Update to version 2.2.7

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rags2ridges
 Type: Package
 Title: Ridge Estimation of Precision Matrices from High-Dimensional Data
-Version: 2.2.6
+Version: 2.2.7
 Maintainer: Carel F.W. Peeters <carel.peeters@wur.nl>
 Authors@R: c(
     person(given = c("Carel", "F.W."),
@@ -37,6 +37,6 @@ Suggests:
     testthat,
     knitr,
     rmarkdown
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Encoding: UTF-8
 VignetteBuilder: knitr

NAMESPACE

@@ -57,21 +57,17 @@ export(optPenalty.fused.auto)
 export(optPenalty.fused.grid)
 export(optPenalty.kCV)
 export(optPenalty.kCVauto)
-export(optPenaltyPchordal)
 export(pcor)
 export(pooledP)
 export(pooledS)
 export(pruneMatrix)
 export(ridgeP)
 export(ridgeP.fused)
 export(ridgePathS)
-export(ridgePchordal)
-export(ridgePsign)
 export(ridgeS)
 export(rmvnormal)
 export(sparsify)
 export(sparsify.fused)
-export(support4ridgeP)
 export(symm)
 import(Rcpp)
 import(igraph)
@@ -112,8 +108,6 @@ importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,rug)
 importFrom(graphics,text)
-importFrom(igraph,graph.adjacency)
-importFrom(igraph,igraph.to.graphNEL)
 importFrom(methods,as)
 importFrom(methods,hasArg)
 importFrom(methods,is)

NEWS.md

@@ -1,7 +1,24 @@
 # News for Package [rags2ridges](https://cran.r-project.org/package=rags2ridges)
 
 
+# Version 2.2.7
+
+## Adjustments:
+  * Functions optPenaltyPchordal, ridgePchordal, ridgePsign, and support4ridgeP (temporarily) deprecated (for major adjustments)
+
+## Documentation:
+  * Fixed URLs.
+
+
+# Version 2.2.6
+
+## Documentation:
+  * Canonicalization of URLs.
+  * Update of published papers 
+
+
 # Version 2.2.5
+
 ## Documentation:
   * Improved documentation and added new [pkgdown](https://cran.r-project.org/package=pkgdown) documentation website.
   * NEWS file moved to markdown format instead of .Rd and available on the website

R/rags2ridges.R

@@ -3750,7 +3750,7 @@ if (getRversion() >= "2.15.1") utils::globalVariables(c("X1", "X2", "value"))
 #' color scale for matrix entries in the negative range. \code{highColor}
 #' determines the color scale for matrix entries in the positive range. For the
 #' colors supported by the arguments \code{lowColor} and \code{highColor}, see
-#' \url{https://stat.columbia.edu/~tzheng/files/Rcolor.pdf}. White entries in
+#' \url{https://www.nceas.ucsb.edu/sites/default/files/2020-04/colorPaletteCheatsheet.pdf}. White entries in
 #' the plot represent the midscale value of 0. One can opt to set the diagonal
 #' entries to the midscale color of white when one is interested in
 #' (heatmapping) the off-diagonal elements only. To achieve this, set
@@ -3929,7 +3929,7 @@ edgeHeat <- function(M, lowColor = "blue", highColor = "red", textsize = 10,
 #' If \code{prune = TRUE} the vertices of degree 0 (vertices not implicated by
 #' any edge) are removed. For the colors supported by the arguments
 #' \code{Vcolor}, \code{VBcolor}, \code{VLcolor}, \code{pEcolor}, and
-#' \code{nEcolor} see \url{https://stat.columbia.edu/~tzheng/files/Rcolor.pdf}.
+#' \code{nEcolor} see \url{https://www.nceas.ucsb.edu/sites/default/files/2020-04/colorPaletteCheatsheet.pdf}.
 #'
 #' @param M (Possibly sparsified) precision \code{matrix}
 #' @param type A \code{character} indicating the type of graph to be produced.
@@ -4482,7 +4482,7 @@ GGMnetworkStats <- function(sparseP, as.table = FALSE){
 #' TRUE}. If \code{prune = TRUE} the vertices of degree 0 (vertices not
 #' implicated by any edge) are removed. For the colors supported by the
 #' arguments \code{nodecol}, \code{Vcolor}, and \code{VBcolor}, see
-#' \url{https://stat.columbia.edu/~tzheng/files/Rcolor.pdf}.
+#' \url{https://www.nceas.ucsb.edu/sites/default/files/2020-04/colorPaletteCheatsheet.pdf}.
 #'
 #' @param P0 Sparse (possibly standardized) precision matrix.
 #' @param node1 A \code{numeric} specifying an endpoint. The numeric should