Deprecations

NAMESPACE

@@ -51,8 +51,6 @@ S3method(DropTip,Splits)
 S3method(DropTip,list)
 S3method(DropTip,multiPhylo)
 S3method(DropTip,phylo)
-S3method(EnforceOutgroup,character)
-S3method(EnforceOutgroup,phylo)
 S3method(KeepTip,"NULL")
 S3method(KeepTip,Splits)
 S3method(KeepTip,list)
@@ -264,7 +262,6 @@ export(AddTip)
 export(AddTipEverywhere)
 export(AddUnconstrained)
 export(AllAncestors)
-export(AllDescendantEdges)
 export(AllTipLabels)
 export(AncestorEdge)
 export(ApePostorder)
@@ -293,7 +290,6 @@ export(DropTipPhylo)
 export(EdgeAncestry)
 export(EdgeDistances)
 export(EndSentence)
-export(EnforceOutgroup)
 export(ExtractTaxa)
 export(Hamming)
 export(IC1Spr)
@@ -375,8 +371,6 @@ export(PhyDatToMatrix)
 export(PhyDatToString)
 export(PhyToString)
 export(PhydatToString)
-export(PhylogeneticInfo)
-export(PhylogeneticInformation)
 export(PolarizeSplits)
 export(Postorder)
 export(PostorderOrder)
@@ -411,7 +405,6 @@ export(SampleOne)
 export(SingleTaxonTree)
 export(SisterSize)
 export(SortTree)
-export(SpectrumLegend)
 export(SplitConflicts)
 export(SplitConsistent)
 export(SplitFrequency)
@@ -476,7 +469,6 @@ importFrom(RCurl,url.exists)
 importFrom(Rdpack,reprompt)
 importFrom(ape,all.equal.phylo)
 importFrom(ape,as.phylo)
-importFrom(ape,bind.tree)
 importFrom(ape,cophenetic.phylo)
 importFrom(ape,edgelabels)
 importFrom(ape,is.rooted)
@@ -495,10 +487,6 @@ importFrom(grDevices,rgb)
 importFrom(graphics,legend)
 importFrom(graphics,lines)
 importFrom(graphics,par)
-importFrom(graphics,segments)
-importFrom(graphics,strheight)
-importFrom(graphics,strwidth)
-importFrom(graphics,text)
 importFrom(methods,new)
 importFrom(methods,setClass)
 importFrom(methods,setMethod)

NEWS.md

@@ -7,7 +7,9 @@
 - Require R 3.6
 - Remove R.cache dependency: `UnrootedKeys()` now uses a native cache implementation.
 - Remove deprecated functions `TreeSplits()`, `ForestSplits()`, `SplitNumber()`,
-  `in.Splits()`.
+  `in.Splits()`, `AllDescendantEdges()`, `PhylogeneticInfo()`,
+  `.EnforceOutgroup()`, `SpectrumLegend()`.
+- Remove deprecated C++ macro `TREETOOLS_SPLITLIST_INIT`.
 
 
 # TreeTools 1.16.1 (2025-08-24) #

R/RoguePlot.R

@@ -247,7 +247,7 @@ RoguePlot <- function(trees, tip, p = 1, plot = TRUE,
                              fat, thin),
          ...)
     if (legend != "none") {
-      PlotTools::SpectrumLegend(
+      SpectrumLegend(
         legend,
         bty = "n",
         palette = pal,

R/helper_functions.R

@@ -98,92 +98,3 @@ replicate64 <- function(n, expr, simplify = "array") {
   sapply64(integer(n), eval.parent(substitute(function(...) expr)),
            simplify = simplify)
 }
-
-#nocov start
-#' Produce a legend for continuous gradient scales
-#' 
-#' Prints an annotated vertical bar coloured according to a continuous palette.
-#' 
-#' This function is now deprecated; it has been superseded by the more capable
-#' [`PlotTools::SpectrumLegend()`] and will be removed in a future release.
-# Deprecation notice added in TreeTools 1.9.2 (2023-04-25)
-#' 
-#' @param x0,y0,x1,y1 Coordinates of the bottom-left and top-right end of the
-#' bar.
-#' @param absolute Logical specifying whether `x` and `y` values denote
-#' coordinates (`TRUE`) or relative position, where (0, 0) denotes the
-#' bottom-left of the plot area and (1, 1) the top right.
-#' @param legend Character vector with which to label points on `palette`.
-#' @param palette Colour palette to depict.
-#' @param lwd,lty,lend Additional parameters to [`segments()`],
-#' controlling line style.
-#' @param cex Character expansion factor relative to current `par("cex")`.
-#' @param text.col Colour used for the legend text.
-#' @param font,text.font Font used for the legend text; see [`text()`].
-#' @param title Text to display 
-#' @param title.col Colour for title; defaults to `text.col[1]`.
-#' @param title.cex Expansion factor(s) for the title, defaults to `cex[1]`.
-#' @param title.adj Horizontal adjustment for title: see the help for
-#' `par("adj")`.
-#' @param title.font Font used for the legend title.
-#' @param pos,\dots Additional parameters to [`text()`].
-#' 
-#' @template MRS
-#' @importFrom graphics segments strheight strwidth text
-#' @keywords internal
-#' @export
-SpectrumLegend <- function(x0 = 0.05, y0 = 0.05,
-                           x1 = x0, y1 = y0 + 0.2,
-                           absolute = FALSE,
-                           legend = character(0), palette,
-                           lwd = 4, lty = 1, lend = "square", cex = 1,
-                           text.col = par("col"),
-                           font = NULL, text.font = font,
-                           title = NULL, title.col = text.col[1], 
-                           title.cex = cex[1], title.adj = 0.5, title.font = 2,
-                           pos = 4,
-                           ...) {
-
-  .Deprecated("PlotTools::SpectrumLegend", package = "PlotTools")
-
-  nCol <- length(palette)
-
-  if (!absolute) {
-    corners <- par("usr") # x0 x1 y0 y1
-    xRange <- corners[2] - corners[1]
-    yRange <- corners[4] - corners[3]
-
-    # Order is important: lazy evaluation will set x1 = modified x0
-    x1 <- corners[1] + (x1 * xRange)
-    x0 <- corners[1] + (x0 * xRange)
-    y1 <- corners[3] + (y1 * yRange)
-    y0 <- corners[3] + (y0 * yRange)
-  }
-
-  segX <- x0 + ((x1 - x0) * 0:nCol / nCol)
-  segY <- y0 + ((y1 - y0) * 0:nCol / nCol)
-
-  nPlus1 <- nCol + 1L
-  segments(segX[-nPlus1], segY[-nPlus1],
-           segX[-1], segY[-1],
-           col = palette,
-           lwd = lwd, lty = lty, lend = lend)
-  text(seq(x0, x1, length.out = length(legend)),
-       seq(y0, y1, length.out = length(legend)),
-       col = text.col,
-       cex = cex,
-       font = text.font,
-       legend, pos = pos, ...)
-  if (!is.null(title)) {
-    text(mean(x0, x1) + (max(strwidth(legend)) / ifelse(pos == 2, -2, 2)),
-         max(y0, y1) + prod(
-           par("lheight"),
-           strheight("")
-         ),
-         title,
-         pos = 3,
-         cex = title.cex, adj = title.adj, font = title.font, col = title.col,
-         ...)
-  }
-}
-#nocov end

R/match.R

@@ -6,9 +6,6 @@
 #' a logical vector indicating whether there is a match or not for each
 #' split in its left operand.
 #'
-#' `in.Splits()` is an alias for `%in%`, included for backwards compatibility.
-#' It is deprecated and will be removed in a future release.
-#'
 #' @param x,table Object of class `Splits`.
 #' @param nomatch Integer value that will be used in place of `NA` in the case
 #' where no match is found.

R/tree_descendants.R

@@ -100,19 +100,6 @@ DescendantTips <- function(parent, child, edge = NULL,
   }
 }
 
-#' @rdname DescendantEdges
-#'
-#' @return `AllDescendantEdges()` is deprecated; use `DescendantEdges()`
-#' instead.
-#' It returns a matrix of class logical, with row _N_ specifying whether each
-#' edge is a descendant of edge _N_ (or the edge itself).
-#'
-#' @export
-AllDescendantEdges <- function(parent, child, nEdge = length(parent)) {
-  .Deprecated("DescendantEdges")
-  .AllDescendantEdges(parent, child, nEdge)
-}
-
 .AllDescendantEdges <- function(parent, child, nEdge = length(parent)) {
   ret <- diag(nEdge) == 1
   blankLogical <- logical(nEdge)

R/tree_generation.R

@@ -482,75 +482,7 @@ ConstrainedNJ <- function(dataset, constraint, weight = 1L,
   tree
 }
 
-#nocov begin
-#' Generate a tree with a specified outgroup
-#'
-#' **Deprecated.** This function will be removed in a future version of
-#' \pkg{TreeTools}.
-#' Use `RootTree()` instead.
-#'
-#' Given a tree or a list of taxa, `EnforceOutgroup()` rearranged the ingroup
-#' and outgroup taxa such that the two are sister taxa across the root, without
-#' changing the relationships within the ingroup or within the outgroup.
-#'
-#' @param tree Either a tree of class \code{phylo}; or (for `EnforceOutgroup()`)
-#' a character vector listing the names of all the taxa in the tree, from which
-#' a random tree will be generated.
-#' @param outgroup Character vector containing the names of taxa to include in
-#' the outgroup.
-#'
-#' @return `EnforceOutgroup()` returned a tree of class `phylo` where all
-#' outgroup taxa are sister to all remaining taxa, without modifying the
-#' ingroup topology.
-#'
-# @examples
-# tree <- EnforceOutgroup(letters[1:9], letters[1:3])
-# plot(tree)
-#
-#' @seealso For a more robust implementation, see [`RootTree()`], which will
-#' eventually replace this function
-#' ([#30](https://github.com/ms609/TreeTools/issues/30)).
-#'
-#' @template MRS
-#' @family tree manipulation
-#' @export
-EnforceOutgroup <- function(tree, outgroup) UseMethod("EnforceOutgroup")
-
-#' @importFrom ape bind.tree
-.EnforceOutgroup <- function(tree, outgroup, taxa) {
-  .Deprecated("RootTree")
-  if (length(outgroup) == 1L) {
-    return(RootTree(tree, outgroup))
-  }
-
-  ingroup <- taxa[!(taxa %fin% outgroup)]
-  if (!all(outgroup %fin% taxa) ||
-      length(ingroup) + length(outgroup) != length(taxa)) {
-    stop("All outgroup taxa must occur in tree")
-  }
-
-  ingroup.branch <- DropTip(tree, outgroup)
-  outgroup.branch <- DropTip(tree, ingroup)
-
-  result <- RootTree(bind.tree(outgroup.branch, ingroup.branch, 0, 1),
-                     outgroup)
-  RenumberTips(Renumber(result), taxa)
-}
-
-#' @rdname EnforceOutgroup
-#' @export
-EnforceOutgroup.phylo <- function(tree, outgroup) {
-  .EnforceOutgroup(tree, outgroup, tree[["tip.label"]])
-}
-
-#' @rdname EnforceOutgroup
-#' @export
-EnforceOutgroup.character <- function(tree, outgroup) {
-  taxa <- tree
-  .EnforceOutgroup(RandomTree(taxa, taxa[1]), outgroup, taxa)
-}
-#nocov end
-
+# Wrap an edge matrix as a tree in preorder
 .PreorderTree <- function(edge,
                           tip.label,
                           Nnode =  dim(edge)[[1]] + 1 - length(tip.label)) {

R/tree_information.R

@@ -78,13 +78,6 @@ Log2TreesMatchingTree <- function(tree) {
 #' @export
 CladisticInfo <- function(x) UseMethod("CladisticInfo")
 
-#' @rdname CladisticInfo
-#' @export
-PhylogeneticInfo <- function(x) {                                               # nocov start
-  .Deprecated("CladisticInfo()")
-  UseMethod("CladisticInfo")
-}                                                                               # nocov end
-
 #' @rdname CladisticInfo
 #' @export
 CladisticInfo.phylo <- function(x) {
@@ -105,10 +98,6 @@ CladisticInfo.list <- function(x) vapply(x, CladisticInfo, 0)
 #' @export
 CladisticInfo.multiPhylo <- CladisticInfo.list
 
-
-#' @rdname CladisticInfo
-#' @export
-PhylogeneticInformation <- PhylogeneticInfo
 #' @rdname CladisticInfo
 #' @export
 CladisticInformation <- CladisticInfo

R/tree_numbering.R

@@ -74,12 +74,11 @@ RenumberTree <- function(parent, child, weight) {
 
 #' @rdname Reorder
 #'
-#' @param \dots Deprecated; included for compatibility with previous versions.
 #' @return `RenumberEdges()` formats the output of `RenumberTree()` into a list
 #' whose two entries correspond to the new parent and child vectors,
 #' in preorder.
 #' @export
-RenumberEdges <- function(parent, child, ...) {
+RenumberEdges <- function(parent, child) {
   oenn <- .Call(`_TreeTools_preorder_edges_and_nodes`, parent, child)
 
   # Return:

R/tree_shape.R

@@ -237,7 +237,7 @@ UnrootedTreeKey <- function(tree, asInteger = FALSE) {
 .unrooted_keys_cache <- new.env(parent = emptyenv())
 
 #' @rdname TreeShape
-#' @param \dots Depreciated (2025-09); retained for backward compatibility.
+#' @param \dots Deprecated (2025-09); retained for backward compatibility.
 #' @return `UnrootedKeys()` returns a vector of integers corresponding to the
 #' keys (not shape numbers) of unrooted tree shapes with `nTip` tips.
 #' It is a wrapper to `.UnrootedKeys()`, with memoization, meaning that results

inst/include/TreeTools/SplitList.h

@@ -25,18 +25,6 @@ using splitbit = uint_fast64_t;
   splitbit(x(split, ((bin) * input_bins_per_bin) + (offset)))
 #define INBIN(r_bin, bin) ((INSUBBIN((bin), (r_bin))) << (R_BIN_SIZE * (r_bin)))
 
-// Retained for backward compatibility; not required since 1.15.0.9006
-#define TREETOOLS_SPLITLIST_INIT __attribute__((constructor))  \
-void _treetools_initialize_bitcounts() {                       \
-  for (int i = 65536; i--; ) {                                 \
-    int16 n_bits = 0;                                          \
-    for (int j = 16; j--; ) {                                  \
-      if (i & (1 << j)) n_bits += 1;                           \
-    }                                                          \
-    TreeTools::bitcounts[i] = n_bits;                          \
-  }                                                            \
-}                                                              \
-
 namespace TreeTools {
 
   constexpr int input_bins_per_bin = SL_BIN_SIZE / R_BIN_SIZE;