export(CatPCA)
 export(PCA)
 export(PCO)
 export(alpha.bags)
 export(axes)
-export(axes_coordinates)
 export(biplot)
 export(classification)
 export(classify)
@@ -34,13 +34,16 @@ export(legend.type)
 export(means)
 export(newaxes)
 export(newsamples)
+export(nom.axes)
+export(ord.axes)
 export(prediction)
 export(reflect)
 export(regress)
 export(rotate)
 export(samples)
 export(sqrtManhattan)
 export(translate_axes)
+importFrom(Rcpp,sourceCpp)
 importFrom(grDevices,chull)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,grey)

R/CA.R

@@ -18,13 +18,19 @@
 #' \item{Z}{Combined data frame of the row and column coordinates.}
 #' \item{r}{Numer of levels in the row factor.}
 #' \item{c}{Numer of levels in the column factor.}
+#' \item{Dr}{Diagonal matrix of row profiles.}
+#' \item{Dc}{Diagonal matrix of column profiles.}
+#' \item{Drh}{Weighted row profiles.}
+#' \item{Dch}{Weighted column profiles.}
 #' \item{rowcoor}{Row coordinates based on the selected \code{variant}.}
 #' \item{colcoor}{Column coordinates based on the selected \code{variant}.}
-#' \item{P}{Correspondence Matrix}
+#' \item{P}{Correspondence Matrix.}
 #' \item{Smat}{Standardised Pearson residuals.}
 #' \item{SVD}{Singular value decomposition solution: \code{d, u, v}.}
-#' \item{qual}{Quality of the approximation.}
+#' \item{e.vects}{Depending on what was specified in \code{CA} argument.}
+#' \item{dim.biplot}{The dimension of the biplot.}
 #' \item{lambda.val}{The computed lambda value if lambda-scaling is requested.}
+#' \item{gamma}{Contribution of the singular values, based on the CA variant.}
 #'
 #' @seealso [biplot()]
 #'
@@ -130,10 +136,10 @@ CA.biplot <- function(bp, dim.biplot = c(2,1,3), e.vects = 1:ncol(bp$X), variant
   bp$Z <- Z
   bp$r <- r
   bp$c <- c
+  bp$Dr <- Dr
   bp$Dc <- Dc
-  bp$Rc <- Dr
-  bp$Dch <- Dch
   bp$Drh <- Drh
+  bp$Dch <- Dch
   bp$rowcoor <- rowcoor         
   bp$colcoor <- colcoor
   bp$P <- P