Increment version to 2.6.0; update NEWS

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: pedtools
 Title: Creating and Working with Pedigrees and Marker Data
-Version: 2.5.0.9000
+Version: 2.6.0
 Authors@R: 
     person("Magnus Dehli", "Vigeland", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9134-4962"))

NEWS.md

@@ -1,22 +1,24 @@
-# dev
+# pedtools 2.6.0
+
+This is a large release with several new features, including a few (relatively minor) breaking changes.
 
 ## Breaking changes
 
-* In pedigree plots, Long labels are now automatically folded to an approximate width of 12 characters by default. Use the new argument `foldLabs` to adjust the folding width, or to switch off folding (`foldLabs = FALSE`).
+* In pedigree plots, long labels are now automatically folded to an approximate width of 12 characters by default. Use the new argument `foldLabs` to adjust the folding width, or to switch off folding (`foldLabs = FALSE`).
 
-* When adding children or parents to a pedigree, the default labelling of new individuals has been simplified. The new labels are now always the smallest integers not already in use. (Previous versions used "NN_1", "NN_2", etc for pedigrees with nonnumeric labels.)
+* When adding children or parents to a pedigree, the default labelling of new individuals has been simplified. The new labels are now always the smallest integers not already in use. (Previous versions used "NN_1", "NN_2", etc for pedigrees with non-numeric labels.)
 
 * `labels(x)` now always returns a character vector, also when `x` is a list of pedigrees. Use `labels(x, unlist = FALSE)` to retain the old behaviour.
 
 ## New features
 
-* `addChildren(x, ...)` and friends now works across components of `x`, when `x` is a list of pedigrees. For instance: `singletons(1:2, sex = 1:2) |> addSon(1:2)`.
+* `addChildren(x, ...)`, and its companions `addSon()` and `addDaughter()`, now works across components of `x`, when `x` is a list of pedigrees. For instance, this now works as expected: `singletons(1:2, sex = 1:2) |> addSon(1:2)`.
 
 * New function `addChild()` is similar to `addSon()` and `addDaughter()`, but allows the sex to be set programmatically, also to `sex = 0`.
 
 * `plot.ped()` gains argument `textAnnot` allowing highly customisable text annotations around and inside pedigree symbols.
 
-* `ancestors()`, `descendants()`, `commonAncestors()` and `commonDescendants()` gain a new argument `maxGen` indicating to limit the analysis to a given number of generations.
+* `ancestors()`, `descendants()`, `commonAncestors()` and `commonDescendants()` gain a new argument `maxGen` limiting the analysis to the given number of generations.
 
 * `transferMarkers()` gains the argument `checkAttrs` for checking consistency of marker attributes across pedigree components.
 

R/ped_utils.R

@@ -375,7 +375,7 @@ generateLabs = function(x, n = 1, avoid = NULL, prefix = "") {
   .mysetdiff(cand, taken)[seq_len(n)]
 }
 
-# TODO: Delete?
+# TODO: Delete - no longer used. Replaced by generateLabs
 # Utility function for generating numbered "NN" labels.
 # Returns "NN_i" where i increments largest j occurring as NN_j, NN.j or NN-j in input.
 nextNN = function(labs) { # labs a character vector

R/utils.R

@@ -142,8 +142,8 @@ listIdentical = function(x) {
 
 
 # Fold a single string at roughly the given width; try to break at nice places
-# TODO: Not optimised (and probably reinventing the wheel here).
-# Better idea: Start with strsplit(s, "")
+# Not optimised, and probably reinventing the wheel here.
+# Perhaps better idea: Start with strsplit(s, "")
 smartfold = function(s, width = 10, breakAt = c(' ', '-', '.', ':', ')', ']')) {
   width = as.integer(max(width, 2))
   nch = nchar(s)
@@ -153,7 +153,7 @@ smartfold = function(s, width = 10, breakAt = c(' ', '-', '.', ':', ')', ']')) {
   res = character(0)
   remaining = s
   while(nch >= width + 3) {
-    b = width # default next brea, if no better
+    b = width # default next break, if no better
     for (ch in breakAt) {
       pos = gregexpr(ch, remaining, fixed = TRUE)[[1]] |> as.integer() # all positions
       goodpos = pos[pos >= width - 2 & pos <= width + 3 & pos <= nch - 3]