* 2015-06-27(Tal Galili) fix url |6b6bafd| 
|  inst/ignored/Introduction to dendextend.html | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-06-27(Tal Galili) fix dpi to get smaller vignettes |f53c729| 
|  vignettes/Cluster_Analysis.Rmd | 2 +-
|  vignettes/introduction.Rmd     | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2015-06-27(Tal Galili) fix: prune.hclust: no visible binding for global variable 'x' unbranch.hclust: no visible binding for global variable 'x' |30804af| 
|  R/prune.R    | 2 +-
|  R/unbranch.R | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-06-27(Tal Galili) updated for 1.0.0. |69c26b4| 
|  ChangeLog | 316 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  18 +++-
|  2 files changed, 333 insertions(+), 1 deletion(-)

* 2015-06-27(Tal Galili) update date |a85432c| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-06-27(Tal Galili) object -> dend  for: shuffle |ec62d71| 
|  NEWS           |  2 +-
|  R/untangle.R   | 30 +++++++++++++++---------------
|  man/shuffle.Rd | 12 ++++++------
|  3 files changed, 22 insertions(+), 22 deletions(-)

* 2015-06-27(Tal Galili) x -> dend  for: unbranch |541d5ef| 
|  NEWS            |  2 +-
|  R/unbranch.R    | 26 +++++++++++++-------------
|  man/unbranch.Rd | 10 +++++-----
|  3 files changed, 19 insertions(+), 19 deletions(-)

* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2  for: tanglegram |5517d9b| 
|  NEWS              |   2 +-
|  R/tanglegram.R    | 136 ++++++++++++++++++++++++++--------------------------
|  man/tanglegram.Rd |  14 +++---
|  3 files changed, 76 insertions(+), 76 deletions(-)

* 2015-06-27(Tal Galili) x -> dend  for: prune |8660626| 
|  NEWS              |  2 +-
|  R/prune.R         | 94 ++++++++++++++++++++++++++---------------------------
|  man/prune.Rd      | 12 +++----
|  man/prune_leaf.Rd |  4 +--
|  4 files changed, 56 insertions(+), 56 deletions(-)

* 2015-06-27(Tal Galili) intersect_trees x1/x2 -> dend1/dend2 |e87987d| 
|  NEWS                   |  3 +--
|  R/prune.R              | 22 +++++++++++-----------
|  man/intersect_trees.Rd |  6 +++---
|  3 files changed, 15 insertions(+), 16 deletions(-)

* 2015-06-27(Tal Galili) object -> dend  for: labels_colors |a306bb1| 
|  NEWS                 |  1 +
|  R/labels_colors.R    | 28 ++++++++++++++--------------
|  man/labels_colors.Rd |  6 +++---
|  3 files changed, 18 insertions(+), 17 deletions(-)

* 2015-06-27(Tal Galili) x -> dend  for: get_nodes_xy |3f50252| 
|  NEWS                | 2 +-
|  R/get_nodes_xy.R    | 6 ++++--
|  man/get_nodes_xy.Rd | 4 ++--
|  3 files changed, 7 insertions(+), 5 deletions(-)

* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2  for: untangle_random_search |9fa317f| 
|  NEWS                          |  2 +-
|  R/untangle.R                  | 32 ++++++++++++++++----------------
|  man/untangle_random_search.Rd |  6 +++---
|  3 files changed, 20 insertions(+), 20 deletions(-)

* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2  for: entanglement |5610519| 
|  NEWS                |  2 +-
|  R/entanglement.R    | 88 +++++++++++++++++++++++++--------------------------
|  man/entanglement.Rd | 14 ++++----
|  3 files changed, 52 insertions(+), 52 deletions(-)

* 2015-06-27(Tal Galili) y to dend2 |2e653c5| 
|  R/distinct_edges.R              | 34 +++++++++++++++++-----------------
|  man/dend_diff.Rd                |  4 ++--
|  man/distinct_edges.Rd           |  6 +++---
|  man/highlight_distinct_edges.Rd |  4 ++--
|  4 files changed, 24 insertions(+), 24 deletions(-)

* 2015-06-27(Tal Galili) x -> dend  for: dend_diff, dist.dendlist, distinct_edges, highlight_distinct_edges, partition_leaves |1da678e| 
|  NEWS                            |  2 +-
|  R/distinct_edges.R              | 94 +++++++++++++++++++--------------------
|  man/dend_diff.Rd                |  8 ++--
|  man/dist.dendlist.Rd            |  4 +-
|  man/distinct_edges.Rd           |  6 +--
|  man/highlight_distinct_edges.Rd | 10 ++---
|  man/partition_leaves.Rd         |  4 +-
|  7 files changed, 64 insertions(+), 64 deletions(-)

* 2015-06-27(Tal Galili) tree -> dend  for: cutree_1h.dendrogram, cutree_1k.dendrogram, heights_per_k.dendrogram |7ec15a4| 
|  NEWS                            |  2 +-
|  R/cutree.dendrogram.R           | 95 ++++++++++++++++++++-------------------
|  man/cutree_1h.dendrogram.Rd     |  6 +--
|  man/cutree_1k.dendrogram.Rd     |  4 +-
|  man/heights_per_k.dendrogram.Rd |  4 +-
|  5 files changed, 57 insertions(+), 54 deletions(-)

* 2015-06-27(Tal Galili) tree -> dend  for: dendextend_cut_lower_fun |d13b9c6| 
|  NEWS                 |  2 +-
|  R/cut_lower_fun.R    | 24 ++++++++++++------------
|  man/cut_lower_fun.Rd | 10 +++++-----
|  3 files changed, 18 insertions(+), 18 deletions(-)

* 2015-06-27(Tal Galili) tree1/tree2 -> dend1/dend2  for: cor_cophenetic |4c987d3| 
|  NEWS                  |  2 +-
|  R/cor_cophenetic.R    | 40 ++++++++++++++++++++--------------------
|  man/cor_cophenetic.Rd | 10 +++++-----
|  3 files changed, 26 insertions(+), 26 deletions(-)

* 2015-06-27(Tal Galili) cor_bakers_gamma: tree1/2 -> dend1/2 |9641738| 
|  NEWS                               |  2 +-
|  R/cor_bakers_gamma.R               | 76 ++++++++++++++++++------------------
|  man/bakers_gamma_for_2_k_matrix.Rd |  6 +--
|  man/cor_bakers_gamma.Rd            | 12 +++---
|  4 files changed, 48 insertions(+), 48 deletions(-)

* 2015-06-27(Tal Galili)       * x -> dend  for: cor.dendlist       * tree1/tree2 -> dend1/dend2  for: cor_FM_index, cor_common_nodes |b62be29| 
|  NEWS                    |  2 ++
|  R/cor.dendlist.R        | 38 +++++++++++++++++++-------------------
|  man/cor.dendlist.Rd     |  6 +++---
|  man/cor_FM_index.Rd     |  6 +++---
|  man/cor_common_nodes.Rd |  6 +++---
|  5 files changed, 30 insertions(+), 28 deletions(-)

* 2015-06-27(Tal Galili) bug fix (renaming object to dend) |952667f| 
|  R/branches_attr_by.R | 2 +-
|  R/distinct_edges.R   | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-06-27(Tal Galili) tree -> dend  for:                color_branches, color_labels_by_labels, color_labels, get_branches_heights, dendextend_get_branches_heights |7fd2a2c| 
|  NEWS                         |   2 +
|  R/attr_access.R              |  16 +++----
|  R/color_branches.R           | 100 ++++++++++++++++++++---------------------
|  R/set.dendrogram.R           |   6 +--
|  man/color_branches.Rd        |  10 ++---
|  man/color_labels.Rd          |   6 +--
|  man/get_branches_heights.Rd  |   4 +-
|  man/rank_order.dendrogram.Rd |   2 +-
|  8 files changed, 74 insertions(+), 72 deletions(-)

* 2015-06-27(Tal Galili) object -> dend  for: |95856ed| 
|  NEWS                                     |  13 +-
|  R/ape.R                                  |   1 +
|  R/attr_access.R                          | 194 ++++++++++++++---------------
|  inst/tests/test-attr_access.R            |   2 +-
|  man/assign_values_to_branches_edgePar.Rd |  12 +-
|  man/assign_values_to_leaves_edgePar.Rd   |  10 +-
|  man/assign_values_to_leaves_nodePar.Rd   |   6 +-
|  man/assign_values_to_nodes_nodePar.Rd    |   4 +-
|  man/get_leaves_attr.Rd                   |   4 +-
|  man/get_leaves_branches_attr.Rd          |   4 +-
|  man/get_leaves_branches_col.Rd           |   4 +-
|  man/get_leaves_edgePar.Rd                |   4 +-
|  man/get_leaves_nodePar.Rd                |   4 +-
|  man/get_nodes_attr.Rd                    |   4 +-
|  man/remove_branches_edgePar.Rd           |   4 +-
|  man/remove_leaves_nodePar.Rd             |   4 +-
|  man/remove_nodes_nodePar.Rd              |   4 +-
|  17 files changed, 145 insertions(+), 133 deletions(-)

* 2015-06-27(Tal Galili) roxygen 4.1.1 |b1723fe| 
|  NAMESPACE                                  | 2 +-
|  man/Bk.Rd                                  | 2 +-
|  man/Bk_permutations.Rd                     | 2 +-
|  man/Bk_plot.Rd                             | 2 +-
|  man/DendSer.dendrogram.Rd                  | 2 +-
|  man/FM_index.Rd                            | 2 +-
|  man/FM_index_R.Rd                          | 2 +-
|  man/FM_index_permutation.Rd                | 2 +-
|  man/FM_index_profdpm.Rd                    | 2 +-
|  man/all.equal.dendrogram.Rd                | 2 +-
|  man/all_couple_rotations_at_k.Rd           | 2 +-
|  man/all_unique.Rd                          | 2 +-
|  man/as.dendlist.Rd                         | 2 +-
|  man/as.phylo.dendrogram.Rd                 | 2 +-
|  man/as_hclust_fixed.Rd                     | 2 +-
|  man/assign_dendextend_options.Rd           | 2 +-
|  man/assign_values_to_branches_edgePar.Rd   | 2 +-
|  man/assign_values_to_leaves_edgePar.Rd     | 2 +-
|  man/assign_values_to_leaves_nodePar.Rd     | 2 +-
|  man/assign_values_to_nodes_nodePar.Rd      | 2 +-
|  man/bakers_gamma_for_2_k_matrix.Rd         | 2 +-
|  man/branches_attr_by_clusters.Rd           | 2 +-
|  man/branches_attr_by_labels.Rd             | 2 +-
|  man/click_rotate.Rd                        | 2 +-
|  man/collapse_branch.Rd                     | 2 +-
|  man/color_branches.Rd                      | 2 +-
|  man/color_labels.Rd                        | 2 +-
|  man/colored_bars.Rd                        | 2 +-
|  man/common_subtrees_clusters.Rd            | 2 +-
|  man/cor.dendlist.Rd                        | 2 +-
|  man/cor_FM_index.Rd                        | 2 +-
|  man/cor_bakers_gamma.Rd                    | 2 +-
|  man/cor_common_nodes.Rd                    | 2 +-
|  man/cor_cophenetic.Rd                      | 2 +-
|  man/count_terminal_nodes.Rd                | 2 +-
|  man/cut_lower_fun.Rd                       | 2 +-
|  man/cutree-methods.Rd                      | 2 +-
|  man/cutree_1h.dendrogram.Rd                | 2 +-
|  man/cutree_1k.dendrogram.Rd                | 2 +-
|  man/d3dendro_options.Rd                    | 2 +-
|  man/d3dendrogram.Rd                        | 2 +-
|  man/dend_diff.Rd                           | 2 +-
|  man/dendextend-package.Rd                  | 2 +-
|  man/dendextend_labels.dendrogram.Rd        | 2 +-
|  man/dendextend_options.Rd                  | 2 +-
|  man/dendlist.Rd                            | 2 +-
|  man/dist.dendlist.Rd                       | 2 +-
|  man/dist_long.Rd                           | 2 +-
|  man/distinct_edges.Rd                      | 2 +-
|  man/duplicate_leaf.Rd                      | 2 +-
|  man/entanglement.Rd                        | 2 +-
|  man/fac2num.Rd                             | 2 +-
|  man/fix_members_attr.dendrogram.Rd         | 2 +-
|  man/flatten.dendrogram.Rd                  | 2 +-
|  man/flip_leaves.Rd                         | 2 +-
|  man/get_branches_heights.Rd                | 2 +-
|  man/get_childrens_heights.Rd               | 2 +-
|  man/get_leaves_attr.Rd                     | 2 +-
|  man/get_leaves_branches_attr.Rd            | 2 +-
|  man/get_leaves_branches_col.Rd             | 2 +-
|  man/get_leaves_edgePar.Rd                  | 2 +-
|  man/get_leaves_nodePar.Rd                  | 2 +-
|  man/get_nodes_attr.Rd                      | 2 +-
|  man/get_nodes_xy.Rd                        | 2 +-
|  man/get_root_branches_attr.Rd              | 2 +-
|  man/ggdend.Rd                              | 2 +-
|  man/hang.dendrogram.Rd                     | 2 +-
|  man/heights_per_k.dendrogram.Rd            | 2 +-
|  man/highlight_distinct_edges.Rd            | 2 +-
|  man/identify.dendrogram.Rd                 | 2 +-
|  man/intersect_trees.Rd                     | 2 +-
|  man/is.dendlist.Rd                         | 2 +-
|  man/is.dendrogram.Rd                       | 2 +-
|  man/is.hclust.Rd                           | 2 +-
|  man/is.natural.number.Rd                   | 2 +-
|  man/is.phylo.Rd                            | 2 +-
|  man/is_null_list.Rd                        | 2 +-
|  man/khan.Rd                                | 2 +-
|  man/labels-assign.Rd                       | 2 +-
|  man/labels_colors.Rd                       | 2 +-
|  man/ladderize.Rd                           | 2 +-
|  man/leaf_Colors.Rd                         | 2 +-
|  man/lowest_common_branch.Rd                | 2 +-
|  man/match_order_by_labels.Rd               | 2 +-
|  man/match_order_dendrogram_by_old_order.Rd | 2 +-
|  man/na_locf.Rd                             | 2 +-
|  man/nleaves.Rd                             | 2 +-
|  man/nnodes.Rd                              | 2 +-
|  man/noded_with_condition.Rd                | 2 +-
|  man/order.dendrogram-assign.Rd             | 2 +-
|  man/order.hclust.Rd                        | 2 +-
|  man/partition_leaves.Rd                    | 2 +-
|  man/pipe.Rd                                | 2 +-
|  man/plot_horiz.dendrogram.Rd               | 2 +-
|  man/prune.Rd                               | 2 +-
|  man/prune_common_subtrees.dendlist.Rd      | 2 +-
|  man/prune_leaf.Rd                          | 2 +-
|  man/pvclust_show_signif.Rd                 | 2 +-
|  man/pvclust_show_signif_gradient.Rd        | 2 +-
|  man/raise.dendrogram.Rd                    | 2 +-
|  man/rank_branches.Rd                       | 2 +-
|  man/rank_order.dendrogram.Rd               | 2 +-
|  man/rank_values_with_clusters.Rd           | 2 +-
|  man/rect.dendrogram.Rd                     | 2 +-
|  man/remove_branches_edgePar.Rd             | 2 +-
|  man/remove_leaves_nodePar.Rd               | 2 +-
|  man/remove_nodes_nodePar.Rd                | 2 +-
|  man/rllply.Rd                              | 2 +-
|  man/rotate.Rd                              | 2 +-
|  man/rotate_DendSer.Rd                      | 2 +-
|  man/sample.dendrogram.Rd                   | 2 +-
|  man/shuffle.Rd                             | 2 +-
|  man/sort_2_clusters_vectors.Rd             | 2 +-
|  man/sort_dist_mat.Rd                       | 2 +-
|  man/sort_levels_values.Rd                  | 2 +-
|  man/tanglegram.Rd                          | 2 +-
|  man/theme_dendro.Rd                        | 2 +-
|  man/unbranch.Rd                            | 2 +-
|  man/unclass_dend.Rd                        | 2 +-
|  man/untangle.Rd                            | 2 +-
|  man/untangle_DendSer.Rd                    | 2 +-
|  man/untangle_random_search.Rd              | 2 +-
|  man/untangle_step_rotate_1side.Rd          | 2 +-
|  man/untangle_step_rotate_2side.Rd          | 2 +-
|  man/which_leaf.Rd                          | 2 +-
|  man/which_node.Rd                          | 2 +-
|  126 files changed, 126 insertions(+), 126 deletions(-)

* 2015-06-27(Tal Galili) object -> dend |8a2f94a| 
|  R/set.dendrogram.R | 80 ++++++++++++++++++++++++++--------------------------
|  man/set.Rd         | 16 +++++------
|  2 files changed, 48 insertions(+), 48 deletions(-)

* 2015-06-24(Tal Galili) Added d3heatmap example to vignette + as suggests to DESCRIPTION |f8a4926| 
|  DESCRIPTION                |  1 +
|  vignettes/introduction.Rmd | 33 ++++++++++++++++++++++++++++++++-
|  2 files changed, 33 insertions(+), 1 deletion(-)

* 2015-06-23(Tal Galili) moved assign_dendextend_options to ".onLoad" - this now allows the use of dendextend::some_func |bf35c68| 
|  DESCRIPTION            |  2 +-
|  NEWS                   |  3 ++-
|  R/dendextend_options.R | 45 +++++++++++++++++++++++++++++++++++++++++++--
|  R/zzz.R                | 17 ++++++++++++++---
|  vignettes/FAQ.Rmd      | 13 +++++++++++++
|  5 files changed, 73 insertions(+), 7 deletions(-)

* 2015-06-07(Tal Galili) Added VignetteIndexEntry information (and Sys.Date) |5adda4c| 
|  vignettes/Cluster_Analysis.Rmd | 6 +++++-
|  vignettes/FAQ.Rmd              | 5 +++++
|  vignettes/introduction.Rmd     | 1 +
|  3 files changed, 11 insertions(+), 1 deletion(-)

* 2015-06-07(Tal Galili) Update instructions on viewing the vignette |4ca1df8| 
|  R/zzz.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-06-06(Tal Galili) Better format. |89a8aee| 
|  README.md                                    |    2 +-
|  inst/ignored/Introduction to dendextend.html | 1218 ++++++++++++++++++++++++
|  inst/ignored/introduction.html               | 1218 ------------------------
|  vignettes/introduction.Rmd                   |    4 +-
|  4 files changed, 1221 insertions(+), 1221 deletions(-)

* 2015-06-06(Tal Galili) misc |b8c68cd| 
|  ChangeLog | 892 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  14 +-
|  2 files changed, 900 insertions(+), 6 deletions(-)

* 2015-06-06(Tal Galili) Fix "CRAN URL not in canonical form" |59b2397| 
|  DESCRIPTION                    |  2 +-
|  R/bk_method.R                  |  2 +-
|  R/colored_bars.R               |  2 +-
|  R/distinct_edges.R             |  2 +-
|  R/ggdendro.R                   |  2 +-
|  R/magrittr.R                   |  4 ++--
|  R/pvclust.R                    |  2 +-
|  README.md                      |  2 +-
|  inst/ignored/introduction.html | 12 ++++++------
|  man/colored_bars.Rd            |  2 +-
|  vignettes/introduction.Rmd     | 12 ++++++------
|  11 files changed, 22 insertions(+), 22 deletions(-)

* 2015-06-06(Tal Galili) Fix " \usage lines wider than 90 characters:" |36a9a84| 
|  R/cor_cophenetic.R    | 4 +++-
|  man/cor_cophenetic.Rd | 4 +++-
|  2 files changed, 6 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) Fix doc problems in cor_cophenetic |f2cd040| 
|  R/cor_cophenetic.R    | 4 ++--
|  man/cor_cophenetic.Rd | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2015-06-06(Tal Galili) Fix cor_cophenetic.dendlist method |35ce2ce| 
|  R/cor_cophenetic.R | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) Updated html with the khan analysis |19ca6e7| 
|  ...ts - enhanced with the dendextend package.html | 80 +++++++++++++++++++--
|  1 file changed, 76 insertions(+), 4 deletions(-)

* 2015-06-06(Tal Galili) Added the "khan" dataset analysis. |02db42c| 
|  NEWS                           |   2 +-
|  vignettes/Cluster_Analysis.Rmd | 128 +++++++++++++++++++++++++++++++++++++++
|  2 files changed, 129 insertions(+), 1 deletion(-)

* 2015-06-06(Tal Galili) Added nleaves.dendlist |5ef24b1| 
|  NAMESPACE      |  1 +
|  NEWS           |  1 +
|  R/nleaves.R    | 13 ++++++++++++-
|  man/nleaves.Rd |  5 ++++-
|  4 files changed, 18 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) added - prune_common_subtrees.dendlist - Prune trees to their common subtrees |86b8eb9| 
|  NAMESPACE                             |  1 +
|  NEWS                                  |  2 +-
|  R/prune.R                             | 33 +++++++++++++++++++++++++++++++++
|  man/prune_common_subtrees.dendlist.Rd | 27 +++++++++++++++++++++++++++
|  4 files changed, 62 insertions(+), 1 deletion(-)

* 2015-06-06(Tal Galili) cor_cophenetic - changed method to method_coef (so it could be updated when using cor.dendlist) |f2bd51b| 
|  NEWS                  |  2 +-
|  R/cor_cophenetic.R    | 10 +++++-----
|  man/cor_cophenetic.Rd |  2 +-
|  3 files changed, 7 insertions(+), 7 deletions(-)

* 2015-06-06(Tal Galili) untangle now has a new "labels" method, and it is now the default. |712bcd6| 
|  NEWS            |  1 +
|  R/untangle.R    | 21 ++++++++++++++++-----
|  man/untangle.Rd |  4 ++--
|  3 files changed, 19 insertions(+), 7 deletions(-)

* 2015-06-06(Tal Galili) clean code a bit from comments |becc43e| 
|  R/untangle.R | 557 ++++++++++++++++++++++++++++-----------------------------
|  1 file changed, 273 insertions(+), 284 deletions(-)

* 2015-06-06(Tal Galili) Adding Bk_plot to see also of Bk |674a498| 
|  R/bk_method.R | 2 +-
|  man/Bk.Rd     | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) Generated by roxygen2 (4.1.1.9000) |7acec1b| 
|  NAMESPACE                                  | 2 +-
|  man/Bk.Rd                                  | 2 +-
|  man/Bk_permutations.Rd                     | 2 +-
|  man/Bk_plot.Rd                             | 2 +-
|  man/DendSer.dendrogram.Rd                  | 2 +-
|  man/FM_index.Rd                            | 2 +-
|  man/FM_index_R.Rd                          | 2 +-
|  man/FM_index_permutation.Rd                | 2 +-
|  man/FM_index_profdpm.Rd                    | 2 +-
|  man/all.equal.dendrogram.Rd                | 2 +-
|  man/all_couple_rotations_at_k.Rd           | 2 +-
|  man/all_unique.Rd                          | 2 +-
|  man/as.dendlist.Rd                         | 2 +-
|  man/as.phylo.dendrogram.Rd                 | 2 +-
|  man/as_hclust_fixed.Rd                     | 2 +-
|  man/assign_dendextend_options.Rd           | 2 +-
|  man/assign_values_to_branches_edgePar.Rd   | 2 +-
|  man/assign_values_to_leaves_edgePar.Rd     | 2 +-
|  man/assign_values_to_leaves_nodePar.Rd     | 2 +-
|  man/assign_values_to_nodes_nodePar.Rd      | 2 +-
|  man/bakers_gamma_for_2_k_matrix.Rd         | 2 +-
|  man/branches_attr_by_clusters.Rd           | 2 +-
|  man/branches_attr_by_labels.Rd             | 2 +-
|  man/click_rotate.Rd                        | 2 +-
|  man/collapse_branch.Rd                     | 2 +-
|  man/color_branches.Rd                      | 2 +-
|  man/color_labels.Rd                        | 2 +-
|  man/colored_bars.Rd                        | 2 +-
|  man/common_subtrees_clusters.Rd            | 2 +-
|  man/cor.dendlist.Rd                        | 2 +-
|  man/cor_FM_index.Rd                        | 2 +-
|  man/cor_bakers_gamma.Rd                    | 2 +-
|  man/cor_common_nodes.Rd                    | 2 +-
|  man/cor_cophenetic.Rd                      | 2 +-
|  man/count_terminal_nodes.Rd                | 2 +-
|  man/cut_lower_fun.Rd                       | 2 +-
|  man/cutree-methods.Rd                      | 2 +-
|  man/cutree_1h.dendrogram.Rd                | 2 +-
|  man/cutree_1k.dendrogram.Rd                | 2 +-
|  man/d3dendro_options.Rd                    | 2 +-
|  man/d3dendrogram.Rd                        | 2 +-
|  man/dend_diff.Rd                           | 2 +-
|  man/dendextend-package.Rd                  | 2 +-
|  man/dendextend_labels.dendrogram.Rd        | 2 +-
|  man/dendextend_options.Rd                  | 2 +-
|  man/dendlist.Rd                            | 2 +-
|  man/dist.dendlist.Rd                       | 2 +-
|  man/dist_long.Rd                           | 2 +-
|  man/distinct_edges.Rd                      | 2 +-
|  man/duplicate_leaf.Rd                      | 2 +-
|  man/entanglement.Rd                        | 2 +-
|  man/fac2num.Rd                             | 2 +-
|  man/fix_members_attr.dendrogram.Rd         | 2 +-
|  man/flatten.dendrogram.Rd                  | 2 +-
|  man/flip_leaves.Rd                         | 2 +-
|  man/get_branches_heights.Rd                | 2 +-
|  man/get_childrens_heights.Rd               | 2 +-
|  man/get_leaves_attr.Rd                     | 2 +-
|  man/get_leaves_branches_attr.Rd            | 2 +-
|  man/get_leaves_branches_col.Rd             | 2 +-
|  man/get_leaves_edgePar.Rd                  | 2 +-
|  man/get_leaves_nodePar.Rd                  | 2 +-
|  man/get_nodes_attr.Rd                      | 2 +-
|  man/get_nodes_xy.Rd                        | 2 +-
|  man/get_root_branches_attr.Rd              | 2 +-
|  man/ggdend.Rd                              | 2 +-
|  man/hang.dendrogram.Rd                     | 2 +-
|  man/heights_per_k.dendrogram.Rd            | 2 +-
|  man/highlight_distinct_edges.Rd            | 2 +-
|  man/identify.dendrogram.Rd                 | 2 +-
|  man/intersect_trees.Rd                     | 2 +-
|  man/is.dendlist.Rd                         | 2 +-
|  man/is.dendrogram.Rd                       | 2 +-
|  man/is.hclust.Rd                           | 2 +-
|  man/is.natural.number.Rd                   | 2 +-
|  man/is.phylo.Rd                            | 2 +-
|  man/is_null_list.Rd                        | 2 +-
|  man/labels-assign.Rd                       | 2 +-
|  man/labels_colors.Rd                       | 2 +-
|  man/ladderize.Rd                           | 2 +-
|  man/leaf_Colors.Rd                         | 2 +-
|  man/lowest_common_branch.Rd                | 2 +-
|  man/match_order_by_labels.Rd               | 2 +-
|  man/match_order_dendrogram_by_old_order.Rd | 2 +-
|  man/na_locf.Rd                             | 2 +-
|  man/nleaves.Rd                             | 2 +-
|  man/nnodes.Rd                              | 2 +-
|  man/noded_with_condition.Rd                | 2 +-
|  man/order.dendrogram-assign.Rd             | 2 +-
|  man/order.hclust.Rd                        | 2 +-
|  man/partition_leaves.Rd                    | 2 +-
|  man/pipe.Rd                                | 2 +-
|  man/plot_horiz.dendrogram.Rd               | 2 +-
|  man/prune.Rd                               | 2 +-
|  man/prune_leaf.Rd                          | 2 +-
|  man/pvclust_show_signif.Rd                 | 2 +-
|  man/pvclust_show_signif_gradient.Rd        | 2 +-
|  man/raise.dendrogram.Rd                    | 2 +-
|  man/rank_branches.Rd                       | 2 +-
|  man/rank_order.dendrogram.Rd               | 2 +-
|  man/rank_values_with_clusters.Rd           | 2 +-
|  man/rect.dendrogram.Rd                     | 2 +-
|  man/remove_branches_edgePar.Rd             | 2 +-
|  man/remove_leaves_nodePar.Rd               | 2 +-
|  man/remove_nodes_nodePar.Rd                | 2 +-
|  man/rllply.Rd                              | 2 +-
|  man/rotate.Rd                              | 2 +-
|  man/rotate_DendSer.Rd                      | 2 +-
|  man/sample.dendrogram.Rd                   | 2 +-
|  man/set.Rd                                 | 2 +-
|  man/shuffle.Rd                             | 2 +-
|  man/sort_2_clusters_vectors.Rd             | 2 +-
|  man/sort_dist_mat.Rd                       | 2 +-
|  man/sort_levels_values.Rd                  | 2 +-
|  man/tanglegram.Rd                          | 2 +-
|  man/theme_dendro.Rd                        | 2 +-
|  man/unbranch.Rd                            | 2 +-
|  man/unclass_dend.Rd                        | 2 +-
|  man/untangle.Rd                            | 2 +-
|  man/untangle_DendSer.Rd                    | 2 +-
|  man/untangle_random_search.Rd              | 2 +-
|  man/untangle_step_rotate_1side.Rd          | 2 +-
|  man/untangle_step_rotate_2side.Rd          | 2 +-
|  man/which_leaf.Rd                          | 2 +-
|  man/which_node.Rd                          | 2 +-
|  125 files changed, 125 insertions(+), 125 deletions(-)

* 2015-06-06(Tal Galili) Adding the khan dataset to the package. |56baf12| 
|  DESCRIPTION   |   3 +-
|  NEWS          |   6 ++--
|  R/data.R      | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  data/khan.rda | Bin 0 -> 114677 bytes
|  man/khan.Rd   |  80 +++++++++++++++++++++++++++++++++++++++++++
|  5 files changed, 189 insertions(+), 4 deletions(-)

* 2015-06-06(Tal Galili) more links |e14dc3a| 
|  README.md | 6 ++----
|  1 file changed, 2 insertions(+), 4 deletions(-)

* 2015-06-06(Tal Galili) update links to the newer vignettes |b56e833| 
|  README.md                      |  6 ++++--
|  vignettes/Cluster_Analysis.Rmd | 14 ++++++++++++++
|  2 files changed, 18 insertions(+), 2 deletions(-)

* 2015-06-06(Tal Galili) got "codecov.io" to work. |a4e4443| 
|  README.md | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-06-05(Tal Galili) adding covr (to try to get some code coverage) |112fca3| 
|  DESCRIPTION | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2015-06-05(Tal Galili) update travis.yml - Change lang to r (and some more things), and see if it still works. |21e5d93| 
|  .travis.yml | 31 ++++++-------------------------
|  1 file changed, 6 insertions(+), 25 deletions(-)

* 2015-05-24(Tal Galili) Date |e9dfd54| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-05-24(Tal Galili) Update news since version 0.18.3 |424cd2b| 
|  NEWS.md | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 105 insertions(+)

* 2015-05-24(Tal Galili) fix typos |7cb02c6| 
|  vignettes/introduction.Rmd | 12 ++++++------
|  1 file changed, 6 insertions(+), 6 deletions(-)

* 2015-05-24(Tal Galili) updated vignettes to have smaller dpi (so that the file sizes will be more reasonable) |39e3c21| 
|  vignettes/Cluster_Analysis.Rmd |  6 +++---
|  vignettes/FAQ.Rmd              | 15 +++++++++++++++
|  vignettes/introduction.Rmd     |  8 ++++----
|  3 files changed, 22 insertions(+), 7 deletions(-)

* 2015-05-24(Tal Galili) html versions of the vignettes |a2204c5| 
|  inst/ignored/Frequantly asked questions.html      | 325 +++++++++++
|  ...ts - enhanced with the dendextend package.html | 574 ++++++++++++++++++++
|  inst/ignored/introduction.html                    | 412 ++++----------
|  3 files changed, 1014 insertions(+), 297 deletions(-)

* 2015-05-24(Tal Galili) misc |4718cb5| 
|  vignettes/Cluster_Analysis.Rmd | 1 +
|  1 file changed, 1 insertion(+)

* 2015-05-24(Tal Galili) Fix typos |6334236| 
|  vignettes/Cluster_Analysis.Rmd | 24 ++++++++++++------------
|  1 file changed, 12 insertions(+), 12 deletions(-)

* 2015-05-24(Tal Galili) Added "animals - Attributes of Animals" section to cluster_analysis.Rmd |5dd94fc| 
|  NEWS                           |   1 +
|  vignettes/Cluster_Analysis.Rmd | 115 +++++++++++++++++++++++++++++++++++++++
|  2 files changed, 116 insertions(+)

* 2015-05-24(Tal Galili) cor_FM_index - Correlation of FM_index for some k (similar to Bk actually). This is added to cor.dendlist |58eeedc| 
|  NAMESPACE           |  1 +
|  NEWS                |  3 +++
|  R/cor.dendlist.R    | 59 +++++++++++++++++++++++++++++++++++++++++++++------
|  man/cor.dendlist.Rd | 10 +++++----
|  man/cor_FM_index.Rd | 39 ++++++++++++++++++++++++++++++++++
|  5 files changed, 101 insertions(+), 11 deletions(-)

* 2015-05-24(Tal Galili) added "cluster" as suggest |b6b1d35| 
|  DESCRIPTION | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) Vignette - added the votes.repub analysis (Votes for Republican Candidate in Presidential Elections) |9ddce80| 
|  vignettes/Cluster_Analysis.Rmd | 205 ++++++++++++++++++++++++++++++++++++++-
|  1 file changed, 200 insertions(+), 5 deletions(-)

* 2015-05-24(Tal Galili) exclude any cache folder in vignette or git |fbd747b| 
|  .Rbuildignore | 1 +
|  .gitignore    | 2 +-
|  2 files changed, 2 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) remove un-needed new line (cat("\n")) |062c9c4| 
|  inst/tests/test-distinct_edges.R | 2 +-
|  inst/tests/test-entanglement.R   | 2 +-
|  inst/tests/test-ggdend.R         | 2 +-
|  3 files changed, 3 insertions(+), 3 deletions(-)

* 2015-05-24(Tal Galili) added a link to cor_common_nodes from cor.dendlist |4844174| 
|  R/cor.dendlist.R    | 3 ++-
|  man/cor.dendlist.Rd | 3 ++-
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2015-05-24(Tal Galili) untangle_random_search/untangle_step_rotate_2side/untangle_best_k_to_rotate_by_2side_backNforth - |c9129c6| 
|  NEWS         | 3 ++-
|  R/untangle.R | 6 +++---
|  2 files changed, 5 insertions(+), 4 deletions(-)

* 2015-05-24(Tal Galili) Added Iris analysis to cluster_analysis.Rmd |e444b56| 
|  vignettes/Cluster_Analysis.Rmd | 293 ++++++++++++++++++++++++++++++++++-----
|  1 file changed, 261 insertions(+), 32 deletions(-)

* 2015-05-24(Tal Galili) misc |e404aa9| 
|  R/color_branches.R | 4 +++-
|  R/tanglegram.R     | 1 +
|  R/zzz.R            | 3 +++
|  man/tanglegram.Rd  | 3 ++-
|  4 files changed, 9 insertions(+), 2 deletions(-)

* 2015-05-24(Tal Galili) a warning for a common bug that happened. |6a16ace| 
|  R/branches_attr_by.R | 4 ++++
|  1 file changed, 4 insertions(+)

* 2015-05-24(Tal Galili) cor_common_nodes - a new correlation measure between dendrograms. |4b2410a| 
|  NAMESPACE               |  1 +
|  NEWS                    |  1 +
|  R/cor.dendlist.R        | 60 +++++++++++++++++++++++++++++++++++++++++++----
|  man/cor.dendlist.Rd     |  6 ++---
|  man/cor_common_nodes.Rd | 43 +++++++++++++++++++++++++++++++++
|  5 files changed, 104 insertions(+), 7 deletions(-)

* 2015-05-24(Tal Galili) Moved FAQ from introduction.Rmd to FAQ.Rmd |f20096a| 
|  NEWS                       |   2 +-
|  vignettes/FAQ.Rmd          | 818 +++++++++++++++++++++++++++++++++++++++++++
|  vignettes/introduction.Rmd | 809 ------------------------------------------
|  3 files changed, 819 insertions(+), 810 deletions(-)

* 2015-05-24(Tal Galili) set - added "rank_branches" |33e838c| 
|  NEWS               | 2 ++
|  R/set.dendrogram.R | 3 +++
|  man/set.Rd         | 1 +
|  3 files changed, 6 insertions(+)

* 2015-05-24(Tal Galili) tanglegram - new parameter: faster. |728deab| 
|  NEWS              |  4 +++-
|  R/tanglegram.R    | 10 ++++++++++
|  man/tanglegram.Rd |  4 ++++
|  3 files changed, 17 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) moved lines to their right place. |085aff4| 
|  NEWS | 12 ++++++------
|  1 file changed, 6 insertions(+), 6 deletions(-)

* 2015-05-24(Tal Galili) move a line around. |aba3dfb| 
|  R/tanglegram.R | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) untangle.dendlist - now preserve the names in the dendlist |cf5a1ae| 
|  NEWS         | 4 +++-
|  R/untangle.R | 4 ++++
|  2 files changed, 7 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) Added MASS (for using parcoord in the examples) |6f34c1a| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-24(Tal Galili) dendlist - added the `which` parameter (for indicating which elements in the dendlist to pick out) |f6edbbc| 
|  NEWS            |  1 +
|  R/dendlist.R    | 18 +++++++++++++++---
|  man/dendlist.Rd | 11 +++++++----
|  3 files changed, 23 insertions(+), 7 deletions(-)

* 2015-05-24(Tal Galili) untangle.dendlist - can now return a dendlist with more than two elements. |9fe8e48| 
|  NEWS            |  1 +
|  R/untangle.R    | 13 ++++++++++++-
|  man/untangle.Rd |  3 +++
|  3 files changed, 16 insertions(+), 1 deletion(-)

* 2015-05-24(Tal Galili) ladderize - added the `which` parameter (for indicating which elements in the dendlist to ladderize) |4f93598| 
|  NEWS             |  1 +
|  R/rotate.R       | 14 ++++++++++----
|  man/ladderize.Rd |  6 +++++-
|  3 files changed, 16 insertions(+), 5 deletions(-)

* 2015-05-24(Tal Galili) remove the warning when creating an empty dendlist |532fb37| 
|  NEWS                       |  2 +-
|  R/dendlist.R               |  2 +-
|  inst/tests/test-dendlist.R | 25 ++++++++++++++-----------
|  3 files changed, 16 insertions(+), 13 deletions(-)

* 2015-05-23(Tal Galili) Rename file to be "cluster analysis" |aa156c6| 
|  vignettes/Cluster_Analysis.Rmd | 103 +++++++++++++++++++++++++++++++++++++++
|  vignettes/Iris_Analysis.Rmd    |  88 ---------------------------------
|  2 files changed, 103 insertions(+), 88 deletions(-)

* 2015-05-23(Tal Galili) Moved the "Iris analysis" from the introduction vignette to a seperate Rmd file. |25ed06f| 
|  vignettes/Iris_Analysis.Rmd | 88 +++++++++++++++++++++++++++++++++++++++++++
|  vignettes/introduction.Rmd  | 83 ----------------------------------------
|  2 files changed, 88 insertions(+), 83 deletions(-)

* 2015-05-23(Tal Galili) Added some explenations of the tanglegram when used with the coloring of the branches and lines. |8c639f4| 
|  vignettes/introduction.Rmd | 54 ++++++++++++++++++++++++++++++++++++++------
|  1 file changed, 47 insertions(+), 7 deletions(-)

* 2015-05-23(Tal Galili) Added tests for rank_values_with_clusters |b6660a5| 
|  NEWS                              |  2 +-
|  inst/tests/test-common_subtrees.R | 49 +++++++++++++++++++++++++++++++++++++
|  2 files changed, 50 insertions(+), 1 deletion(-)

* 2015-05-23(Tal Galili) added context |0e3ae60| 
|  inst/tests/test-dendlist.R | 3 +++
|  1 file changed, 3 insertions(+)

* 2015-05-23(Tal Galili) Decided this will be version 1.0.0 and not 0.19.0 |25c19e1| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 2 +-
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2015-05-23(Tal Galili) Fix "common_subtrees_color_branches" to make sure everyone are using the same colors. |36f22d3| 
|  R/tanglegram.R    | 75 ++++++++++++++++++++++++++++++++++-------------------
|  man/tanglegram.Rd | 10 ++++---
|  2 files changed, 55 insertions(+), 30 deletions(-)

* 2015-05-23(Tal Galili) color_branches - now uses branches_attr_by_clusters with "all" labels needing to fit a group for the branches to be colors. |9e27f28| 
|  R/color_branches.R | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2015-05-23(Tal Galili)    * branches_attr_by_clusters -       * can now accept a vector of values with the length of the labels.       * new parameter "branches_changed_have_which_labels" - allows the user the decide if the change in parameters will be for branches with all/any of the labels (useful for tanglegram - since we would like to color common subtrees with all of the labels, not just any.) |b2fd1d0| 
|  NEWS                             |  4 +++
|  R/branches_attr_by.R             | 70 ++++++++++++++++++++++++++++++++------
|  man/branches_attr_by_clusters.Rd | 16 +++++++--
|  3 files changed, 77 insertions(+), 13 deletions(-)

* 2015-05-23(Tal Galili) Added rank_values_with_clusters - Rank a vector based on clusters (important for various functions.) |97787ac| 
|  NAMESPACE                        |  1 +
|  NEWS                             |  2 +-
|  R/common_subtrees.R              | 52 ++++++++++++++++++++++++++++++++++----
|  man/rank_values_with_clusters.Rd | 37 +++++++++++++++++++++++++++
|  4 files changed, 86 insertions(+), 6 deletions(-)

* 2015-05-22(Tal Galili) Fix: ggplot.ggdend: no visible global function definition for |ff33554| 
|  R/ggdend.R | 1 +
|  1 file changed, 1 insertion(+)

* 2015-05-22(Tal Galili) Fix: Codoc mismatches from documentation object 'ggdend': |7161cd7| 
|  R/ggdend.R    | 6 ++++--
|  man/ggdend.Rd | 5 ++++-
|  2 files changed, 8 insertions(+), 3 deletions(-)

* 2015-05-22(Tal Galili) fix: \examples lines wider than 100 characters: |ca11269| 
|  R/attr_access.R                          | 4 +++-
|  man/assign_values_to_branches_edgePar.Rd | 4 +++-
|  2 files changed, 6 insertions(+), 2 deletions(-)

* 2015-05-22(Tal Galili) added test for ggdend |d00f01a| 
|  inst/tests/test-ggdend.R | 50 ++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 50 insertions(+)

* 2015-05-22(Tal Galili) added get_nodes_attr test |788def3| 
|  inst/tests/test-attr_access.R | 13 +++++++++++++
|  1 file changed, 13 insertions(+)

* 2015-05-22(Tal Galili) plot.ggdend - added support to plot nodes |bd2e1a9| 
|  NEWS       |  4 +++-
|  R/ggdend.R | 28 +++++++++++++++++++++++++++-
|  2 files changed, 30 insertions(+), 2 deletions(-)

* 2015-05-22(Tal Galili) Fix ggdend to now deal with edgePar and nodePar being lists. (now the vignette doesn't crash) |d20f2d0| 
|  R/ggdend.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++---------
|  1 file changed, 48 insertions(+), 9 deletions(-)

* 2015-05-22(Tal Galili) Fix test to now account for edgePar and nodePar are lists. |2c608bf| 
|  inst/tests/test-attr_access.R      |  4 +++-
|  inst/tests/test-branches_attr_by.R | 10 ++++++++++
|  inst/tests/test-set.dendrogram.R   | 15 ++++++++-------
|  3 files changed, 21 insertions(+), 8 deletions(-)

* 2015-05-22(Tal Galili) made sure that the end of the vector in "dendextend_heights_per_k.dendrogram" will give the tree size (and not 0) as its name. |60cac76| 
|  R/cutree.dendrogram.R               |  5 +++++
|  inst/tests/test-cutree.dendrogram.R | 30 +++++++++++++++++++++++++++++-
|  2 files changed, 34 insertions(+), 1 deletion(-)

* 2015-05-22(Tal Galili) Date |f5ef241| 
|  NEWS | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-22(Tal Galili) Fix link |adeabab| 
|  vignettes/introduction.Rmd | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-22(Tal Galili) Date |5dbf21c| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-22(Tal Galili) Parameters are now stored as a list for (allows for branches to have colors/linetype/linewidth, some are numeric and some character): assign_values_to_branches_edgePar / assign_values_to_leaves_nodePar / assign_values_to_leaves_edgePar / assign_values_to_nodes_nodePar - the parameters are stored as a list in edgePar/nodePar (instead of a vector). Discovered thanks to Martin Maechler.  Fixes: "Error in segments(x0, y0, x1, y1, col = col, lty = lty, lwd = lwd) : invalid line type: must be length 2, 4, 6 or 8" |4bf8f20| 
|  NEWS                                     |  2 ++
|  R/attr_access.R                          | 29 +++++++++++++++++++++--------
|  inst/tests/test-branches_attr_by.R       | 23 +++++++++++++++++------
|  man/assign_values_to_branches_edgePar.Rd | 14 +++++++++++++-
|  tests/test-all.R                         | 16 ++++++++++++----
|  5 files changed, 65 insertions(+), 19 deletions(-)

* 2015-05-22(Tal Galili) Added doc to common_subtrees_clusters |a6b4cb0| 
|  NAMESPACE                       |  1 +
|  R/common_subtrees.R             | 53 +++++++++++++++++++++++----------------
|  man/common_subtrees_clusters.Rd | 44 ++++++++++++++++++++++++++++++++
|  3 files changed, 77 insertions(+), 21 deletions(-)

* 2015-05-22(Tal Galili) tanglegram - have doc match code. |d86f957| 
|  R/tanglegram.R    | 7 ++++---
|  man/tanglegram.Rd | 4 +++-
|  2 files changed, 7 insertions(+), 4 deletions(-)

* 2015-05-22(Tal Galili) Fix "color_branches: no visible binding for global variable 'cols'" |64a8bba| 
|  R/color_branches.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-22(Tal Galili) labels.dendrogram is now working through dendextend_options("labels.dendrogram"). The defualt is the new dendextend_labels.dendrogram (which is just stats:::labels.dendrogram), but this allows the package dendextendRcpp to change the function used by the package (without masking the function in base R) - thus making both me, and CRAN, happy :) |ae602a9| 
|  NAMESPACE                           |  1 +
|  NEWS                                |  4 +++-
|  R/dendextend_options.R              |  1 +
|  R/stats_imports.R                   | 35 +++++++++++++++++++++++++++++++++++
|  R/zzz.R                             |  4 +++-
|  man/dendextend_labels.dendrogram.Rd | 28 ++++++++++++++++++++++++++++
|  6 files changed, 71 insertions(+), 2 deletions(-)

* 2015-05-22(Tal Galili) rect.dendrogram - deals with the case we want to use k for which k+1 is not defined. |61eeded| 
|  NEWS                              |  3 ++-
|  R/rect.dendrogram.R               | 21 +++++++++++++++++++--
|  inst/tests/test-rect.dendrogram.R | 26 ++++++++++++++++++++++++++
|  man/rect.dendrogram.Rd            |  8 ++++++++
|  4 files changed, 55 insertions(+), 3 deletions(-)

* 2015-05-19(Tal Galili) tanglegram - Added new parameters: common_subtrees_color_lines and common_subtrees_color_branches to color connecting-lines and/or the dendrograms themsleves, to help detect commonly shared subtrees. |7394cba| 
|  NEWS              |  2 +-
|  R/tanglegram.R    | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++--
|  man/tanglegram.Rd | 29 +++++++++++++++++++++
|  3 files changed, 100 insertions(+), 3 deletions(-)

* 2015-05-19(Tal Galili) common_subtrees_clusters - a (currently hidden) function to get clusters for labels of common subtrees between two trees. |22c3235| 
|  NEWS                  |   3 +
|  R/common_subtrees.R   | 175 ++++++++++++++++++++++++++++++++++++++++++++++++
|  man/distinct_edges.Rd |   1 +
|  tests/test-all.R      |   2 -
|  4 files changed, 179 insertions(+), 2 deletions(-)

* 2015-05-18(Tal Galili) tanglegram - turned "highlight_distinct_edges = FALSE". This is due to a bug in R that causes plot.dendrogram to crash when trying to plot a tree with both lty and some character color for the branch. |cfebab3| 
|  NEWS           | 2 +-
|  R/tanglegram.R | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-05-18(Tal Galili) color_branches - gained a new "cluster" parameter to allow for easy uneven coloring of branches (using branches_attr_by_clusters). This is not a new feature, as it is an attempt to have the user access more options from one place (i.e.: color_branches). |5d601b0| 
|  DESCRIPTION                      |  2 +-
|  NEWS                             |  6 ++-
|  R/branches_attr_by.R             |  2 +-
|  R/color_branches.R               | 81 ++++++++++++++++++++++++++++----------
|  man/branches_attr_by_clusters.Rd |  2 +-
|  man/color_branches.Rd            | 20 +++++++++-
|  6 files changed, 87 insertions(+), 26 deletions(-)

* 2015-05-18(Tal Galili) roxygen2 (4.0.2) -> roxygen2 (4.1.1) |81c0709| 
|  NAMESPACE                                  | 2 +-
|  man/Bk.Rd                                  | 3 ++-
|  man/Bk_permutations.Rd                     | 3 ++-
|  man/Bk_plot.Rd                             | 3 ++-
|  man/DendSer.dendrogram.Rd                  | 3 ++-
|  man/FM_index.Rd                            | 3 ++-
|  man/FM_index_R.Rd                          | 3 ++-
|  man/FM_index_permutation.Rd                | 3 ++-
|  man/FM_index_profdpm.Rd                    | 3 ++-
|  man/all.equal.dendrogram.Rd                | 3 ++-
|  man/all_couple_rotations_at_k.Rd           | 3 ++-
|  man/all_unique.Rd                          | 3 ++-
|  man/as.dendlist.Rd                         | 3 ++-
|  man/as.phylo.dendrogram.Rd                 | 3 ++-
|  man/as_hclust_fixed.Rd                     | 3 ++-
|  man/assign_dendextend_options.Rd           | 3 ++-
|  man/assign_values_to_branches_edgePar.Rd   | 3 ++-
|  man/assign_values_to_leaves_edgePar.Rd     | 3 ++-
|  man/assign_values_to_leaves_nodePar.Rd     | 3 ++-
|  man/assign_values_to_nodes_nodePar.Rd      | 3 ++-
|  man/bakers_gamma_for_2_k_matrix.Rd         | 3 ++-
|  man/branches_attr_by_clusters.Rd           | 3 ++-
|  man/branches_attr_by_labels.Rd             | 3 ++-
|  man/click_rotate.Rd                        | 3 ++-
|  man/collapse_branch.Rd                     | 3 ++-
|  man/color_branches.Rd                      | 3 ++-
|  man/color_labels.Rd                        | 3 ++-
|  man/colored_bars.Rd                        | 3 ++-
|  man/cor.dendlist.Rd                        | 3 ++-
|  man/cor_bakers_gamma.Rd                    | 3 ++-
|  man/cor_cophenetic.Rd                      | 3 ++-
|  man/count_terminal_nodes.Rd                | 3 ++-
|  man/cut_lower_fun.Rd                       | 3 ++-
|  man/cutree-methods.Rd                      | 3 ++-
|  man/cutree_1h.dendrogram.Rd                | 3 ++-
|  man/cutree_1k.dendrogram.Rd                | 3 ++-
|  man/d3dendro_options.Rd                    | 3 ++-
|  man/d3dendrogram.Rd                        | 3 ++-
|  man/dend_diff.Rd                           | 3 ++-
|  man/dendextend-package.Rd                  | 3 ++-
|  man/dendextend_options.Rd                  | 3 ++-
|  man/dendlist.Rd                            | 3 ++-
|  man/dist.dendlist.Rd                       | 3 ++-
|  man/dist_long.Rd                           | 3 ++-
|  man/distinct_edges.Rd                      | 3 ++-
|  man/duplicate_leaf.Rd                      | 3 ++-
|  man/entanglement.Rd                        | 3 ++-
|  man/fac2num.Rd                             | 3 ++-
|  man/fix_members_attr.dendrogram.Rd         | 3 ++-
|  man/flatten.dendrogram.Rd                  | 3 ++-
|  man/flip_leaves.Rd                         | 3 ++-
|  man/get_branches_heights.Rd                | 3 ++-
|  man/get_childrens_heights.Rd               | 3 ++-
|  man/get_leaves_attr.Rd                     | 3 ++-
|  man/get_leaves_branches_attr.Rd            | 3 ++-
|  man/get_leaves_branches_col.Rd             | 3 ++-
|  man/get_leaves_edgePar.Rd                  | 3 ++-
|  man/get_leaves_nodePar.Rd                  | 3 ++-
|  man/get_nodes_attr.Rd                      | 3 ++-
|  man/get_nodes_xy.Rd                        | 3 ++-
|  man/get_root_branches_attr.Rd              | 3 ++-
|  man/ggdend.Rd                              | 3 ++-
|  man/hang.dendrogram.Rd                     | 3 ++-
|  man/heights_per_k.dendrogram.Rd            | 3 ++-
|  man/highlight_distinct_edges.Rd            | 3 ++-
|  man/identify.dendrogram.Rd                 | 3 ++-
|  man/intersect_trees.Rd                     | 3 ++-
|  man/is.dendlist.Rd                         | 3 ++-
|  man/is.dendrogram.Rd                       | 3 ++-
|  man/is.hclust.Rd                           | 3 ++-
|  man/is.natural.number.Rd                   | 3 ++-
|  man/is.phylo.Rd                            | 3 ++-
|  man/is_null_list.Rd                        | 3 ++-
|  man/labels-assign.Rd                       | 3 ++-
|  man/labels_colors.Rd                       | 3 ++-
|  man/ladderize.Rd                           | 3 ++-
|  man/leaf_Colors.Rd                         | 3 ++-
|  man/lowest_common_branch.Rd                | 3 ++-
|  man/match_order_by_labels.Rd               | 3 ++-
|  man/match_order_dendrogram_by_old_order.Rd | 3 ++-
|  man/na_locf.Rd                             | 3 ++-
|  man/nleaves.Rd                             | 3 ++-
|  man/nnodes.Rd                              | 3 ++-
|  man/noded_with_condition.Rd                | 3 ++-
|  man/order.dendrogram-assign.Rd             | 3 ++-
|  man/order.hclust.Rd                        | 3 ++-
|  man/partition_leaves.Rd                    | 3 ++-
|  man/pipe.Rd                                | 3 ++-
|  man/plot_horiz.dendrogram.Rd               | 3 ++-
|  man/prune.Rd                               | 3 ++-
|  man/prune_leaf.Rd                          | 3 ++-
|  man/pvclust_show_signif.Rd                 | 3 ++-
|  man/pvclust_show_signif_gradient.Rd        | 3 ++-
|  man/raise.dendrogram.Rd                    | 3 ++-
|  man/rank_branches.Rd                       | 3 ++-
|  man/rank_order.dendrogram.Rd               | 3 ++-
|  man/rect.dendrogram.Rd                     | 3 ++-
|  man/remove_branches_edgePar.Rd             | 3 ++-
|  man/remove_leaves_nodePar.Rd               | 3 ++-
|  man/remove_nodes_nodePar.Rd                | 3 ++-
|  man/rllply.Rd                              | 3 ++-
|  man/rotate.Rd                              | 3 ++-
|  man/rotate_DendSer.Rd                      | 3 ++-
|  man/sample.dendrogram.Rd                   | 3 ++-
|  man/set.Rd                                 | 3 ++-
|  man/shuffle.Rd                             | 3 ++-
|  man/sort_2_clusters_vectors.Rd             | 3 ++-
|  man/sort_dist_mat.Rd                       | 3 ++-
|  man/sort_levels_values.Rd                  | 3 ++-
|  man/tanglegram.Rd                          | 6 ++++--
|  man/theme_dendro.Rd                        | 3 ++-
|  man/unbranch.Rd                            | 3 ++-
|  man/unclass_dend.Rd                        | 3 ++-
|  man/untangle.Rd                            | 3 ++-
|  man/untangle_DendSer.Rd                    | 3 ++-
|  man/untangle_random_search.Rd              | 3 ++-
|  man/untangle_step_rotate_1side.Rd          | 3 ++-
|  man/untangle_step_rotate_2side.Rd          | 3 ++-
|  man/which_leaf.Rd                          | 3 ++-
|  man/which_node.Rd                          | 3 ++-
|  120 files changed, 241 insertions(+), 121 deletions(-)

* 2015-05-18(Tal Galili) tanglegram - tiny clarification about color_lines |3fe5dd9| 
|  R/tanglegram.R | 1 +
|  1 file changed, 1 insertion(+)

* 2015-05-18(Tal Galili) distinct_edges - a simpler R code |47975fb| 
|  R/distinct_edges.R | 6 ++++--
|  1 file changed, 4 insertions(+), 2 deletions(-)

* 2015-05-18(Tal Galili) Fix: as.hclust.pvclust: no visible binding for global variable ‘object’ |c3ada78| 
|  R/pvclust.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-17(Tal Galili) Fix coveralls badge |c5fcb1c| 
|  README.md | 4 +---
|  1 file changed, 1 insertion(+), 3 deletions(-)

* 2015-05-17(Tal Galili) Added coveralls and CRAN status |6948645| 
|  .travis.yml | 4 ++++
|  NEWS        | 2 ++
|  README.md   | 3 +++
|  3 files changed, 9 insertions(+)

* 2015-05-17(Tal Galili) Added Code of conduct |fd5a95a| 
|  .Rbuildignore |  3 ++-
|  CONDUCT.md    | 25 +++++++++++++++++++++++++
|  NEWS          |  5 +++++
|  R/zzz.R       | 11 +++++++++++
|  README.md     |  6 ++++++
|  5 files changed, 49 insertions(+), 1 deletion(-)

* 2015-05-17(Tal Galili)  Fix "Objects in \usage without \alias in documentation object". For ‘prune.rpart’ and ‘sort.dendlist’. |872678a| 
|  NEWS          | 1 +
|  R/prune.R     | 1 +
|  R/rotate.R    | 1 +
|  man/prune.Rd  | 1 +
|  man/rotate.Rd | 1 +
|  5 files changed, 5 insertions(+)

* 2015-05-17(Tal Galili) as.hclust.pvclust - use "x" instead of "object", to avoid "checking S3 generic/method consistency ... WARNING" |12c1c08| 
|  NEWS        | 1 +
|  R/pvclust.R | 2 +-
|  2 files changed, 2 insertions(+), 1 deletion(-)

* 2015-05-17(Tal Galili) Fix "'::' or ':::' import not declared from: ‘rpart’" by adding rpart to DESCRIPTION. |e8a85e7| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 8 ++++++++
|  2 files changed, 10 insertions(+), 2 deletions(-)

* 2015-05-17(Tal Galili) version bump 0.18.8 |ca2a085| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  README.md   | 4 ++--
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2015-05-17(Tal Galili) identify.dendrogram - parameter horiz now works (fixes #4) |0cf59c3| 
|  NEWS                       |  3 +++
|  R/rect.dendrogram.R        | 16 +++++++++++++---
|  man/identify.dendrogram.Rd |  6 +++++-
|  3 files changed, 21 insertions(+), 4 deletions(-)

* 2015-05-16(Tal Galili) tiny fix |117e2b2| 
|  README.md | 1 +
|  1 file changed, 1 insertion(+)

* 2015-05-16(Tal Galili) Another tweak to the install of packages |9afdd03| 
|  README.md | 10 ++++++----
|  1 file changed, 6 insertions(+), 4 deletions(-)

* 2015-05-16(Tal Galili) Simplafy github installation code a bit. |29215cb| 
|  README.md | 15 ++++-----------
|  1 file changed, 4 insertions(+), 11 deletions(-)

* 2015-05-16(Tal Galili) Added a Vectorize example (fixes #6) |df95472| 
|  R/rect.dendrogram.R    | 2 ++
|  man/rect.dendrogram.Rd | 2 ++
|  2 files changed, 4 insertions(+)

* 2015-05-16(Tal Galili) rect.dendrogram - make the heights of the rects be in the middle of the two clusters so that they would look nicer. Added prop_k_height to state which proportion of the height the rect should be (between k and k+1 heights). Also added upper_rect to allow the user to customize the exact height. (this closes issue #6) |4526d46| 
|  DESCRIPTION            |  7 ++++---
|  NEWS                   |  4 ++--
|  R/rect.dendrogram.R    | 16 +++++++++++++---
|  man/rect.dendrogram.Rd |  7 ++++++-
|  4 files changed, 25 insertions(+), 9 deletions(-)

* 2015-05-15(Tal Galili) all.equal.dendrogram - suppress warning for a dend with only 1 item, when using dendextendRcpp. |fb8515c| 
|  NEWS                            |  1 +
|  R/all.equal.R                   | 17 +++++++++++++++--
|  inst/tests/test-cut_lower_fun.R | 14 ++++++++++----
|  3 files changed, 26 insertions(+), 6 deletions(-)

* 2015-05-15(Tal Galili) Fix comments' text |1d22f77| 
|  R/cutree.dendrogram.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-05-15(Tal Galili) all.equal.dendlist - can now compare two dendlist objects to one another, and not only the dendrograms inside one dendlist. (also added new tests that all.equal.dendlist works) |c581e1b| 
|  NEWS                        |  7 +++++++
|  R/all.equal.R               | 19 +++++++++++++++++++
|  inst/tests/test-dendlist.R  | 32 +++++++++++++++++++++++++++++++-
|  man/all.equal.dendrogram.Rd |  5 +++++
|  4 files changed, 62 insertions(+), 1 deletion(-)

* 2015-05-15(Tal Galili) Test commit |6449eb7| 
|  tests/test-all.R | 3 +++
|  1 file changed, 3 insertions(+)

* 2015-05-06(Tal Galili) remove dependancy in VIGNETTE on DendSer (using require instead of library) - bump to 0.18.7 |49a073f| 
|  DESCRIPTION                |  7 +++----
|  NEWS                       |  2 ++
|  vignettes/introduction.Rmd | 30 ++++++++++++++++++------------
|  3 files changed, 23 insertions(+), 16 deletions(-)

* 2015-05-06(Tal Galili) ladderize instead of rotate_DendSer - in the example |729903b| 
|  R/set.dendrogram.R | 4 ++--
|  man/set.Rd         | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2015-05-06(Tal Galili) tanglegram.dendlist - fix it when names is null to have the default be "" |8dbea82| 
|  NEWS           | 1 +
|  R/tanglegram.R | 5 ++++-
|  2 files changed, 5 insertions(+), 1 deletion(-)

* 2015-05-06(Tal Galili) untangle - added method="ladderize" |0c04568| 
|  NEWS            |  7 +++++++
|  R/untangle.R    | 11 ++++++-----
|  man/untangle.Rd |  4 ++--
|  3 files changed, 15 insertions(+), 7 deletions(-)

* 2015-04-25(Tal Galili) library corrplot added to plot cor.dendlist results. Examples added to vignette and function's example. |aea94bc| 
|  DESCRIPTION                | 3 ++-
|  NEWS                       | 3 ++-
|  R/cor.dendlist.R           | 8 +++++++-
|  man/cor.dendlist.Rd        | 8 +++++++-
|  vignettes/introduction.Rmd | 9 +++++++++
|  5 files changed, 27 insertions(+), 4 deletions(-)

* 2015-04-25(Tal Galili) tanglegram.dendlist - now gets main_left and main_right (if they are null) from the names in dendlist (if they exist) |7cc9037| 
|  NEWS              |  3 +++
|  R/tanglegram.R    | 14 +++++++++++---
|  man/tanglegram.Rd |  2 +-
|  3 files changed, 15 insertions(+), 4 deletions(-)

* 2015-04-25(Tal Galili) added example for using "get_leaves_branches_col" in "How to color the branches in heatmap.2?" |c30208f| 
|  NEWS                       | 3 +++
|  vignettes/introduction.Rmd | 8 +++++++-
|  2 files changed, 10 insertions(+), 1 deletion(-)

* 2015-04-25(Tal Galili) Fix get_leaves_branches_attr and also make it simpler. |6017490| 
|  R/attr_access.R | 12 ++++--------
|  1 file changed, 4 insertions(+), 8 deletions(-)

* 2015-04-25(Tal Galili) NEW FUNCTIONS: (version 0.18.6)    * get_leaves_edgePar - Get edgePar of dendrogram's leaves    * get_leaves_branches_attr - Get an attribute of the branches of a dendrogram's leaves    * get_leaves_branches_col - Get the colors of the branches of a dendrogram's leaves. This function is actually the point of the two other functions. It is meant to help match the color of the labels with that of the branches - after running color_branches. |139236d| 
|  DESCRIPTION                     |   4 +-
|  NAMESPACE                       |   3 +
|  NEWS                            |   8 +++
|  R/attr_access.R                 | 141 ++++++++++++++++++++++++++++++++++++++
|  man/get_leaves_branches_attr.Rd |  48 +++++++++++++
|  man/get_leaves_branches_col.Rd  |  44 ++++++++++++
|  man/get_leaves_edgePar.Rd       |  45 ++++++++++++
|  man/get_leaves_nodePar.Rd       |   1 +
|  8 files changed, 292 insertions(+), 2 deletions(-)

* 2015-04-22(Tal Galili) use color_branches instead of set (easier for people - I would guess) |ade1635| 
|  vignettes/introduction.Rmd | 6 ++++--
|  1 file changed, 4 insertions(+), 2 deletions(-)

* 2015-04-22(Tal Galili) VIGNETTE added: "How to color the branches in heatmap.2?" |6127035| 
|  DESCRIPTION                |   4 +-
|  NEWS                       |   7 +
|  vignettes/introduction.Rmd | 632 +++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 641 insertions(+), 2 deletions(-)

* 2015-03-05(Tal Galili) s |17f6568| 
|  README.md | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-03-05(Tal Galili) Added TOC to readme.md |4d083c0| 
|  README.md | 12 +++++++++++-
|  1 file changed, 11 insertions(+), 1 deletion(-)

* 2015-02-14(Tal Galili) Update vignette on github |e0ecc5a| 
|  inst/ignored/introduction.html | 1875 ++++++++++++++++++--------------------
|  1 file changed, 866 insertions(+), 1009 deletions(-)

* 2015-02-14(Tal Galili) moved to knitr::docco_linear (and some fixes to figures height) |6de5e7b| 
|  vignettes/introduction.Rmd | 10 +++++-----
|  1 file changed, 5 insertions(+), 5 deletions(-)

* 2015-02-07(Tal Galili) as.hclust.pvclust |1c3ce5b| 
|  NAMESPACE   |  1 +
|  NEWS        |  1 +
|  R/pvclust.R | 11 ++++++++++-
|  3 files changed, 12 insertions(+), 1 deletion(-)

* 2015-02-07(Tal Galili) Added sort.dendlist |e90a0cd| 
|  DESCRIPTION   |  4 ++--
|  NAMESPACE     |  1 +
|  NEWS          |  1 +
|  R/rotate.R    | 11 +++++++++++
|  man/rotate.Rd |  2 ++
|  5 files changed, 17 insertions(+), 2 deletions(-)

* 2015-02-07(Tal Galili) prune.rpart added |3ae7031| 
|  NAMESPACE    |  1 +
|  NEWS         | 10 ++++++++++
|  R/prune.R    |  8 ++++++++
|  man/prune.Rd |  2 ++
|  4 files changed, 21 insertions(+)

* 2015-01-31(Tal Galili) Bump to 0.18.3 |86adb2a| 
|  ChangeLog | 13 +++++++++++++
|  R/zzz.R   |  2 +-
|  2 files changed, 14 insertions(+), 1 deletion(-)

* 2015-01-31(Tal Galili) require -> requireNamespace |6dcc805| 
|  .Rbuildignore   | 2 +-
|  R/bk_method.R   | 2 +-
|  R/rainbow_fun.R | 2 +-
|  3 files changed, 3 insertions(+), 3 deletions(-)

* 2015-01-31(Tal Galili) update NEWS.md and changelog |e8b9e78| 
|  ChangeLog | 42 ++++++++++++++++++++++++++++++++++++++++++
|  NEWS      |  2 +-
|  NEWS.md   | 20 ++++++++++++++++++++
|  R/zzz.R   |  2 +-
|  4 files changed, 64 insertions(+), 2 deletions(-)

* 2015-01-31(Tal Galili) Fix "Please use :: or requireNamespace() instead." by commenting out all "library", since using "::" is enough! |fc73295| 
|  NEWS                  |   6 +
|  R/DendSer.R           |   2 +-
|  R/ape.R               |   8 +-
|  R/cutree.dendrogram.R |  42 +++---
|  R/ggdend.R            |   4 +-
|  R/ggdendro.R          |   2 +-
|  R/nleaves.R           |   4 +-
|  R/prune.R             |   2 +-
|  R/rotate.R            |   4 +-
|  R/set.dendrogram.R    |   2 +-
|  R/unbranch.R          |   2 +-
|  R/untangle.R          | 358 ++++++++++++++++++++++++------------------------
|  R/zzz.R               |   2 +-
|  13 files changed, 222 insertions(+), 216 deletions(-)

* 2015-01-31(Tal Galili) Fix "title case" for the package's Title in the DESCRIPTION |ccf93c3| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 5 +++++
|  2 files changed, 7 insertions(+), 2 deletions(-)

* 2015-01-31(Tal Galili) Fix "No package encoding and non-ASCII characters in the following R files" |bba4e4c| 
|  R/ggdend.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-31(Tal Galili) Minor doc fix for `collapse_branch` |2f3019b| 
|  DESCRIPTION            | 2 +-
|  NEWS                   | 9 +++++++++
|  R/unbranch.R           | 3 ++-
|  man/collapse_branch.Rd | 3 ++-
|  4 files changed, 14 insertions(+), 3 deletions(-)

* 2015-01-31(Tal Galili) Update NEWS.md and changelog |e0ef4b5| 
|  ChangeLog | 39 +++++++++++++++++++++++++++++++++++++++
|  NEWS.md   | 29 +++++++++++++++++++++++++++++
|  2 files changed, 68 insertions(+)

* 2015-01-31(Tal Galili) collapse_branch to vignette |4cafe05| 
|  NEWS                       |  8 +++++++-
|  vignettes/introduction.Rmd | 17 +++++++++++++++++
|  2 files changed, 24 insertions(+), 1 deletion(-)

* 2015-01-31(Tal Galili) Add ladderize to collapse_branch example |f7043c6| 
|  R/rotate.R             | 2 +-
|  R/unbranch.R           | 8 +++++---
|  man/collapse_branch.Rd | 7 ++++---
|  man/rotate.Rd          | 2 +-
|  4 files changed, 11 insertions(+), 8 deletions(-)

* 2015-01-31(Tal Galili) ###VIGNETTE - new sections!    * Quick functions for FAQ       * How to colour the labels of a dendrogram by an additional factor variable       * How to color a dendrogram's branches/labels based on cluster (i.e.: cutree result)       * Change dendrogram's labels       * Larger font for leaves in a dendrogram       * How to view attributes of a dendrogram    * rotate - explain about sort    * ggplot2 integration (!)    * Comparing trees:       * dend_diff       * all.equal       * dist.dendlist       * cor.dendlist |84335e7| 
|  NEWS                       |  15 +++
|  vignettes/introduction.Rmd | 305 +++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 320 insertions(+)

* 2015-01-31(Tal Galili) `ggplot.ggdend` - support theme = NULL |d94efb6| 
|  NEWS          | 2 +-
|  R/ggdend.R    | 9 ++++++---
|  man/ggdend.Rd | 5 +++--
|  3 files changed, 10 insertions(+), 6 deletions(-)

* 2015-01-31(Tal Galili) Minor .Rd fixes. |d69de40| 
|  R/ggdend.R    | 4 ++--
|  man/ggdend.Rd | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2015-01-31(Tal Galili) `sort.dendrogram` - added a new parameter: type = c("labels", "nodes"), to use `ladderize` for sorting |2d4fe25| 
|  DESCRIPTION   |  4 ++--
|  NEWS          |  8 ++++++++
|  R/rotate.R    | 17 +++++++++++++++--
|  man/rotate.Rd | 11 ++++++++++-
|  4 files changed, 35 insertions(+), 5 deletions(-)

* 2015-01-30(Tal Galili) cheatsheet? |1f2c862| 
|  TODO | 5 +++++
|  1 file changed, 5 insertions(+)

* 2015-01-30(Tal Galili) Updated ChangeLog and NEWS.md |d3b1613| 
|  ChangeLog | 674 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
|  NEWS.md   | 102 +++++++++
|  2 files changed, 768 insertions(+), 8 deletions(-)

* 2015-01-30(Tal Galili) Fix package date. |10d25e2| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2015-01-29(Tal Galili) Fix various doc errors. |369cce9| 
|  R/rotate.R       | 19 ++++++++++---------
|  man/ladderize.Rd |  6 +++---
|  man/rotate.Rd    |  8 ++++----
|  3 files changed, 17 insertions(+), 16 deletions(-)

* 2015-01-29(Tal Galili) Fix "ggplot.ggdend: no visible global function definition for ‘aes_string’" error |f5b34b7| 
|  R/ggdend.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-29(Tal Galili) `ladderize` - Ladderize a Tree (reorganizes the internal structure of the tree to get the ladderized effect when plotted) |9120507| 
|  NAMESPACE        |   4 ++
|  NEWS             |   1 +
|  R/rotate.R       | 116 +++++++++++++++++++++++++++++++++++++++++++++++++++--
|  man/ladderize.Rd |  47 ++++++++++++++++++++++
|  man/rotate.Rd    |   4 +-
|  5 files changed, 167 insertions(+), 5 deletions(-)

* 2015-01-29(Tal Galili) Use aes_string instead of aes! |70ab17c| 
|  R/ggdend.R | 13 ++++++++-----
|  1 file changed, 8 insertions(+), 5 deletions(-)

* 2015-01-29(Tal Galili) Fix as.ggdend - to get the col/cex of the labels correctly. |174e12f| 
|  R/ggdend.R | 7 +++++--
|  1 file changed, 5 insertions(+), 2 deletions(-)

* 2015-01-29(Tal Galili) Fix "Missing link or links in documentation object" error |e8713e5| 
|  R/ape.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-29(Tal Galili) Fix "lines wider than 100 characters:" error |a035228| 
|  R/distinct_edges.R              | 4 +++-
|  man/as.phylo.dendrogram.Rd      | 2 +-
|  man/highlight_distinct_edges.Rd | 4 +++-
|  3 files changed, 7 insertions(+), 3 deletions(-)

* 2015-01-29(Tal Galili) Fix many "no visible global function definition for ..." errors. |c028b06| 
|  R/ggdend.R    | 42 ++++++++++++++++++++++++++++++++----------
|  man/ggdend.Rd | 18 ++++++++++--------
|  2 files changed, 42 insertions(+), 18 deletions(-)

* 2015-01-29(Tal Galili) Fix theme_dendro: no visible global function definition for 'element_text' |4e30954| 
|  R/ggdendro.R | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2015-01-29(Tal Galili) fix collapse_branch: no visible binding for global variable ‘dend_node’ |c51c27e| 
|  R/unbranch.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-29(Tal Galili) Fix Codoc mismatches in prepare.ggdend |c87b7d8| 
|  R/ggdend.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-29(Tal Galili) ggplot.ggdend: leaf_labels -> labels |5f6e090| 
|  R/ggdend.R | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2015-01-29(Tal Galili) DESCRIPTION: Moved ape and ggplot2 to "Suggests" packages - so that I could refer to them in the vignette/help pages. |9f54d6a| 
|  DESCRIPTION | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2015-01-29(Tal Galili) Rename dist_fun.R to dist_long.R |6ed91cc| 
|  NEWS          |  1 +
|  R/dist_fun.R  | 62 ---------------------------------------------------------
|  R/dist_long.R | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/unbranch.R  |  1 +
|  4 files changed, 64 insertions(+), 62 deletions(-)

* 2015-01-29(Tal Galili) `collapse_branch` - simplifies a tree with branches lower than some tollerance level |691c490| 
|  NAMESPACE              |  1 +
|  NEWS                   |  1 +
|  R/unbranch.R           | 90 ++++++++++++++++++++++++++++++++++++++++++++++++
|  man/collapse_branch.Rd | 38 ++++++++++++++++++++
|  4 files changed, 130 insertions(+)

* 2015-01-29(Tal Galili) Fix "Error in plot.xy(xy.coords(x, y), type = type, ...) : " when dend has graphical parameters. |480b0fc| 
|  R/ggdendro.R | 16 ++++++++++++++++
|  1 file changed, 16 insertions(+)

* 2015-01-29(Tal Galili) Fix: Error in eval(expr, envir, enclos) : object 'cex' not found In addition: Warning message: In is.na(data$labels$cex) :   is.na() applied to non-(list or vector) of type 'NULL' |50ab05a| 
|  R/ggdend.R | 22 +++++++++++++++++-----
|  1 file changed, 17 insertions(+), 5 deletions(-)

* 2015-01-29(Tal Galili) `remove_nodes_nodePar` - as the name implies... |3584e7c| 
|  NAMESPACE                   |  1 +
|  NEWS                        |  2 ++
|  R/attr_access.R             | 37 ++++++++++++++++++++++++++++++++++++-
|  man/remove_nodes_nodePar.Rd | 33 +++++++++++++++++++++++++++++++++
|  4 files changed, 72 insertions(+), 1 deletion(-)

* 2015-01-28(Tal Galili) fix namespace issues (using S3 for a non-imported package is NOT wise, and results in the main function not seeing the new S3 function implemented...) |bc5c1ee| 
|  NAMESPACE     |  4 ++--
|  R/ggdend.R    | 14 ++++++++------
|  man/ggdend.Rd |  4 ++--
|  3 files changed, 12 insertions(+), 10 deletions(-)

* 2015-01-28(Tal Galili) Added theme_dendro as the default theme for ggplot.ggdend |0dfc218| 
|  R/ggdend.R    | 16 +++++++---------
|  man/ggdend.Rd |  4 +++-
|  2 files changed, 10 insertions(+), 10 deletions(-)

* 2015-01-28(Tal Galili) Organize NEWS |c41aeba| 
|  NEWS | 31 +++++++++++++++++--------------
|  1 file changed, 17 insertions(+), 14 deletions(-)

* 2015-01-28(Tal Galili) Importing `theme_dendro` from the ggdendro package |d4f6552| 
|  NAMESPACE           |  1 +
|  R/ggdend.R          |  2 +-
|  R/ggdendro.R        | 32 ++++++++++++++++++++++++++++++++
|  man/ggdend.Rd       |  3 +++
|  man/theme_dendro.Rd | 24 ++++++++++++++++++++++++
|  5 files changed, 61 insertions(+), 1 deletion(-)

* 2015-01-28(Tal Galili) Mention ggplot2 -> plot.ly in the ggdend doc. |5340107| 
|  R/ggdend.R    | 22 ++++++++++++++++++++--
|  man/ggdend.Rd | 22 ++++++++++++++++++++--
|  2 files changed, 40 insertions(+), 4 deletions(-)

* 2015-01-27(Tal Galili) `prepare.ggdend` - fills a ggdend object with various default values (to be later used when plotted)  (this function was extrected from ggplot.ggdend) |5fffec4| 
|  NAMESPACE     |  1 +
|  NEWS          |  1 +
|  R/ggdend.R    | 82 +++++++++++++++++++++++++++++++++------------------------
|  man/ggdend.Rd | 24 ++++++++++++-----
|  4 files changed, 67 insertions(+), 41 deletions(-)

* 2015-01-27(Tal Galili) Thanks to Andrie de Vries, dendextend now enhances ggplot2 :) |13647d4| 
|  DESCRIPTION | 7 +++++--
|  1 file changed, 5 insertions(+), 2 deletions(-)

* 2015-01-27(Tal Galili) Adding documentation to ggdend and friends! |64a21a9| 
|  NAMESPACE     |   5 +++
|  NEWS          |   3 +-
|  R/ggdend.R    | 121 ++++++++++++++++++++++++++++++++++++++++++++++++++------
|  man/ggdend.Rd |  99 ++++++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 216 insertions(+), 12 deletions(-)

* 2015-01-27(Tal Galili) Added a working (at least partially) version of ggplot.ggdend |e54200a| 
|  R/ggdend.R | 246 +++++++++++++++++++++++++++++++++++++++++++++++++----------
|  1 file changed, 205 insertions(+), 41 deletions(-)

* 2015-01-27(Tal Galili) `as.ggdend.dendrogram` - turns a dendrogram to the ggdend class, ready to be plotted with ggplot2. |9cc9761| 
|  NEWS       |   2 +
|  R/ggdend.R | 241 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 243 insertions(+)

* 2015-01-27(Tal Galili) `get_leaves_nodePar` - a new function that Get's the nodePar of dendrogram's leaves (designed to help with as.ggdend) |57192cd| 
|  NAMESPACE                     |  1 +
|  NEWS                          |  2 +-
|  R/attr_access.R               | 45 +++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-attr_access.R | 22 ++++++++++++++++++++
|  man/get_leaves_nodePar.Rd     | 40 ++++++++++++++++++++++++++++++++++++
|  5 files changed, 109 insertions(+), 1 deletion(-)

* 2015-01-27(Tal Galili) Added the file ggdendro.R with the dendrogram_data function (imported from the ggdendro package) |08d69d6| 
|  NEWS         |   3 ++
|  R/ggdendro.R | 165 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 168 insertions(+)

* 2015-01-26(Tal Galili) renamed imports_stats.R to stats_imports.R |27068c4| 
|  NEWS              |   1 +
|  R/imports_stats.R | 285 ----------------------------------------------------
|  R/stats_imports.R | 285 ++++++++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 286 insertions(+), 285 deletions(-)

* 2015-01-26(Tal Galili) cor.dendlist and dist.dendlist - their matrix now includes dend names in col/row names. |951968a| 
|  R/cor.dendlist.R     | 4 +++-
|  R/distinct_edges.R   | 5 ++++-
|  man/cor.dendlist.Rd  | 2 +-
|  man/dist.dendlist.Rd | 2 +-
|  4 files changed, 9 insertions(+), 4 deletions(-)

* 2015-01-26(Tal Galili) Add ggdendro example for creating a radial plot :) |efaf335| 
|  R/ape.R                    | 12 ++++++++++++
|  man/as.phylo.dendrogram.Rd | 19 ++++++++++++++++++-
|  2 files changed, 30 insertions(+), 1 deletion(-)

* 2015-01-26(Tal Galili) export as.phylo.dendrogram in a way that actually works... |c8b69de| 
|  NAMESPACE                  |  1 +
|  NEWS                       |  2 +-
|  R/ape.R                    | 47 +++++++++++++++++++++++++++++++++++++++++---
|  R/noded_with_condition.R   |  2 +-
|  man/as.phylo.dendrogram.Rd | 35 +++++++++++++++++++++++++++++++++
|  man/which_node.Rd          |  1 +
|  6 files changed, 83 insertions(+), 5 deletions(-)

* 2015-01-26(Tal Galili) get_nodes_attr with id example |d2464f6| 
|  vignettes/introduction.Rmd | 1 +
|  1 file changed, 1 insertion(+)

* 2015-01-26(Tal Galili) Fix "Error in missing(id) : 'missing' can only be used for arguments" in get_nodes_attr |e912cc3| 
|  R/attr_access.R | 8 +++++---
|  1 file changed, 5 insertions(+), 3 deletions(-)

* 2015-01-26(Tal Galili) magrittr is imported there is no longer a need for "library(magrittr)" in examples. |8210261| 
|  R/branches_attr_by.R           | 1 -
|  R/dist_fun.R                   | 1 -
|  R/get_nodes_xy.R               | 1 -
|  R/noded_with_condition.R       | 2 --
|  R/set.dendrogram.R             | 1 -
|  man/branches_attr_by_labels.Rd | 1 -
|  man/dist_long.Rd               | 1 -
|  man/get_nodes_xy.Rd            | 1 -
|  man/noded_with_condition.Rd    | 1 -
|  man/set.Rd                     | 1 -
|  man/which_leaf.Rd              | 1 -
|  11 files changed, 12 deletions(-)

* 2015-01-26(Tal Galili) `which_node` - a new function which finds Which node is common to a group of labels |fbaef43| 
|  NAMESPACE                |  1 +
|  NEWS                     |  2 ++
|  R/noded_with_condition.R | 46 ++++++++++++++++++++++++++++++++++++++++++++++
|  man/which_node.Rd        | 43 +++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 92 insertions(+)

* 2015-01-26(Tal Galili) update `get_nodes_attr` - added the "id" parameter (to get attributes of only a subset of id's) |de61889| 
|  NEWS                          |  1 +
|  R/attr_access.R               | 26 +++++++++++++++++++++++---
|  inst/tests/test-attr_access.R |  5 +++++
|  man/get_nodes_attr.Rd         |  8 +++++++-
|  4 files changed, 36 insertions(+), 4 deletions(-)

* 2015-01-26(Tal Galili) Rename `get_branches_attr` to be `get_root_branches_attr` |3e38822| 
|  NAMESPACE                                |  2 +-
|  NEWS                                     |  2 +-
|  R/attr_access.R                          |  4 ++--
|  R/unbranch.R                             | 12 +++++-----
|  inst/tests/test-unbranch.R               |  6 ++---
|  man/assign_values_to_branches_edgePar.Rd |  2 +-
|  man/get_branches_attr.Rd                 | 38 ------------------------------
|  man/get_root_branches_attr.Rd            | 38 ++++++++++++++++++++++++++++++
|  man/remove_branches_edgePar.Rd           |  2 +-
|  9 files changed, 53 insertions(+), 53 deletions(-)

* 2015-01-26(Tal Galili) minor docs update and version bump |5ac4ac6| 
|  DESCRIPTION                     | 4 ++--
|  R/distinct_edges.R              | 1 -
|  man/dend_diff.Rd                | 2 ++
|  man/highlight_distinct_edges.Rd | 1 -
|  4 files changed, 4 insertions(+), 4 deletions(-)

* 2015-01-26(Tal Galili) Made dend_diff work with dendlist |4fd37af| 
|  NAMESPACE          |  2 ++
|  NEWS               |  2 +-
|  R/distinct_edges.R | 46 ++++++++++++++++++++++++++++++++++++++++++----
|  man/dend_diff.Rd   | 19 +++++++++++++++----
|  4 files changed, 60 insertions(+), 9 deletions(-)

* 2015-01-26(Tal Galili) Made highlight_distinct_edges work with dendlist (and added a nice iris example) |edcae3a| 
|  NAMESPACE                       |  2 ++
|  NEWS                            |  2 +-
|  R/distinct_edges.R              | 51 +++++++++++++++++++++++++++++++++++++--
|  man/highlight_distinct_edges.Rd | 34 +++++++++++++++++++++++---
|  4 files changed, 82 insertions(+), 7 deletions(-)

* 2015-01-25(Tal Galili) `cutree_1h.dendrogram` and `cutree_1k.dendrogram` - will now create clusters as the number of items if k==nleaves(tree) or if h<0. This is both consistent with stats::hclust, but it also "makes sense" (since this is well defined for ANY tree) |7afd28e| 
|  NEWS                                |  1 +
|  R/cutree.dendrogram.R               | 21 ++++++++++++++++++++-
|  inst/tests/test-cut_lower_fun.R     |  9 +++++++++
|  inst/tests/test-cutree.dendrogram.R | 33 ++++++++++++++++++++++++---------
|  inst/tests/test-distinct_edges.R    |  1 +
|  5 files changed, 55 insertions(+), 10 deletions(-)

* 2015-01-25(Tal Galili) `cutree` - now produces warnings if it returns 0's. i.e.: when it can't cut the tree based on the required parameter. (following isue #5 reported by grafab) |fce5319| 
|  NEWS                                |  2 +-
|  R/cutree.dendrogram.R               | 13 ++++++++++---
|  inst/tests/test-cutree.dendrogram.R | 24 ++++++++++++++++++++++++
|  man/cutree-methods.Rd               |  7 ++++++-
|  4 files changed, 41 insertions(+), 5 deletions(-)

* 2015-01-25(Tal Galili) Various doc .Rd fixes. |45b21e0| 
|  NAMESPACE                       |  1 -
|  R/ape.R                         |  2 +-
|  R/distinct_edges.R              | 12 ++++++------
|  R/tanglegram.R                  |  1 +
|  man/dend_diff.Rd                |  2 +-
|  man/distinct_edges.Rd           |  2 +-
|  man/highlight_distinct_edges.Rd |  6 +++---
|  man/partition_leaves.Rd         |  2 +-
|  man/tanglegram.Rd               |  1 +
|  9 files changed, 15 insertions(+), 14 deletions(-)

* 2015-01-25(Tal Galili) `tanglegram` - a new highlight_distinct_edges parameter (default is TRUE) |7a7e758| 
|  NEWS              | 1 +
|  R/tanglegram.R    | 6 ++++++
|  man/tanglegram.Rd | 2 ++
|  3 files changed, 9 insertions(+)

* 2015-01-25(Tal Galili) New function: all.equal.dendrogram/all.equal.dendlist - Global Comparison of two (or more) dendrograms |8edaa3b| 
|  NAMESPACE                   |   2 +
|  NEWS                        |   1 +
|  R/all.equal.R               | 157 ++++++++++++++++++++++++++++++++++++++++++
|  man/all.equal.dendrogram.Rd |  65 +++++++++++++++++
|  4 files changed, 225 insertions(+)

* 2015-01-25(Tal Galili) `labels<-.dendrogram` - no longer forces as.character conversion |6a6223b| 
|  NEWS                             | 1 +
|  R/labels.R                       | 3 ++-
|  inst/tests/test-set.dendrogram.R | 5 ++++-
|  3 files changed, 7 insertions(+), 2 deletions(-)

* 2015-01-25(Tal Galili) minor test fix |0b8b076| 
|  inst/tests/test-distinct_edges.R | 11 ++++++++---
|  1 file changed, 8 insertions(+), 3 deletions(-)

* 2015-01-25(Tal Galili) use ave instead of ward in hclust (make sure the change to ward.D will no longer cause issues) |a220126| 
|  inst/tests/test-unbranch.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2015-01-25(Tal Galili) New functions (with doc and tests):    * partition_leaves - A list with labels for each subtree (edge)    * distinct_edges - Finds the edges present in the first tree but not in the second    * highlight_distinct_edges - Highlight distint edges in a tree (compared to another one)    * dend_diff - Plots two trees side by side, highlighting edges unique to each tree in red.    * dist.dendlist - Topological Distances Between Two dendrograms (currently only the Robinson-Foulds distance) |05b4ebc| 
|  NAMESPACE                        |   5 +
|  NEWS                             |  17 ++-
|  R/distinct_edges.R               | 291 +++++++++++++++++++++++++++++++++++++
|  inst/tests/test-distinct_edges.R |  39 +++++
|  man/dend_diff.Rd                 |  42 ++++++
|  man/dist.dendlist.Rd             |  38 +++++
|  man/distinct_edges.Rd            |  36 +++++
|  man/highlight_distinct_edges.Rd  |  49 +++++++
|  man/partition_leaves.Rd          |  43 ++++++
|  9 files changed, 559 insertions(+), 1 deletion(-)

* 2015-01-25(Tal Galili) Small document update to assign_values_to_branches_edgePar |330ed91| 
|  R/attr_access.R                          | 3 ++-
|  man/assign_values_to_branches_edgePar.Rd | 3 ++-
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2015-01-25(Tal Galili) cor.dendlist - Correlation matrix between a list of trees. |a3d8371| 
|  NAMESPACE           |  1 +
|  NEWS                |  2 ++
|  R/cor.dendlist.R    | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/cor.dendlist.Rd | 43 ++++++++++++++++++++++++++++
|  4 files changed, 123 insertions(+)

* 2015-01-24(Tal Galili) A new phylo method for `labels` and `labels<-` |f51e36a| 
|  DESCRIPTION          |  2 +-
|  NAMESPACE            |  2 ++
|  NEWS                 |  7 ++++++-
|  R/labels.R           | 38 ++++++++++++++++++++++++++++++++++++++
|  man/labels-assign.Rd |  6 ++++++
|  5 files changed, 53 insertions(+), 2 deletions(-)

* 2015-01-24(Tal Galili) `nleaves.phylo` - no longer require conversion to a dendrogram in order to compute. |8b5dad4| 
|  R/nleaves.R | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2015-01-21(Tal Galili) 1) new file ape.R - to which I moved `as.dendrogram.phylo` and `as.phylo.dendrogram` functions to. |e94bd9b| 
|  DESCRIPTION      |  4 ++--
|  NAMESPACE        |  1 +
|  NEWS             |  7 +++++++
|  R/ape.R          | 42 ++++++++++++++++++++++++++++++++++++++++++
|  R/nleaves.R      | 22 ----------------------
|  tests/test-all.R |  2 ++
|  6 files changed, 54 insertions(+), 24 deletions(-)

* 2014-12-08(Tal Galili) Bump to 0.17.6 |a4d0561| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 8 ++++++++
|  2 files changed, 10 insertions(+), 2 deletions(-)

* 2014-12-08(Tal Galili) roxygen2 from 4.0.1 to 4.0.2 |b46267b| 
|  man/Bk.Rd                                  |  2 +-
|  man/Bk_permutations.Rd                     |  2 +-
|  man/Bk_plot.Rd                             |  2 +-
|  man/DendSer.dendrogram.Rd                  |  2 +-
|  man/FM_index.Rd                            |  2 +-
|  man/FM_index_R.Rd                          |  2 +-
|  man/FM_index_permutation.Rd                |  2 +-
|  man/FM_index_profdpm.Rd                    |  2 +-
|  man/all_couple_rotations_at_k.Rd           |  2 +-
|  man/all_unique.Rd                          |  2 +-
|  man/as.dendlist.Rd                         |  2 +-
|  man/as_hclust_fixed.Rd                     |  2 +-
|  man/assign_dendextend_options.Rd           |  2 +-
|  man/assign_values_to_branches_edgePar.Rd   |  2 +-
|  man/assign_values_to_leaves_edgePar.Rd     |  2 +-
|  man/assign_values_to_leaves_nodePar.Rd     |  2 +-
|  man/assign_values_to_nodes_nodePar.Rd      |  2 +-
|  man/bakers_gamma_for_2_k_matrix.Rd         |  2 +-
|  man/branches_attr_by_clusters.Rd           |  2 +-
|  man/branches_attr_by_labels.Rd             |  2 +-
|  man/click_rotate.Rd                        |  6 +++---
|  man/color_branches.Rd                      |  2 +-
|  man/color_labels.Rd                        |  8 ++++----
|  man/colored_bars.Rd                        |  2 +-
|  man/cor_bakers_gamma.Rd                    |  6 +++---
|  man/cor_cophenetic.Rd                      |  6 +++---
|  man/count_terminal_nodes.Rd                |  2 +-
|  man/cut_lower_fun.Rd                       |  2 +-
|  man/cutree-methods.Rd                      |  6 +++---
|  man/cutree_1h.dendrogram.Rd                | 10 +++++-----
|  man/cutree_1k.dendrogram.Rd                |  2 +-
|  man/d3dendro_options.Rd                    |  2 +-
|  man/d3dendrogram.Rd                        |  2 +-
|  man/dendextend-package.Rd                  |  2 +-
|  man/dendextend_options.Rd                  |  2 +-
|  man/dendlist.Rd                            |  2 +-
|  man/duplicate_leaf.Rd                      |  2 +-
|  man/entanglement.Rd                        |  6 +++---
|  man/fac2num.Rd                             |  2 +-
|  man/fix_members_attr.dendrogram.Rd         |  2 +-
|  man/flatten.dendrogram.Rd                  |  2 +-
|  man/flip_leaves.Rd                         |  2 +-
|  man/get_branches_attr.Rd                   |  2 +-
|  man/get_branches_heights.Rd                |  2 +-
|  man/get_childrens_heights.Rd               |  2 +-
|  man/get_leaves_attr.Rd                     |  2 +-
|  man/get_nodes_attr.Rd                      |  2 +-
|  man/get_nodes_xy.Rd                        |  2 +-
|  man/hang.dendrogram.Rd                     |  2 +-
|  man/heights_per_k.dendrogram.Rd            |  2 +-
|  man/identify.dendrogram.Rd                 |  2 +-
|  man/intersect_trees.Rd                     |  2 +-
|  man/is.dendlist.Rd                         |  2 +-
|  man/is.dendrogram.Rd                       |  2 +-
|  man/is.hclust.Rd                           |  2 +-
|  man/is.natural.number.Rd                   |  2 +-
|  man/is.phylo.Rd                            |  2 +-
|  man/is_null_list.Rd                        |  2 +-
|  man/labels-assign.Rd                       |  6 +++---
|  man/labels_colors.Rd                       |  2 +-
|  man/leaf_Colors.Rd                         |  2 +-
|  man/lowest_common_branch.Rd                |  2 +-
|  man/match_order_by_labels.Rd               |  2 +-
|  man/match_order_dendrogram_by_old_order.Rd |  2 +-
|  man/na_locf.Rd                             |  2 +-
|  man/nleaves.Rd                             |  6 +++---
|  man/nnodes.Rd                              |  2 +-
|  man/noded_with_condition.Rd                |  2 +-
|  man/order.dendrogram-assign.Rd             |  2 +-
|  man/order.hclust.Rd                        |  2 +-
|  man/pipe.Rd                                |  2 +-
|  man/plot_horiz.dendrogram.Rd               |  2 +-
|  man/prune.Rd                               |  6 +++---
|  man/prune_leaf.Rd                          |  2 +-
|  man/pvclust_show_signif.Rd                 |  2 +-
|  man/pvclust_show_signif_gradient.Rd        |  2 +-
|  man/raise.dendrogram.Rd                    |  2 +-
|  man/rank_branches.Rd                       |  2 +-
|  man/rank_order.dendrogram.Rd               |  2 +-
|  man/rect.dendrogram.Rd                     |  6 +++---
|  man/remove_branches_edgePar.Rd             |  2 +-
|  man/remove_leaves_nodePar.Rd               |  2 +-
|  man/rllply.Rd                              |  2 +-
|  man/rotate.Rd                              |  6 +++---
|  man/rotate_DendSer.Rd                      |  2 +-
|  man/sample.dendrogram.Rd                   |  2 +-
|  man/set.Rd                                 |  6 +++---
|  man/shuffle.Rd                             |  6 +++---
|  man/sort_2_clusters_vectors.Rd             |  2 +-
|  man/sort_dist_mat.Rd                       |  2 +-
|  man/sort_levels_values.Rd                  |  2 +-
|  man/tanglegram.Rd                          |  6 +++---
|  man/unbranch.Rd                            |  6 +++---
|  man/unclass_dend.Rd                        |  2 +-
|  man/untangle.Rd                            |  6 +++---
|  man/untangle_DendSer.Rd                    |  2 +-
|  man/untangle_random_search.Rd              |  2 +-
|  man/untangle_step_rotate_1side.Rd          |  2 +-
|  man/untangle_step_rotate_2side.Rd          |  2 +-
|  man/which_leaf.Rd                          |  2 +-
|  100 files changed, 137 insertions(+), 137 deletions(-)

* 2014-12-08(Tal Galili) dist_long - Turns a dist object to a "long" table. |a5fee75| 
|  NAMESPACE        |  4 +++-
|  R/dist_fun.R     | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/dist_long.Rd | 28 ++++++++++++++++++++++++
|  3 files changed, 94 insertions(+), 1 deletion(-)

* 2014-12-08(Tal Galili) Update text (per request by CRAN) |46697aa| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-12-08(Tal Galili) text editing |5afb4dd| 
|  vignettes/introduction.Rmd | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-10-04(Tal Galili) Ignore ^\.travis.yml$ when building the package. |45cba35| 
|  .Rbuildignore | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2014-10-04(Tal Galili) Adding .travis.yml |6e17ba3| 
|  .travis.yml | 24 ++++++++++++++++++++++++
|  README.md   |  3 +++
|  2 files changed, 27 insertions(+)

* 2014-09-22(Tal Galili) VIGNETTE - fix several typos and grammatical mistakes. |7e41e50| 
|  NAMESPACE                  |  2 +-
|  NEWS                       |  3 +++
|  TODO                       | 61 ++++++++++++++++++++++++++++++++++++++++++++
|  vignettes/introduction.Rmd | 26 +++++++++----------
|  4 files changed, 78 insertions(+), 14 deletions(-)

* 2014-09-22(Tal Galili) Fixing - \usage lines wider than 90 characters |fff3e9f| 
|  NEWS                    | 3 ++-
|  R/cor_bakers_gamma.R    | 6 ++++--
|  man/cor_bakers_gamma.Rd | 6 ++++--
|  3 files changed, 10 insertions(+), 5 deletions(-)

* 2014-09-22(Tal Galili) Several bug fixes to the docs. |45bf641| 
|  NAMESPACE               |  2 +-
|  NEWS                    | 11 ++++++++
|  R/cor_bakers_gamma.R    | 18 ++++++++++++-
|  R/dendlist.R            | 64 +++++++++++++++++++++++++++++++----------------
|  R/set.dendrogram.R      |  1 +
|  man/cor_bakers_gamma.Rd | 13 ++++++++--
|  man/dendlist.Rd         | 14 +++++++++++
|  man/plot.dendlist.Rd    | 34 -------------------------
|  man/set.Rd              |  1 +
|  9 files changed, 98 insertions(+), 60 deletions(-)

* 2014-09-22(Tal Galili) Fixing tests as well. (with as.hclust for sub dends. |bf0fd2b| 
|  NEWS                                |  2 +-
|  inst/tests/test-cutree.dendrogram.R | 86 +++++++++++++++++------------------
|  inst/tests/test-labels-assign.R     |  3 +-
|  3 files changed, 46 insertions(+), 45 deletions(-)

* 2014-09-22(Tal Galili) `order.dendrogram<-` - commenting off an example which (as of R 3.1.1-patched) produces an error (as it should). |4a672fa| 
|  DESCRIPTION                    |  4 ++--
|  NEWS                           | 10 ++++++++++
|  R/labels.R                     |  4 ++--
|  R/zzz.R                        |  1 +
|  man/order.dendrogram-assign.Rd |  4 ++--
|  5 files changed, 17 insertions(+), 6 deletions(-)

* 2014-09-20(Tal Galili) Added set.data.table - informs the user of the conflict in "set" between dendextend and data.table. |e167228| 
|  DESCRIPTION        |  5 +++--
|  NAMESPACE          |  1 +
|  NEWS               |  2 ++
|  R/set.dendrogram.R | 10 ++++++++++
|  man/set.Rd         |  2 ++
|  5 files changed, 18 insertions(+), 2 deletions(-)

* 2014-09-20(Tal Galili) added sessionInfo to VIGNETTE |f34c02a| 
|  NEWS                       | 8 ++++++++
|  vignettes/introduction.Rmd | 8 ++++++++
|  2 files changed, 16 insertions(+)

* 2014-08-26(Tal Galili) full name credit. |16ee14d| 
|  NEWS | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-08-26(Tal Galili) link to the bug report, and thanked varmara. |0e10459| 
|  NEWS | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-08-26(Tal Galili) color_labels - now can handle the coloring of labels when the function is without k and h, but that it is not possible to cut the tree to nleaves items (due to several leaves with 0 height). This is done by not doing any cutting in such cases, and just directly using labels_colors. (added tests) |734fe99| 
|  DESCRIPTION                     |  4 ++--
|  NEWS                            |  7 +++++++
|  R/color_branches.R              |  8 ++++++--
|  inst/tests/test-labels_colors.R | 35 +++++++++++++++++++++++++++++++++++
|  man/color_labels.Rd             |  3 ---
|  5 files changed, 50 insertions(+), 7 deletions(-)

* 2014-08-25(Tal Galili) Version 0.17.2 (updated NEWS DESCRIPTION, etc) |fa1dba2| 
|  DESCRIPTION |  4 ++--
|  NEWS        |  7 +++++--
|  NEWS.md     | 19 +++++++++++++++++--
|  TODO        | 11 ++++++++++-
|  4 files changed, 34 insertions(+), 7 deletions(-)

* 2014-08-25(Tal Galili) Add to introduction.Rmd how to install the package from github. |0ecf3af| 
|  README.md                  |  6 +-----
|  vignettes/introduction.Rmd | 40 ++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 41 insertions(+), 5 deletions(-)

* 2014-08-25(Tal Galili) Added the function assign_values_to_leaves_edgePar |8ff1d61| 
|  NAMESPACE                              |  1 +
|  R/attr_access.R                        | 92 +++++++++++++++++++++++++++++++-
|  man/assign_values_to_leaves_edgePar.Rd | 52 ++++++++++++++++++
|  3 files changed, 144 insertions(+), 1 deletion(-)

* 2014-08-23(Tal Galili) capitalize R Core Team |48b8f6d| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-08-23(Tal Galili) Added cor_bakers_gamma.dendlist |08e0276| 
|  NAMESPACE            | 1 +
|  NEWS                 | 6 +++++-
|  R/cor_bakers_gamma.R | 7 +++++++
|  TODO                 | 3 +++
|  4 files changed, 16 insertions(+), 1 deletion(-)

* 2014-08-23(Tal Galili) VIGNETTE Fix some typos and mistakes |33316b3| 
|  NEWS                       | 11 +++++++++--
|  vignettes/introduction.Rmd |  8 ++++----
|  2 files changed, 13 insertions(+), 6 deletions(-)

* 2014-08-19(Tal Galili) more editing, and thanks. |d47c870| 
|  NEWS    |  1 +
|  R/zzz.R | 29 +++++++++++++++++------------
|  2 files changed, 18 insertions(+), 12 deletions(-)

* 2014-08-19(Tal Galili) compacted ‘dendextend-tutorial.pdf’ from 725Kb to 551Kb |5944f4e| 
|  DESCRIPTION                      |   2 +-
|  NEWS                             |  15 +++++++++++++
|  NEWS.md                          |  15 +++++++++++++
|  R/zzz.R                          |  42 ++++++++++++++++++++++++++++++++++---
|  inst/doc/dendextend-tutorial.pdf | Bin 754947 -> 564592 bytes
|  5 files changed, 70 insertions(+), 4 deletions(-)

* 2014-08-19(Tal Galili) updated |6c952e3| 
|  ChangeLog | 37 +++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  4 ++++
|  2 files changed, 41 insertions(+)

* 2014-08-19(Tal Galili) Have the package build the vignette. |8653ed9| 
|  DESCRIPTION | 1 +
|  NEWS        | 1 +
|  2 files changed, 2 insertions(+)

* 2014-08-19(Tal Galili) Update the location of vignettes on github. |ec66fa0| 
|  README.md | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2014-08-19(Tal Galili) Fixed introduction.html to not overlap the bounderies of the code area. |7d47c9e| 
|  vignettes/introduction.Rmd | 37 ++++++++++++++++++++++++-------------
|  1 file changed, 24 insertions(+), 13 deletions(-)

* 2014-08-19(Tal Galili) Created a copy of "introduction.html" in inst/ignored (so people could see it on github) |0a1195a| 
|  .Rbuildignore                  |    7 +-
|  NEWS                           |    2 +-
|  inst/ignored/introduction.html | 1543 ++++++++++++++++++++++++++++++++++++++
|  3 files changed, 1549 insertions(+), 3 deletions(-)

* 2014-08-19(Tal Galili) Moved dendextend-tutorial.rnw to vignettes\disabled - so it is still there, but not compiled. Also moved dendextend-tutorial.pdf to inst\doc - so there is a copy of this older vignette, but without needed to run it with all the benchmarks... (it is also compressed) |5558f2c| 
|  NEWS                                       |    3 +
|  R/zzz.R                                    |    7 +-
|  inst/doc/dendextend-tutorial.pdf           |  Bin 0 -> 754947 bytes
|  vignettes/dendextend-tutorial.pdf          | 9793 --------------------------
|  vignettes/dendextend-tutorial.rnw          | 2024 ------
|  vignettes/disabled/dendextend-tutorial.rnw | 2024 ++++++
|  6 files changed, 2031 insertions(+), 11820 deletions(-)

* 2014-08-19(Tal Galili) erased file |a97af45| 
|  R/dendlist - Copy.R | 275 --------------------------------------------------
|  1 file changed, 275 deletions(-)

* 2014-08-19(Tal Galili) Update NEWS.md and ChangeLog before CRAN release. for 0.17.0 |4e47159| 
|  ChangeLog | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   | 11 ++++++---
|  2 files changed, 82 insertions(+), 3 deletions(-)

* 2014-08-19(Tal Galili) Moved ggdendro, labeltodendro, dendroextras, ape to "Enhances:" in DESCRIPTION. (include fixing tests, and adding library - so to through errors in case the package is not available) |992d09d| 
|  DESCRIPTION              | 11 ++++++-----
|  NAMESPACE                |  1 -
|  NEWS                     |  2 +-
|  R/DendSer.R              |  2 +-
|  R/bk_method.R            |  2 +-
|  R/dendextend-package.R   |  2 +-
|  R/nleaves.R              |  6 +++---
|  R/prune.R                |  2 +-
|  R/pvclust.R              |  2 +-
|  R/rotate.R               |  2 +-
|  R/unbranch.R             |  2 +-
|  inst/tests/test-rotate.R |  2 +-
|  12 files changed, 18 insertions(+), 18 deletions(-)

* 2014-08-19(Tal Galili) Added spaces to docs |d4ce41a| 
|  man/as.dendlist.Rd | 22 ----------------------
|  1 file changed, 22 deletions(-)

* 2014-08-19(Tal Galili) new function: `rainbow_fun` - uses rainbow_hcl, or rainbow (if colorspace is not available) |f71d025| 
|  DESCRIPTION          |   2 +-
|  NEWS                 |   9 +-
|  R/branches_attr_by.R |   4 +-
|  R/color_branches.R   |  14 +--
|  R/colored_bars.R     |   1 +
|  R/dendlist - Copy.R  | 275 +++++++++++++++++++++++++++++++++++++++++++++++++
|  R/labels_colors.R    |   4 +-
|  R/rainbow_fun.R      |  33 ++++++
|  man/as.dendlist.Rd   |  22 ++++
|  man/colored_bars.Rd  |   1 +
|  10 files changed, 345 insertions(+), 20 deletions(-)

* 2014-08-19(Tal Galili) Break lines which were too long. |fd1f130| 
|  R/pvclust.R                         | 8 ++++++--
|  man/pvclust_show_signif.Rd          | 4 +++-
|  man/pvclust_show_signif_gradient.Rd | 4 +++-
|  3 files changed, 12 insertions(+), 4 deletions(-)

* 2014-08-19(Tal Galili) Added warn = dendextend_options("warn") to docs |94bd5f4| 
|  R/cutree.dendrogram.R | 5 +++--
|  man/cutree-methods.Rd | 5 +++--
|  2 files changed, 6 insertions(+), 4 deletions(-)

* 2014-08-19(Tal Galili) edgeText is not needed here. |9a4441e| 
|  R/get_nodes_xy.R | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2014-08-19(Tal Galili) laply -> lapply , and some tree to dend fixes. |4167e7b| 
|  R/untangle.R | 10 +++++-----
|  1 file changed, 5 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili) paramters to parameters |b4097c8| 
|  DESCRIPTION                | 2 +-
|  vignettes/introduction.Rmd | 8 ++++----
|  2 files changed, 5 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili) The following files are already in R: 'jss.bst', 'jss.cls' and I remove them from the package. |954508e| 
|  .Rbuildignore | 2 ++
|  1 file changed, 2 insertions(+)

* 2014-08-18(Tal Galili) all.unique to all_unique in the example. |a100582| 
|  R/color_branches.R | 10 +++++-----
|  man/all_unique.Rd  | 10 +++++-----
|  2 files changed, 10 insertions(+), 10 deletions(-)

* 2014-08-18(Tal Galili) Update various files |6bc8a22| 
|  .Rbuildignore        |   5 +-
|  ChangeLog            | 404 +++++++++++++++++++++++++++++++++++++++++++++++++
|  DESCRIPTION          |   2 +-
|  NEWS.md              |  52 +++++++
|  TODO                 |   8 +
|  vignettes/.gitignore |   3 +-
|  6 files changed, 470 insertions(+), 4 deletions(-)

* 2014-08-18(Tal Galili) cutree.hclust - added a dummy parameter |786c408| 
|  R/cutree.dendrogram.R | 1 +
|  1 file changed, 1 insertion(+)

* 2014-08-18(Tal Galili) Added a dendextendRcpp section. (and removed the not-working ggdendro section) |3d381da| 
|  vignettes/introduction.Rmd | 38 ++++++--------------------------------
|  1 file changed, 6 insertions(+), 32 deletions(-)

* 2014-08-18(Tal Galili) `cutree.dendrogram` - added a parameter (NA_to_0L) to control it. Also, make `Bk` work with cutree(NA_to_0L = FALSE) |b33a2a7| 
|  NEWS                  | 3 ++-
|  R/bk_method.R         | 4 ++--
|  R/cutree.dendrogram.R | 6 +++++-
|  man/cutree-methods.Rd | 4 ++++
|  4 files changed, 13 insertions(+), 4 deletions(-)

* 2014-08-18(Tal Galili) vignettes: Cophenetic correlation and Bk plots. |9cdc2d5| 
|  vignettes/introduction.Rmd | 133 ++++++++++++++++++++++++++++++++++++++++++-
|  1 file changed, 131 insertions(+), 2 deletions(-)

* 2014-08-18(Tal Galili) vignettes: Correlation measures - Baker's Gamma Index |b12f2df| 
|  vignettes/introduction.Rmd | 68 ++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 68 insertions(+)

* 2014-08-18(Tal Galili) vignettes: tanglegram |6666a97| 
|  vignettes/introduction.Rmd | 139 +++++++++++++++++++++++++++++++++++++++++--
|  1 file changed, 135 insertions(+), 4 deletions(-)

* 2014-08-18(Tal Galili) Fixing how the tests are printed by adding cat("\n") |6d5169c| 
|  inst/tests/test-entanglement.R | 3 +++
|  1 file changed, 3 insertions(+)

* 2014-08-18(Tal Galili) Test in set.dendrogram needed - dendextend_options("warn", TRUE) |576f951| 
|  inst/tests/test-set.dendrogram.R | 23 ++++++++++++++++++-----
|  1 file changed, 18 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili) Test for Color recycling needed - dendextend_options("warn", TRUE) |006168a| 
|  inst/tests/test-labels_colors.R | 2 ++
|  1 file changed, 2 insertions(+)

* 2014-08-18(Tal Galili) Rename all.unique to all_unique |3411cc2| 
|  NAMESPACE                 |  3 ++-
|  NEWS                      |  4 ++--
|  R/color_branches.R        | 27 ++++++++++++++++++++-------
|  inst/tests/test-general.R |  9 +++++----
|  man/all.unique.Rd         | 32 --------------------------------
|  man/all_unique.Rd         | 32 ++++++++++++++++++++++++++++++++
|  6 files changed, 61 insertions(+), 46 deletions(-)

* 2014-08-18(Tal Galili) `cutree.dendrogram` - replaces NA values with 0L - adjust the tests. |49a4bd8| 
|  NEWS                                | 2 +-
|  inst/tests/test-cutree.dendrogram.R | 8 ++++----
|  2 files changed, 5 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili)    * `untangle_step_rotate_1side` - added "leaves_matching_method" parameter.    * `entanglement.dendrogram` - changed the default of "leaves_matching_method" to be "labels" (slower, but safer for the user...) |f77b4b6| 
|  NEWS                              |  2 ++
|  R/entanglement.R                  |  7 ++++---
|  R/untangle.R                      | 37 ++++++++++++++++++++++++++++++-------
|  man/entanglement.Rd               |  7 ++++---
|  man/untangle_random_search.Rd     |  4 ++--
|  man/untangle_step_rotate_1side.Rd | 19 ++++++++++++++++++-
|  6 files changed, 60 insertions(+), 16 deletions(-)

* 2014-08-18(Tal Galili) tanglegram: Changed the deafult in cex_main to 2 |d02bd09| 
|  R/tanglegram.R    | 4 ++--
|  man/tanglegram.Rd | 2 +-
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2014-08-18(Tal Galili) `untangle` - has a default to method (DendSet) |424b02d| 
|  NEWS            | 1 +
|  R/untangle.R    | 9 +++++++--
|  man/untangle.Rd | 4 +++-
|  3 files changed, 11 insertions(+), 3 deletions(-)

* 2014-08-18(Tal Galili) `set.dendrogram` - added a "labels_to_char" option. |6f6f0cf| 
|  NEWS               | 1 +
|  R/set.dendrogram.R | 4 ++++
|  man/set.Rd         | 2 ++
|  3 files changed, 7 insertions(+)

* 2014-08-18(Tal Galili) vignettes: pvclust, and dendlist sections. |fe7206c| 
|  vignettes/introduction.Rmd | 72 ++++++++++++++++++++++++++++++++++++--------
|  1 file changed, 60 insertions(+), 12 deletions(-)

* 2014-08-18(Tal Galili) New function: `head.dendlist` |bd03014| 
|  NAMESPACE    |  1 +
|  NEWS         |  1 +
|  R/dendlist.R | 15 +++++++++++++++
|  3 files changed, 17 insertions(+)

* 2014-08-18(Tal Galili) update pvrect2 - if we'd ever want one with adjustable lower rects... |07866e2| 
|  R/pvclust.R | 15 ++++++++++++---
|  1 file changed, 12 insertions(+), 3 deletions(-)

* 2014-08-18(Tal Galili) Added pvrect2 - a copy of pvrect |185e6bf| 
|  R/pvclust.R | 109 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 109 insertions(+)

* 2014-08-18(Tal Galili) vignettes: "Enhancing other packages" examples for DendSer, gplots and dynamicTreeCut |69d0a52| 
|  vignettes/introduction.Rmd | 92 ++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 92 insertions(+)

* 2014-08-18(Tal Galili) Added is.infinite2 and used it so to avoid endless warnings over type coercion... |b778982| 
|  R/attr_access.R | 22 +++++++++++++++++-----
|  R/dendlist.R    |  2 +-
|  2 files changed, 18 insertions(+), 6 deletions(-)

* 2014-08-18(Tal Galili) `assign_values_to_branches_edgePar`, `assign_values_to_nodes_nodePar`, `assign_values_to_leaves_nodePar` - now ignores "Inf" also when it is a character by adding as.numeric (and not only if it is numeric!) (this might be a problem if someone would try to update a label with the name "Inf"). |a6a2a78| 
|  NEWS                             |  4 ++++
|  R/attr_access.R                  | 11 ++++++++---
|  R/branches_attr_by.R             |  2 +-
|  man/branches_attr_by_clusters.Rd |  2 +-
|  4 files changed, 14 insertions(+), 5 deletions(-)

* 2014-08-18(Tal Galili) A new test for `assign_values_to_branches_edgePar` - make sure it deals with Inf and "Inf". |9036ac1| 
|  inst/tests/test-branches_attr_by.R | 76 ++++++++++++++++++++++++++++++++++++
|  1 file changed, 76 insertions(+)

* 2014-08-17(Tal Galili) Made sure "rotate_DendSer" shows in the docs. |1409976| 
|  R/DendSer.R               | 6 +++---
|  man/DendSer.dendrogram.Rd | 2 +-
|  man/dendlist.Rd           | 2 +-
|  man/rotate_DendSer.Rd     | 2 +-
|  man/untangle_DendSer.Rd   | 2 +-
|  5 files changed, 7 insertions(+), 7 deletions(-)

* 2014-08-17(Tal Galili) Adding DendSer.R (moving functions into it) |c9f589b| 
|  NEWS         |   1 +
|  R/DendSer.R  | 130 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/untangle.R | 110 ------------------------------------------------
|  3 files changed, 131 insertions(+), 110 deletions(-)

* 2014-08-17(Tal Galili) vignettes: Adding extra bars and rectangles |9040574| 
|  vignettes/introduction.Rmd | 66 ++++++++++++++++++++++++++++++++++++++++++--
|  1 file changed, 64 insertions(+), 2 deletions(-)

* 2014-08-17(Tal Galili) `colored_bars` - fix for multiple bars to work. +have scale default be better for multiple bars. |2feadad| 
|  NEWS                |  3 ++-
|  R/colored_bars.R    | 28 ++++++++++++++++++++--------
|  man/colored_bars.Rd | 13 +++++++++----
|  3 files changed, 31 insertions(+), 13 deletions(-)

* 2014-08-16(Tal Galili) `rect.dendrogram` - Made sure the heights are working properly! |636a223| 
|  NEWS                |  1 +
|  R/rect.dendrogram.R | 22 +++++++++++++++-------
|  2 files changed, 16 insertions(+), 7 deletions(-)

* 2014-08-16(Tal Galili) rect.dendrogram - fix a bug with the location of the rect's (using "tree" and not "dend") |792929f| 
|  NEWS                | 2 +-
|  R/rect.dendrogram.R | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2014-08-16(Tal Galili) `intersect_trees` - now returns a dendlist. |b2fa915| 
|  NEWS                   | 1 +
|  R/prune.R              | 4 ++--
|  man/intersect_trees.Rd | 2 +-
|  3 files changed, 4 insertions(+), 3 deletions(-)

* 2014-08-16(Tal Galili) Rename files: trim.R -> prune.R |83f6388| 
|  NEWS      |   1 +
|  R/prune.R | 253 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/trim.R  | 253 ------------------------------------------------------------
|  3 files changed, 254 insertions(+), 253 deletions(-)

* 2014-08-15(Tal Galili) Use "set" in order to not confuse the reader... |6e048d2| 
|  vignettes/introduction.Rmd | 30 ++++++++++++++++++++++--------
|  1 file changed, 22 insertions(+), 8 deletions(-)

* 2014-08-14(Tal Galili) Vignettes: Writing "Changing a dendrogram’s structure" |197d1fd| 
|  vignettes/introduction.Rmd | 64 ++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 64 insertions(+)

* 2014-08-14(Tal Galili) color_branches - warn of missing k only if warn=TRUE |f8677ba| 
|  R/color_branches.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-08-14(Tal Galili) vignettes: moved to dend15 and dend13. Wrote: * Setting a dendrogram's nodes/leaves (points) * Setting a dendrogram's branches |ffb1aaf| 
|  vignettes/introduction.Rmd | 226 +++++++++++++++++++++++++++++++------------
|  1 file changed, 164 insertions(+), 62 deletions(-)

* 2014-08-14(Tal Galili) `branches_attr_by_labels` now uses `dendextend_options("warn")` to decide if to print that labels were coerced into character. |a4fd3ef| 
|  NEWS                 | 1 +
|  R/branches_attr_by.R | 2 +-
|  2 files changed, 2 insertions(+), 1 deletion(-)

* 2014-08-14(Tal Galili) Fix headers. |a3e5f79| 
|  NEWS | 13 ++++++++-----
|  1 file changed, 8 insertions(+), 5 deletions(-)

* 2014-08-14(Tal Galili) `branches_attr_by_clusters` and `branches_attr_by_labels` - moved from using NA to Inf. |2f3f5df| 
|  NEWS                           |  1 +
|  R/branches_attr_by.R           | 16 ++++++++--------
|  man/branches_attr_by_labels.Rd |  4 ++--
|  3 files changed, 11 insertions(+), 10 deletions(-)

* 2014-08-14(Tal Galili) Move the function branches_attr_by_labels between two files |1e65ab0| 
|  NEWS                     |   2 +-
|  R/branches_attr_by.R     | 113 +++++++++++++++++++++++++++++++++++++++++++++
|  R/noded_with_condition.R | 101 ----------------------------------------
|  3 files changed, 114 insertions(+), 102 deletions(-)

* 2014-08-14(Tal Galili) Simplify the introduction, and use if for DESCRIPTION |4142dd9| 
|  DESCRIPTION                | 8 ++++++--
|  NEWS                       | 2 +-
|  vignettes/introduction.Rmd | 8 ++++----
|  3 files changed, 11 insertions(+), 7 deletions(-)

* 2014-08-14(Tal Galili) `colored_bars` - added defaults to make the bars be plotted bellow the labels (+allow the order of the bars to be based on the labels' order) |dc0b710| 
|  NEWS                |  1 +
|  R/colored_bars.R    | 28 ++++++++++++++++++++++++++--
|  man/colored_bars.Rd | 14 +++++++++++---
|  3 files changed, 38 insertions(+), 5 deletions(-)

* 2014-08-14(Tal Galili) `color_branches` - can now work when the labels of the tree are not unique (feature request by Heather Turner - thanks Heather :) ) |5722bcc| 
|  NEWS               |  5 +++--
|  R/color_branches.R | 13 +++++++++++++
|  2 files changed, 16 insertions(+), 2 deletions(-)

* 2014-08-14(Tal Galili) all.unique - check if all elements in a vector are unique (including tests) |0eb8327| 
|  NAMESPACE                 |  1 +
|  NEWS                      |  2 +-
|  R/color_branches.R        | 33 +++++++++++++++++++++++++++++++++
|  inst/tests/test-general.R | 14 ++++++++++++++
|  man/all.unique.Rd         | 32 ++++++++++++++++++++++++++++++++
|  5 files changed, 81 insertions(+), 1 deletion(-)

* 2014-08-14(Tal Galili) vignettes: Explaining depth-first search |b77bded| 
|  vignettes/introduction.Rmd | 153 ++++++++++++++++++++++++++++++++-----------
|  1 file changed, 115 insertions(+), 38 deletions(-)

* 2014-08-11(Tal Galili) Fix lower_rect in rect.dendrogram to work with horiz=TRUE |ac6e2f7| 
|  R/rect.dendrogram.R    | 5 ++++-
|  man/rect.dendrogram.Rd | 5 ++++-
|  2 files changed, 8 insertions(+), 2 deletions(-)

* 2014-08-11(Tal Galili) moving the date. |6d7eb14| 
|  DESCRIPTION | 2 +-
|  NEWS        | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2014-08-11(Tal Galili) `rect.dendrogram` - a new xpd and lower_rect parameters - to control how low the rect will be (for example, below or above the labels). The default is below the labels. |f7e58f6| 
|  NEWS                   |  2 +-
|  R/rect.dendrogram.R    | 32 ++++++++++++++++++++++++++++----
|  man/rect.dendrogram.Rd | 19 ++++++++++++++++---
|  3 files changed, 45 insertions(+), 8 deletions(-)

* 2014-08-10(Tal Galili) Dealing with a missing/junk attribute |12f3566| 
|  R/attr_access.R               | 5 +----
|  inst/tests/test-attr_access.R | 3 +++
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2014-08-10(Tal Galili) `get_nodes_attr` - can now return an array or a list for attributes which include a more complex structure (such as nodePar), by working with lists and adding a "simplify" parameter. |f264362| 
|  NEWS                          |  1 +
|  R/attr_access.R               | 19 +++++++++++++++++--
|  inst/tests/test-attr_access.R |  8 +++++++-
|  man/get_nodes_attr.Rd         |  6 +++++-
|  4 files changed, 30 insertions(+), 4 deletions(-)

* 2014-08-10(Tal Galili) vignettes introduction: added a first draft of explaining depth first |a99955f| 
|  vignettes/introduction.Rmd | 36 +++++++++++++++++++++++++++++++++---
|  1 file changed, 33 insertions(+), 3 deletions(-)

* 2014-08-10(Tal Galili) get_nodes_xy - Get the x-y coordiantes of a dendrogram's nodes |28b8205| 
|  DESCRIPTION         |   4 +-
|  NAMESPACE           |   1 +
|  NEWS                |   5 +
|  R/get_nodes_xy.R    | 253 ++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/get_nodes_xy.Rd |  72 ++++++++++++++
|  5 files changed, 333 insertions(+), 2 deletions(-)

* 2014-08-09(Tal Galili) Changing a dendrogram’s labels |1c2c9d5| 
|  vignettes/introduction.Rmd | 108 +++++++++++++++++++++++++++++++++++++++----
|  1 file changed, 99 insertions(+), 9 deletions(-)

* 2014-08-09(Tal Galili) set.dendrogram - if "what" is missing, return the object as is. |27836ee| 
|  NEWS               | 3 ++-
|  R/set.dendrogram.R | 5 +++++
|  2 files changed, 7 insertions(+), 1 deletion(-)

* 2014-08-09(Tal Galili) set.dendrogram - changed from using `labels_colors<-` to `color_labels` for "labels_colors" (this will now work with using k...) |69c8bcf| 
|  NEWS               | 1 +
|  R/set.dendrogram.R | 3 ++-
|  2 files changed, 3 insertions(+), 1 deletion(-)

* 2014-08-09(Tal Galili) `labels<-.dendrogram` - if value is missing, returning the dendrogram as is (this also affects `set`) |0c9d5fb| 
|  NEWS       | 2 ++
|  R/labels.R | 6 ++++++
|  2 files changed, 8 insertions(+)

* 2014-08-09(Tal Galili) `labels_colors<-` - added if(dendextend_options("warn")) |0585aae| 
|  NEWS              | 1 +
|  R/labels_colors.R | 4 ++--
|  2 files changed, 3 insertions(+), 2 deletions(-)

* 2014-08-09(Tal Galili) set.dendrogram - added nodes_pch, nodes_cex and nodes_col - using `assign_values_to_nodes_nodePar` |c638422| 
|  NEWS               |  1 +
|  R/set.dendrogram.R | 12 ++++++++++++
|  man/set.Rd         |  6 ++++++
|  3 files changed, 19 insertions(+)

* 2014-08-08(Tal Galili) Moved Iris example to the end. And added explenation in the .Rd docs of the different possible options for "what" can get in set.dendrogram. |15c19b7| 
|  vignettes/introduction.Rmd | 160 +++++++++++++++++++++++++++----------------
|  1 file changed, 101 insertions(+), 59 deletions(-)

* 2014-08-08(Tal Galili) set.dendrogram - added explenation in the .Rd docs of the different possible options for "what" |8f65726| 
|  NEWS               |  1 +
|  R/set.dendrogram.R | 21 +++++++++++++++++++++
|  man/set.Rd         | 21 +++++++++++++++++++++
|  3 files changed, 43 insertions(+)

* 2014-08-08(Tal Galili) Added a d3 .Rd |1c70916| 
|  man/d3dendro_options.Rd | 40 ++++++++++++++++++++++++++++++++++++++++
|  man/d3dendrogram.Rd     | 47 +++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 87 insertions(+)

* 2014-08-08(Tal Galili) Introdution vignettes - wrote a decent: tl;dr and Prerequisites (acknowledgement, iris, chaining) |b46135b| 
|  DESCRIPTION                |  29 +++++-----
|  vignettes/introduction.Rmd | 131 +++++++++++++++++++++++++++++--------------
|  2 files changed, 104 insertions(+), 56 deletions(-)

* 2014-08-08(Tal Galili) `cutree.dendrogram` - now replaces NA values with 0L |2061c3e| 
|  NEWS                  | 1 +
|  R/cutree.dendrogram.R | 3 ++-
|  2 files changed, 3 insertions(+), 1 deletion(-)

* 2014-08-08(Tal Galili) `color_branches` - now handles flat trees more gracefully. (returns them as they are) |b999388| 
|  NEWS                  |  2 +-
|  R/color_branches.R    | 17 ++++++++++++++++-
|  man/color_branches.Rd | 12 +++++++++++-
|  3 files changed, 28 insertions(+), 3 deletions(-)

* 2014-08-08(Tal Galili) Include dendextend_options("warn", TRUE) in tests. |c2f7b68| 
|  R/cutree.dendrogram.R               | 4 ++--
|  inst/tests/test-cutree.dendrogram.R | 5 ++++-
|  inst/tests/test-unbranch.R          | 3 +++
|  man/untangle_step_rotate_2side.Rd   | 4 ++--
|  4 files changed, 11 insertions(+), 5 deletions(-)

* 2014-08-08(Tal Galili) untangle_step_rotate_2side` - print_times is now dendextend_options("warn"), |0da7c3f| 
|  NEWS         | 4 +++-
|  R/untangle.R | 2 +-
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2014-08-08(Tal Galili) Update .Rd docs, now that ALL `warn` paramteres are set to dendextend_options("warn") (which is FALSE) |6f4031f| 
|  man/Bk.Rd                                |  9 +++++----
|  man/Bk_permutations.Rd                   |  7 +++++--
|  man/Bk_plot.Rd                           | 10 ++++++----
|  man/FM_index.Rd                          |  6 ++++--
|  man/FM_index_R.Rd                        |  6 ++++--
|  man/FM_index_permutation.Rd              |  7 +++++--
|  man/FM_index_profdpm.Rd                  |  6 ++++--
|  man/assign_values_to_branches_edgePar.Rd | 10 ++++------
|  man/assign_values_to_leaves_nodePar.Rd   | 11 +++++------
|  man/assign_values_to_nodes_nodePar.Rd    | 10 ++++------
|  man/color_labels.Rd                      |  7 +++++--
|  man/cor_bakers_gamma.Rd                  |  6 ++++--
|  man/cut_lower_fun.Rd                     |  8 +++++---
|  man/cutree-methods.Rd                    |  6 ++++--
|  man/cutree_1h.dendrogram.Rd              |  6 ++++--
|  man/cutree_1k.dendrogram.Rd              |  8 +++++---
|  man/dendextend_options.Rd                |  6 ++++++
|  man/get_branches_attr.Rd                 |  7 +++++--
|  man/intersect_trees.Rd                   |  8 +++++---
|  man/sort_2_clusters_vectors.Rd           |  6 ++++--
|  man/sort_levels_values.Rd                |  8 +++++---
|  man/tanglegram.Rd                        |  5 +++--
|  22 files changed, 101 insertions(+), 62 deletions(-)

* 2014-08-08(Tal Galili) ALL `warn` paramteres are no set to dendextend_options("warn") (which is FALSE) |bb759ff| 
|  NEWS                  |  6 ++++++
|  R/attr_access.R       | 30 ++++++++++++-----------------
|  R/bk_method.R         | 50 +++++++++++++++++++++++++++++++------------------
|  R/color_branches.R    | 10 ++++++----
|  R/cor_bakers_gamma.R  | 10 ++++++----
|  R/cor_cophenetic.R    |  2 +-
|  R/cut_lower_fun.R     | 10 ++++++----
|  R/cutree.dendrogram.R | 36 +++++++++++++++++++++--------------
|  R/tanglegram.R        | 11 ++++++-----
|  R/trim.R              |  8 +++++---
|  10 files changed, 102 insertions(+), 71 deletions(-)

* 2014-08-08(Tal Galili) `get_branches_attr` - change "warning" to "warn", and it now works with is.dendrogram, and no longer changes the class of something which is not a dendrogram. |73e4ad0| 
|  R/unbranch.R | 14 ++++++++------
|  1 file changed, 8 insertions(+), 6 deletions(-)

* 2014-08-08(Tal Galili) A new "warn" dendextend_options parameter. logical (FALSE). Should warning be issued? |d491d43| 
|  R/dendextend_options.R | 8 ++++++++
|  1 file changed, 8 insertions(+)

* 2014-08-08(Tal Galili) dendextend_options.R - moved `dendextend_options` functions to it. |8e33740| 
|  NEWS                   |   8 ++++
|  R/dendextend_options.R | 110 +++++++++++++++++++++++++++++++++++++++++++++++
|  R/zzz.R                |  88 -------------------------------------
|  3 files changed, 118 insertions(+), 88 deletions(-)

* 2014-08-07(Tal Galili) A new draft for introduction.Rmd Vignettes |ddc69d9| 
|  vignettes/introduction.Rmd | 187 +++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 187 insertions(+)

* 2014-08-06(Tal Galili) Added pvclust - bump to 0.16.4 |e4cca44| 
|  ChangeLog   | 120 ++++++++++++++++++++++++
|  DESCRIPTION |   5 +-
|  NEWS.md     | 297 +++++++++++++++++++++++++++++++++-------------------------
|  3 files changed, 290 insertions(+), 132 deletions(-)

* 2014-08-06(Tal Galili) NEW FUNCTIONS:    * `as.dendrogram.pvclust` - extract the hclust from a pvclust object, and turns it into a dendrogram.    * `hc2axes` - imported from pvclust, needed for text.pvclust    * `text.pvclust` - imported from pvclust, adds text to a dend plot of a pvclust result    * `pvclust_show_signif` - Shows the significant branches in a dendrogram, based on a pvclust object    * `pvclust_show_signif_gradient` - Shows the gradient of significance of branches in a dendrogram, based on a pvclust object |5677850| 
|  NAMESPACE                           |   4 +
|  NEWS                                |  16 ++
|  R/pvclust.R                         | 281 ++++++++++++++++++++++++++++++++--
|  man/pvclust_show_signif.Rd          |  65 ++++++++
|  man/pvclust_show_signif_gradient.Rd |  58 +++++++
|  5 files changed, 412 insertions(+), 12 deletions(-)

* 2014-08-06(Tal Galili) Move from is.finite to !is.infinite - so to be able to handle characters and not just numbers! |c00faa7| 
|  R/attr_access.R | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2014-08-06(Tal Galili)  `assign_values_to_leaves_nodePar`, `assign_values_to_nodes_nodePar`, `assign_values_to_branches_edgePar` - If the value has `Inf` (instead of NA!) then the value will not be changed. |d44661d| 
|  R/attr_access.R                          | 16 +++++++---------
|  inst/tests/test-set.dendrogram.R         |  8 ++++----
|  man/assign_values_to_branches_edgePar.Rd |  4 +---
|  man/assign_values_to_leaves_nodePar.Rd   |  2 +-
|  man/assign_values_to_nodes_nodePar.Rd    |  6 +++---
|  5 files changed, 16 insertions(+), 20 deletions(-)

* 2014-08-06(Tal Galili) Version bump to 0.16.3 |91b0884| 
|  DESCRIPTION | 9 +++++----
|  1 file changed, 5 insertions(+), 4 deletions(-)

* 2014-08-06(Tal Galili) `assign_values_to_nodes_nodePar` - Assign values to nodePar of dendrogram's nodes |5dbfb56| 
|  NAMESPACE                              |   2 +-
|  NEWS                                   |   6 ++
|  R/attr_access.R                        | 116 +++++++++++++++++++++++++++++--
|  man/assign_values_to_leaves_nodePar.Rd |   6 +-
|  man/assign_values_to_nodes_nodePar.Rd  |  55 +++++++++++++++
|  5 files changed, 177 insertions(+), 8 deletions(-)

* 2014-08-06(Tal Galili) NEWS - updated to use header 2 and 3 instead of 1 and 2 for the markdown version. |a025624| 
|  NEWS | 271 +++++++++++++++++++++++++++++++++--------------------------------
|  1 file changed, 139 insertions(+), 132 deletions(-)

* 2014-08-06(mark) removed export directive |09030d7| 
|  R/d3dendrogram.R | 1 -
|  1 file changed, 1 deletion(-)

* 2014-08-06(mark) Added and documented global options |bfc2809| 
|  NAMESPACE        |  1 +
|  R/d3dendrogram.R | 96 ++++++++++++++++++++++++++++++++++++++++++------------
|  R/zzz.R          |  3 ++
|  3 files changed, 79 insertions(+), 21 deletions(-)

* 2014-08-06(mark) d3dendrogram accepts global options, e.g. node_fill |2d39826| 
|  R/d3dendrogram.R | 89 +++++++++++++++++++++++++++++++++++-------------------
|  1 file changed, 58 insertions(+), 31 deletions(-)

* 2014-08-06(mark) d3dendrogram now opens in (RStudio) viewer by default |10a64b3| 
|  R/d3dendrogram.R | 33 ++++++++++++++++++++++-----------
|  1 file changed, 22 insertions(+), 11 deletions(-)

* 2014-07-29(Tal Galili) require -> library (Thanks Yihui: http://yihui.name/en/2014/07/library-vs-require/) |e676951| 
|  DESCRIPTION                         |  4 +--
|  NEWS                                |  8 ++++++
|  R/as.dendrogram.randomForest.R      |  2 +-
|  R/attr_access.R                     |  6 ++---
|  R/bk_method.R                       |  4 +--
|  R/branches_attr_by.R                |  8 +++---
|  R/color_branches.R                  | 10 ++++----
|  R/colored_bars.R                    |  6 ++---
|  R/cor_bakers_gamma.R                |  4 +--
|  R/cor_cophenetic.R                  |  2 +-
|  R/cut_lower_fun.R                   |  8 +++---
|  R/cutree.dendrogram.R               | 10 ++++----
|  R/d3dendrogram.R                    |  6 ++---
|  R/nleaves.R                         |  8 +++---
|  R/noded_with_condition.R            | 12 ++++-----
|  R/pvclust.R                         |  4 +--
|  R/rotate.R                          |  6 ++---
|  R/set.dendrogram.R                  |  2 +-
|  R/trim.R                            |  2 +-
|  R/unbranch.R                        |  2 +-
|  R/untangle.R                        | 20 +++++++--------
|  R/zzz.R                             | 10 ++++----
|  TODO                                |  4 +++
|  demo/dendextend.R                   |  2 +-
|  inst/tests/test-attr_access.R       |  4 +--
|  inst/tests/test-bk_method.R         |  2 +-
|  inst/tests/test-cor_bakers_gamma.R  |  2 +-
|  inst/tests/test-cor_cophenetic.R    |  2 +-
|  inst/tests/test-cut_lower_fun.R     |  8 +++---
|  inst/tests/test-cutree.dendrogram.R |  8 +++---
|  inst/tests/test-dendlist.R          |  2 +-
|  inst/tests/test-entanglement.R      |  4 +--
|  inst/tests/test-labels-assign.R     |  2 +-
|  inst/tests/test-nleaves.R           |  2 +-
|  inst/tests/test-rotate.R            |  4 +--
|  inst/tests/test-set.dendrogram.R    | 10 ++++----
|  inst/tests/test-trim.R              |  4 +--
|  inst/tests/test-untangle.R          |  4 +--
|  man/DendSer.dendrogram.Rd           |  2 +-
|  man/FM_index.Rd                     |  2 +-
|  man/FM_index_permutation.Rd         |  2 +-
|  man/branches_attr_by_clusters.Rd    |  6 ++---
|  man/branches_attr_by_labels.Rd      |  4 +--
|  man/color_branches.Rd               |  6 ++---
|  man/cor_bakers_gamma.Rd             |  2 +-
|  man/cor_cophenetic.Rd               |  2 +-
|  man/cut_lower_fun.Rd                |  6 ++---
|  man/cutree-methods.Rd               |  2 +-
|  man/cutree_1h.dendrogram.Rd         |  2 +-
|  man/cutree_1k.dendrogram.Rd         |  2 +-
|  man/get_branches_heights.Rd         |  4 +--
|  man/get_nodes_attr.Rd               |  2 +-
|  man/heights_per_k.dendrogram.Rd     |  2 +-
|  man/na_locf.Rd                      |  4 +--
|  man/noded_with_condition.Rd         |  4 +--
|  man/rotate_DendSer.Rd               |  2 +-
|  man/set.Rd                          |  2 +-
|  man/which_leaf.Rd                   |  4 +--
|  vignettes/dendextend-tutorial.rnw   | 48 +++++++++++++++++------------------
|  59 files changed, 165 insertions(+), 153 deletions(-)

* 2014-07-26(Tal Galili) ChangeLog |2257d2c| 
|  ChangeLog | 20 ++++++++++++++++++++
|  1 file changed, 20 insertions(+)

* 2014-07-26(Tal Galili) Comment out example code that won't run. |f39d69e| 
|  NEWS.md     |   7 ++
|  R/pvclust.R | 242 +++++++++++++++++++++++++++++-----------------------------
|  2 files changed, 128 insertions(+), 121 deletions(-)

* 2014-07-26(Tal Galili) Fix: \examples lines wider than 100 characters |051eab6| 
|  DESCRIPTION                      |  2 +-
|  NEWS                             |  7 +++++++
|  R/branches_attr_by.R             |  3 ++-
|  R/noded_with_condition.R         | 30 ++++++++++++++++++++++--------
|  man/branches_attr_by_clusters.Rd |  3 ++-
|  man/branches_attr_by_labels.Rd   | 24 ++++++++++++++++++------
|  man/noded_with_condition.Rd      |  4 +++-
|  7 files changed, 55 insertions(+), 18 deletions(-)

* 2014-07-26(Tal Galili) Update NEWS and ChangeLog |9cd933b| 
|  ChangeLog | 47 +++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   |  8 ++++++--
|  2 files changed, 53 insertions(+), 2 deletions(-)

* 2014-07-26(Tal Galili) added a pvclust example (using a condition on p-value, and heighlighting branches based on that with lwd/col.) |cbbaae3| 
|  NEWS        |   2 +
|  R/pvclust.R | 121 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  TODO        |   1 -
|  3 files changed, 123 insertions(+), 1 deletion(-)

* 2014-07-26(Tal Galili) `na_locf` - Fill Last Observation Carried Forward |5e764d7| 
|  DESCRIPTION    |  2 +-
|  NAMESPACE      |  1 +
|  NEWS           |  4 +--
|  R/pvclust.R    | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/na_locf.Rd | 57 +++++++++++++++++++++++++++++++++++
|  5 files changed, 153 insertions(+), 3 deletions(-)

* 2014-07-26(Tal Galili) `which_leaf` - a new function to tell us Which node is a leaf |3658216| 
|  NAMESPACE                |  1 +
|  NEWS                     |  1 +
|  R/noded_with_condition.R | 35 +++++++++++++++++++++++++++++++++++
|  TODO                     |  1 +
|  man/which_leaf.Rd        | 40 ++++++++++++++++++++++++++++++++++++++++
|  5 files changed, 78 insertions(+)

* 2014-07-26(Tal Galili) `assign_values_to_branches_edgePar` - allow the option to skip leaves |9ec9e1d| 
|  NEWS                                     |  1 +
|  R/attr_access.R                          | 10 ++++++++--
|  man/assign_values_to_branches_edgePar.Rd |  5 ++++-
|  3 files changed, 13 insertions(+), 3 deletions(-)

* 2014-07-26(Tal Galili) branches_attr_by_labels - if dend is not a dendrogram, we should stop and not warn! |591c3b9| 
|  R/noded_with_condition.R | 6 +++++-
|  1 file changed, 5 insertions(+), 1 deletion(-)

* 2014-07-25(Tal Galili) various doc updates. |a8863ab| 
|  ChangeLog                        | 203 +++++++++++++++++++++++++++++++++++++
|  NEWS.md                          |  60 ++++++++++-
|  R/branches_attr_by.R             |   1 +
|  TODO                             |   6 +-
|  man/branches_attr_by_clusters.Rd |   1 +
|  5 files changed, 267 insertions(+), 4 deletions(-)

* 2014-07-25(Tal Galili) Added import for "whisker" for d3dendrogram. |426bd4a| 
|  DESCRIPTION            | 1 +
|  NAMESPACE              | 1 +
|  R/d3dendrogram.R       | 3 ++-
|  R/dendextend-package.R | 1 +
|  4 files changed, 5 insertions(+), 1 deletion(-)

* 2014-07-25(Tal Galili) Updated TODO :) |82524ce| 
|  TODO | 4 ----
|  1 file changed, 4 deletions(-)

* 2014-07-25(Tal Galili) Added ref to plotDendroAndColors |81e15ee| 
|  R/branches_attr_by.R             | 3 ++-
|  R/colored_bars.R                 | 4 ++--
|  man/branches_attr_by_clusters.Rd | 3 ++-
|  man/colored_bars.Rd              | 3 ++-
|  4 files changed, 8 insertions(+), 5 deletions(-)

* 2014-07-25(Tal Galili) For now - version 0.16.0 |4c13ada| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-07-25(Tal Galili) branches_attr_by_clusters - modified the example in the docs a bit (using the original dist matrix for the cutreeDynamic). |04ffde4| 
|  R/branches_attr_by.R             | 16 +++++++++-------
|  man/branches_attr_by_clusters.Rd | 16 +++++++++-------
|  2 files changed, 18 insertions(+), 14 deletions(-)

* 2014-07-25(Tal Galili) `colored_bars` - update docs |6283ece| 
|  NEWS                | 2 +-
|  R/colored_bars.R    | 9 +++++++--
|  man/colored_bars.Rd | 3 +++
|  3 files changed, 11 insertions(+), 3 deletions(-)

* 2014-07-25(Tal Galili) `branches_attr_by_labels` - change the order of some parameters (based on how much I expect users to use each of them.) |efd8c42| 
|  NEWS                           |  1 +
|  R/noded_with_condition.R       | 11 ++++++-----
|  man/branches_attr_by_labels.Rd | 16 +++++++++-------
|  3 files changed, 16 insertions(+), 12 deletions(-)

* 2014-07-25(Tal Galili) Added branches_attr_by_clusters - This function was designed to enable the manipulation (mainly coloring) of branches, based on the results from the cutreeDynamic function (from the {dynamicTreeCut} package). |cf18ef3| 
|  NAMESPACE                        |   1 +
|  NEWS                             |   8 +-
|  R/branches_attr_by.R             | 182 +++++++++++++++++++++++++++++++++++++
|  man/branches_attr_by_clusters.Rd | 111 ++++++++++++++++++++++
|  4 files changed, 300 insertions(+), 2 deletions(-)

* 2014-07-25(Tal Galili) colored_bars - change the order of colors and dend, and allowing for dend to be missing. |4e85359| 
|  NEWS                |  4 ++++
|  R/colored_bars.R    | 19 ++++++++++++-------
|  man/colored_bars.Rd |  7 ++++---
|  3 files changed, 20 insertions(+), 10 deletions(-)

* 2014-07-25(Tal Galili) assign_values_to_branches_edgePar - now can keep existing value, if gets NA. |0c29c7b| 
|  DESCRIPTION                              | 4 ++--
|  NEWS                                     | 8 ++++++++
|  R/attr_access.R                          | 9 ++++++++-
|  R/noded_with_condition.R                 | 8 ++++++--
|  man/assign_values_to_branches_edgePar.Rd | 4 ++++
|  man/branches_attr_by_labels.Rd           | 5 +++--
|  6 files changed, 31 insertions(+), 7 deletions(-)

* 2014-07-24(talgalili) minor fixes |f0306e8| 
|  README.md | 6 ++++--
|  1 file changed, 4 insertions(+), 2 deletions(-)

* 2014-07-24(talgalili) Add options to the methods. |922befd| 
|  R/set.dendrogram.R | 3 +++
|  man/set.Rd         | 3 +++
|  2 files changed, 6 insertions(+)

* 2014-07-24(talgalili) In the docs: \dontrun { -> \dontrun{ |76e215f| 
|  R/noded_with_condition.R       | 4 ++--
|  man/branches_attr_by_labels.Rd | 2 +-
|  man/noded_with_condition.Rd    | 2 +-
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2014-07-24(talgalili) make package installation easier |859ad72| 
|  README.md | 14 ++++++++------
|  1 file changed, 8 insertions(+), 6 deletions(-)

* 2014-07-24(talgalili) Updated DESCRIPTION and NEWS to version 0.15.2 |069acdf| 
|  DESCRIPTION |  5 +++--
|  NEWS        | 11 ++++++++++-
|  2 files changed, 13 insertions(+), 3 deletions(-)

* 2014-07-24(talgalili) set.dendrogram - added new options: by_labels_branches_col, by_labels_branches_lwd, by_labels_branches_lty |0e4e414| 
|  R/set.dendrogram.R | 38 +++++++++++++++++++++++++++++++++++++-
|  man/set.Rd         | 31 ++++++++++++++++++++++++++++++-
|  2 files changed, 67 insertions(+), 2 deletions(-)

* 2014-07-24(talgalili) NEW FUNCTIONS:    * `noded_with_condition` - Find which nodes satisfies a condition    * `branches_attr_by_labels` - Change col/lwd/lty of branches matching labels condition |1c59527| 
|  NAMESPACE                      |   2 +
|  R/noded_with_condition.R       | 184 +++++++++++++++++++++++++++++++++++++++
|  man/branches_attr_by_labels.Rd |  56 ++++++++++++
|  man/noded_with_condition.Rd    |  61 +++++++++++++
|  4 files changed, 303 insertions(+)

* 2014-07-24(talgalili) Minor fixes to get the package to work. Also added some credit, and a more robust installation code to README.md (so it would work on non-Windows OS better) |53046d2| 
|  DESCRIPTION                | 3 ++-
|  README.md                  | 6 ++++--
|  dendextend.Rproj           | 2 +-
|  man/identify.dendrogram.Rd | 2 +-
|  4 files changed, 8 insertions(+), 5 deletions(-)

* 2014-07-24(talgalili) Fix malformed character. |5931a29| 
|  R/zzz.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-07-24(talgalili) Fix malformed character. |8126b0d| 
|  R/rect.dendrogram.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-07-19(Tal Galili) Added Mark van der Loo's first version of d3dendrogram |590e0d7| 
|  R/d3dendrogram.R | 198 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 198 insertions(+)

* 2014-07-19(Tal Galili) Added a heatmap.2 example to set.dendrogram |ce47f54| 
|  R/set.dendrogram.R | 28 ++++++++++++++++++++++++++++
|  man/set.Rd         | 28 ++++++++++++++++++++++++++++
|  2 files changed, 56 insertions(+)

* 2014-07-18(Tal Galili) `rect.dendrogram` - adding paramters for creating text under the clusters, as well as make it easier to plot lines on the rect (density = 7). props to skullkey for his help. |8706a7d| 
|  NEWS                   |  7 +++++++
|  R/rect.dendrogram.R    | 39 +++++++++++++++++++++++++++++++++++----
|  TODO                   | 12 +++++++-----
|  man/rect.dendrogram.Rd | 29 ++++++++++++++++++++++++++++-
|  4 files changed, 77 insertions(+), 10 deletions(-)

* 2014-07-16(Tal Galili) identify.dendrogram - function and docs added. (it might be a bit buggy...) |941521e| 
|  NAMESPACE                  |  1 +
|  NEWS                       |  2 ++
|  R/rect.dendrogram.R        | 78 +++++++++++++++++++++++++++++++++++++++-----
|  man/identify.dendrogram.Rd | 69 +++++++++++++++++++++++++++++++++++++++
|  4 files changed, 141 insertions(+), 9 deletions(-)

* 2014-07-16(Tal Galili) `rect.dendrogram` - just like `rect.hclust`, plus: works for dendrograms, passes `...` to rect for lwd lty etc, now has an horiz parameter! |b290b8b| 
|  NAMESPACE              |   1 +
|  NEWS                   |  11 ++--
|  R/labels.R             |   2 +-
|  R/rect.dendrogram.R    | 136 +++++++++++++++++++++++++++++++++++++++++++----
|  man/rect.dendrogram.Rd |  70 ++++++++++++++++++++++++
|  5 files changed, 206 insertions(+), 14 deletions(-)

* 2014-07-16(Tal Galili) rect.dendrogram - started working on the function. (we start with rect.hclust, and move from there) |3c8aa38| 
|  R/rect.dendrogram.R | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 60 insertions(+)

* 2014-07-16(Tal Galili) order.hclust (new function) - Ordering of the Leaves in a hclust Dendrogram |224f9a0| 
|  NAMESPACE           |  1 +
|  NEWS                |  3 +++
|  R/dendextend.R      |  1 -
|  R/labels.R          | 28 ++++++++++++++++++++++++++++
|  man/order.hclust.Rd | 33 +++++++++++++++++++++++++++++++++
|  5 files changed, 65 insertions(+), 1 deletion(-)

* 2014-07-15(Tal Galili) Rename 2 file names from add->set (set.dendrogram.R and tests-set.dendrogram.R) |6b14d4b| 
|  DESCRIPTION                      |   4 +-
|  NEWS                             |  10 ++
|  R/add.dendrogram.R               | 212 -------------------------------------
|  R/set.dendrogram.R               | 212 +++++++++++++++++++++++++++++++++++++
|  inst/tests/test-add.dendrogram.R | 143 -------------------------
|  inst/tests/test-set.dendrogram.R | 143 +++++++++++++++++++++++++
|  6 files changed, 367 insertions(+), 357 deletions(-)

* 2014-07-15(Tal Galili) Rename from "add" to "set"! |fb77b15| 
|  NAMESPACE                        |   6 +-
|  R/add.dendrogram.R               | 109 ++++++++++++++---------------
|  inst/tests/test-add.dendrogram.R |  46 ++++++-------
|  man/add.Rd                       | 137 -------------------------------------
|  man/set.Rd                       | 137 +++++++++++++++++++++++++++++++++++++
|  5 files changed, 216 insertions(+), 219 deletions(-)

* 2014-07-15(Tal Galili) Rename files - from update to add |e08cccb| 
|  NEWS                                |   7 +-
|  R/add.dendrogram.R                  | 215 ++++++++++++++++++++++++++++++++++
|  R/update.dendrogram.R               | 215 ----------------------------------
|  inst/tests/test-add.dendrogram.R    | 143 ++++++++++++++++++++++
|  inst/tests/test-update.dendrogram.R | 143 ----------------------
|  5 files changed, 362 insertions(+), 361 deletions(-)

* 2014-07-15(Tal Galili) Changed "update" to be "add". To make it easier to read and write... |cd72d1e| 
|  NAMESPACE                           |   5 +-
|  R/update.dendrogram.R               | 118 ++++++++++++++++-------------
|  R/zzz.R                             |   5 ++
|  inst/tests/test-update.dendrogram.R |  46 ++++++------
|  man/add.Rd                          | 137 ++++++++++++++++++++++++++++++++++
|  man/update.dendrogram.Rd            | 135 ---------------------------------
|  6 files changed, 233 insertions(+), 213 deletions(-)

* 2014-07-15(Tal Galili) update: change "with" to "value" (probably a better name for this parameter) |e9f44e6| 
|  R/update.dendrogram.R    | 34 +++++++++++++++++-----------------
|  man/update.dendrogram.Rd |  6 +++---
|  2 files changed, 20 insertions(+), 20 deletions(-)

* 2014-07-14(Tal Galili) is_null_list - making the example donotrun. Reason: I can run this only if I'd make is_null_list exported |d7cfcac| 
|  R/dendlist.R        | 4 ++++
|  TODO                | 1 +
|  man/is_null_list.Rd | 4 ++++
|  3 files changed, 9 insertions(+)

* 2014-07-14(Tal Galili) Updated some docs. |2b98871| 
|  ChangeLog    | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  DESCRIPTION  |  2 +-
|  NEWS         |  2 +-
|  NEWS.md      |  8 ++++--
|  R/magrittr.R | 10 ++++++++
|  R/zzz.R      |  1 +
|  TODO         |  1 -
|  7 files changed, 96 insertions(+), 5 deletions(-)

* 2014-07-14(Tal Galili) Minor doc fixed for: cor_cophenetic, entanglement. as.phylo.dendrogram, untangle.dendlist, and labels.hclust (which required the use of @rdname) |30c5277| 
|  R/cor_cophenetic.R     |  7 +++++--
|  R/dendextend-package.R |  8 ++++++++
|  R/entanglement.R       |  6 +++---
|  R/nleaves.R            |  6 ++----
|  R/untangle.R           |  5 +++--
|  man/cor_cophenetic.Rd  |  4 +++-
|  man/entanglement.Rd    |  4 ++--
|  man/labels-assign.Rd   |  9 +++++++++
|  man/labels.hclust.Rd   | 11 -----------
|  man/shuffle.Rd         |  1 +
|  man/untangle.Rd        |  2 +-
|  11 files changed, 37 insertions(+), 26 deletions(-)

* 2014-07-14(Tal Galili) Added an internal function "zero_range" |58cf6bc| 
|  R/colored_bars.R | 19 +++++++++++++++++++
|  1 file changed, 19 insertions(+)

* 2014-07-14(Tal Galili) Change "" to `` when wrapping a function of style `fo<-`, so to have RStudio pick up on it. |bdca139| 
|  R/labels.R | 24 ++++++++++++++----------
|  1 file changed, 14 insertions(+), 10 deletions(-)

* 2014-07-14(Tal Galili) Moved {magrittr} to the "Imports" section in DESCRIPTION. And imported the %>% function from magrittr (using a trick from the dplyr package) |f2bb8be| 
|  DESCRIPTION  |  4 ++--
|  NAMESPACE    |  3 ++-
|  NEWS         |  3 +++
|  R/magrittr.R | 43 +++++++++++++++++++++++++++++++++++++++++++
|  man/pipe.Rd  | 32 ++++++++++++++++++++++++++++++++
|  5 files changed, 82 insertions(+), 3 deletions(-)

* 2014-07-14(Tal Galili) roxygen2 - Moved from using @S3method to @export (removed 45 warnings from check() ) |e036f50| 
|  NEWS                  |  3 ++-
|  R/cor_bakers_gamma.R  |  6 ++++--
|  R/cutree.dendrogram.R |  4 ++--
|  R/entanglement.R      | 12 ++++++++----
|  R/labels.R            | 12 ++++++------
|  R/nleaves.R           | 27 +++++++++++++++++----------
|  R/rotate.R            | 18 ++++++++++++------
|  R/tanglegram.R        | 12 ++++++++----
|  R/trim.R              |  9 ++++++---
|  R/unbranch.R          |  9 ++++++---
|  R/untangle.R          | 18 ++++++++++++------
|  R/update.dendrogram.R |  3 ++-
|  R/zzz.R               |  1 +
|  TODO                  |  4 ++++
|  man/labels.hclust.Rd  | 11 +++++++++++
|  15 files changed, 101 insertions(+), 48 deletions(-)

* 2014-07-14(Tal Galili) untangle.dendrogram - fix doc, and add \n to massage |0f2afed| 
|  R/untangle.R                      | 4 ++--
|  man/untangle_step_rotate_2side.Rd | 2 +-
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2014-07-14(Tal Galili) Replace expect_that with expect_equal |8a27370| 
|  inst/tests/test-labels-assign.R | 49 +++++++++++++++++++++------------------
|  1 file changed, 27 insertions(+), 22 deletions(-)

* 2014-07-14(Tal Galili) tests - add an option to stop the warnings (I know they are there, so really no point in them keep showing up...) |4862624| 
|  inst/tests/test-update.dendrogram.R | 7 +++++++
|  1 file changed, 7 insertions(+)

* 2014-07-14(Tal Galili) add ` to functions in NEWS |ece7863| 
|  NEWS    | 36 ++++++++++++++++++------------------
|  NEWS.md | 36 ++++++++++++++++++------------------
|  2 files changed, 36 insertions(+), 36 deletions(-)

* 2014-07-14(Tal Galili) Turn news to be more marked down... |b231b9b| 
|  NEWS    | 230 +++++++++++++++++++++++++++++++-------------------------------
|  NEWS.md | 230 +++++++++++++++++++++++++++++++-------------------------------
|  2 files changed, 230 insertions(+), 230 deletions(-)

* 2014-07-14(Tal Galili) update NEWS.md and changelog |5f206dd| 
|  ChangeLog | 232 ++++++++++++++++++++++++++++++++++++++++++++++++++++
|  NEWS.md   | 265 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-----
|  R/zzz.R   |   4 +-
|  3 files changed, 479 insertions(+), 22 deletions(-)

* 2014-07-14(Tal Galili) Updated the README a bit. |8d6bb95| 
|  README.md | 37 +++++++------------------------------
|  1 file changed, 7 insertions(+), 30 deletions(-)

* 2014-07-14(Tal Galili) add .gitignore to not keep the cache and figure folders |5a4028c| 
|  vignettes/.gitignore | 2 ++
|  1 file changed, 2 insertions(+)

* 2014-07-14(Tal Galili) update TODO and ChangeLog |99430e2| 
|  ChangeLog | 400 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  TODO      |  25 ++++
|  2 files changed, 425 insertions(+)

* 2014-07-14(Tal Galili) Remove all extra doc files |8a3a863| 
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    4 -
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|  148 files changed, 3744 insertions(+), 19994 deletions(-)

* 2014-07-14(Tal Galili) Fix the docs of the functions in dendextend which relates to the newer dendextendRcpp (version 0.5.1): cut_lower_fun, get_branches_heights,  heights_per_k.dendrogram |a0382df| 
|  NEWS                            |  6 +++---
|  R/attr_access.R                 | 11 +++++------
|  R/cut_lower_fun.R               | 16 ++++++++--------
|  R/cutree.dendrogram.R           | 25 +++++++++++++------------
|  man/cut_lower_fun.Rd            | 16 ++++++++--------
|  man/get_branches_heights.Rd     | 11 +++++------
|  man/heights_per_k.dendrogram.Rd | 23 ++++++++++++-----------
|  7 files changed, 54 insertions(+), 54 deletions(-)

* 2014-07-13(Tal Galili) Fix typos in vignettes - thank you Bob Muenchen! |96692d2| 
|  DESCRIPTION                       | 16 +++++----
|  NEWS                              |  1 +
|  vignettes/dendextend-tutorial.bib | 10 ++++++
|  vignettes/dendextend-tutorial.rnw | 70 ++++++++++++++++++-------------------
|  4 files changed, 54 insertions(+), 43 deletions(-)

* 2014-07-13(Tal Galili) rotate_DendSer function added - and a bug was fixed in doing so. (also some credit corrections) |b045289| 
|  NAMESPACE                 |  1 +
|  NEWS                      |  2 +-
|  R/untangle.R              | 64 +++++++++++++++++++++++++++++++++++----------
|  man/DendSer.dendrogram.Rd |  8 ++++--
|  man/color_branches.Rd     |  2 +-
|  man/rotate_DendSer.Rd     | 47 +++++++++++++++++++++++++++++++++
|  man/tanglegram.Rd         |  4 +--
|  man/untangle_DendSer.Rd   |  3 ++-
|  8 files changed, 110 insertions(+), 21 deletions(-)

* 2014-07-13(Tal Galili) Vignettes - fixing spelling mistakes. |cc792b7| 
|  vignettes/dendextend-tutorial.rnw | 48 ++++++++++++++++++-------------------
|  1 file changed, 24 insertions(+), 24 deletions(-)

* 2014-07-13(Tal Galili) Update credits. |184907e| 
|  DESCRIPTION        | 8 +++++---
|  R/color_branches.R | 2 +-
|  R/tanglegram.R     | 4 ++--
|  3 files changed, 8 insertions(+), 6 deletions(-)

* 2014-07-13(Tal Galili) Minor doc changes |210cf71| 
|  R/labels.R               | 1 +
|  man/color_branches.Rd    | 1 +
|  man/labels_colors.Rd     | 4 ++++
|  man/update.dendrogram.Rd | 2 +-
|  4 files changed, 7 insertions(+), 1 deletion(-)

* 2014-07-13(Tal Galili) Added tests for update.dendrogram! |ba435a1| 
|  inst/tests/test-update.dendrogram.R | 136 ++++++++++++++++++++++++++++++++++
|  1 file changed, 136 insertions(+)

* 2014-07-13(Tal Galili) update.dendrogram - added .Rd docs :) |208af7d| 
|  NAMESPACE                |   1 +
|  R/update.dendrogram.R    | 297 ++++++++++++++++++++++-----------------------
|  man/update.dendrogram.Rd | 135 +++++++++++++++++++++
|  3 files changed, 282 insertions(+), 151 deletions(-)

* 2014-07-13(Tal Galili) tanglegram - preserve and restore previous par options (will no longer have a tiny plot in the left corner, when using a simple plot after tanglegram) |982053b| 
|  NEWS           | 4 +++-
|  R/tanglegram.R | 5 ++++-
|  2 files changed, 7 insertions(+), 2 deletions(-)

* 2014-07-12(Tal Galili) colored_bars - added docs :) |08a7118| 
|  DESCRIPTION         |   4 +-
|  NAMESPACE           |   2 +-
|  NEWS                |   2 +
|  R/colored_bars.R    | 243 +++++++++++++++++++++++++++++++-------------------
|  man/colored_bars.Rd | 116 ++++++++++++++++++++++++
|  5 files changed, 271 insertions(+), 96 deletions(-)

* 2014-07-12(Tal Galili) color_bars - adding more parameters. Made sure it can now be placed on top of a plot(dend). |a3db1f1| 
|  NAMESPACE        |   1 +
|  NEWS             |   2 +
|  R/color_bars.R   |  64 ----------------
|  R/colored_bars.R | 216 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 219 insertions(+), 64 deletions(-)

* 2014-07-12(Tal Galili) color_bars - make sure to keep and reset the options |c13e95b| 
|  R/color_bars.R | 5 ++++-
|  1 file changed, 4 insertions(+), 1 deletion(-)

* 2014-07-12(Tal Galili) Rename plotHclustColors to color_bars - and made it work with dendrograms |61f854e| 
|  R/color_bars.R | 10 +++++++---
|  1 file changed, 7 insertions(+), 3 deletions(-)

* 2014-07-12(Tal Galili) plotHclustColors - first import into the package |5c5bec8| 
|  R/color_bars.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 57 insertions(+)

* 2014-07-11(Tal Galili) assign_values_to_branches_edgePar - value can now be different than 1 (it now also has a recycle option for the value) |fdc946e| 
|  NEWS                                     |  5 ++++-
|  R/attr_access.R                          | 24 +++++++++++++++++++++---
|  man/assign_values_to_branches_edgePar.Rd |  8 +++++++-
|  3 files changed, 32 insertions(+), 5 deletions(-)

* 2014-07-11(Tal Galili) update.dendrogram added: branches_color, branches_k_color,      branches_col, branches_lwd, branches_lty, clear_branches, clear_leaves |ee7d0c7| 
|  R/update.dendrogram.R | 68 ++++++++++++++++++++++++++++++++++++-------------
|  1 file changed, 50 insertions(+), 18 deletions(-)

* 2014-07-11(Tal Galili) `labels_colors<-` is more robust (for cases with partiel attr in nodePar). Also moved to using is.dendrogram more. |e774148| 
|  NEWS              |  5 +++--
|  R/attr_access.R   |  4 ++--
|  R/labels.R        |  1 +
|  R/labels_colors.R | 25 ++++++++++++++++++++-----
|  4 files changed, 26 insertions(+), 9 deletions(-)

* 2014-07-11(Tal Galili) Fix "is.dendlist" to use inherits instead of class |621dc3d| 
|  R/dendlist.R | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-07-11(Tal Galili) update.dendrogram - added options for: labels_colors, labels_cex, branches_color, hang, leaves_pch, leaves_cex, leaves_col |b29fa80| 
|  NEWS                  |  3 ++-
|  R/attr_access.R       |  8 ++++++-
|  R/labels_colors.R     |  2 ++
|  R/update.dendrogram.R | 58 +++++++++++++++++++++++++++++++++++++++++++------
|  4 files changed, 62 insertions(+), 9 deletions(-)

* 2014-07-11(Tal Galili) plot.dendlist - a wrapper for tangelgram |05d2fc8| 
|  NAMESPACE            |  3 +++
|  NEWS                 |  1 +
|  R/dendlist.R         | 34 ++++++++++++++++++++++++++++++++++
|  man/plot.dendlist.Rd | 34 ++++++++++++++++++++++++++++++++++
|  4 files changed, 72 insertions(+)

* 2014-07-11(Tal Galili) color_branches - now has a default behavior if k is missing. |f37929b| 
|  NEWS               |  5 +++--
|  R/color_branches.R | 31 ++++++++++++++++++-------------
|  2 files changed, 21 insertions(+), 15 deletions(-)

* 2014-07-11(Tal Galili) `labels_colors<-` now has a default behavior if value is missing. |928b499| 
|  NEWS              |  1 +
|  R/labels_colors.R | 11 ++++++++++-
|  2 files changed, 11 insertions(+), 1 deletion(-)

* 2014-07-11(Tal Galili) update.dendrogram - first draft of the function (implements only "labels") |7f76137| 
|  NAMESPACE             |   1 +
|  NEWS                  |   2 +
|  R/update.dendrogram.R | 131 ++++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 134 insertions(+)

* 2014-07-10(Tal Galili) Added cor_cophenetic.dendlist with tests and docs. |3303e4a| 
|  NAMESPACE                          |  1 +
|  R/cor_cophenetic.R                 | 26 ++++++++++++++++++---
|  inst/tests/test-cor_bakers_gamma.R |  2 +-
|  inst/tests/test-cor_cophenetic.R   | 44 ++++++++++++++++++++++++++++++++++++
|  man/cor_cophenetic.Rd              | 19 ++++++++++++----
|  5 files changed, 83 insertions(+), 9 deletions(-)

* 2014-07-10(Tal Galili) Added entanglement.dendlist to the doc |6ae315a| 
|  R/entanglement.R    | 1 +
|  man/entanglement.Rd | 1 +
|  2 files changed, 2 insertions(+)

* 2014-07-10(Tal Galili) Added match.arg for Bk_plot,  cor_cophenetic, entanglement, untangle_random_search, untangle_step_rotate_1side, and untangle_step_rotate_2side |ec129c1| 
|  NEWS                  | 1 +
|  R/bk_method.R         | 3 ++-
|  R/cor_cophenetic.R    | 7 ++++---
|  R/entanglement.R      | 3 ++-
|  R/untangle.R          | 8 +++++---
|  man/cor_cophenetic.Rd | 3 ++-
|  6 files changed, 16 insertions(+), 9 deletions(-)

* 2014-07-10(Tal Galili) Fix untangle tests: untangle_step_rotate_1side now outputs a dendlist, so we needed to extract the first element so to get the same results as before. (also added piping) |75f99af| 
|  inst/tests/test-untangle.R | 18 +++++++++---------
|  1 file changed, 9 insertions(+), 9 deletions(-)

* 2014-07-10(Tal Galili) Piping %>% some examples |1691c78| 
|  R/attr_access.R                            | 10 +++++-----
|  R/color_branches.R                         |  4 ++--
|  R/entanglement.R                           |  4 ++--
|  R/nleaves.R                                |  2 +-
|  R/sample.dendrogram.R                      |  4 ++--
|  R/tanglegram.R                             |  2 +-
|  R/untangle.R                               | 12 ++++++------
|  man/all_couple_rotations_at_k.Rd           |  2 +-
|  man/assign_values_to_branches_edgePar.Rd   |  2 +-
|  man/color_branches.Rd                      |  2 +-
|  man/duplicate_leaf.Rd                      |  2 +-
|  man/flip_leaves.Rd                         |  2 +-
|  man/leaf_Colors.Rd                         |  2 +-
|  man/match_order_by_labels.Rd               |  2 +-
|  man/match_order_dendrogram_by_old_order.Rd |  2 +-
|  man/plot_horiz.dendrogram.Rd               |  2 +-
|  man/rank_branches.Rd                       |  2 +-
|  man/rank_order.dendrogram.Rd               |  2 +-
|  man/remove_branches_edgePar.Rd             |  2 +-
|  man/remove_leaves_nodePar.Rd               |  2 +-
|  man/sample.dendrogram.Rd                   |  2 +-
|  man/shuffle.Rd                             |  2 +-
|  man/untangle_step_rotate_1side.Rd          |  2 +-
|  man/untangle_step_rotate_2side.Rd          |  4 ++--
|  24 files changed, 37 insertions(+), 37 deletions(-)

* 2014-07-10(Tal Galili) Added a TODO file |0fbee3a| 
|  NEWS | 64 -----------------------------------------------------
|  TODO | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 79 insertions(+), 64 deletions(-)

* 2014-07-10(Tal Galili) Fix some spaces around "<-" |c141009| 
|  R/color_branches.R | 18 +++++++++---------
|  R/untangle.R       |  4 ++--
|  2 files changed, 11 insertions(+), 11 deletions(-)

* 2014-07-10(Tal Galili) Rename back from .b to .R |c0fd282| 
|  R/as.dendrogram.randomForest.R                    |   54 +
|  R/as.dendrogram.randomForest.b                    |   54 -
|  R/attr_access.R                                   |  814 ++++++++++++
|  R/attr_access.b                                   |  814 ------------
|  R/bk_method.R                                     | 1098 ++++++++++++++++
|  R/bk_method.b                                     | 1098 ----------------
|  R/color_branches.R                                |  482 +++++++
|  R/color_branches.b                                |  482 -------
|  R/cor_bakers_gamma.R                              |  240 ++++
|  R/cor_bakers_gamma.b                              |  240 ----
|  R/cor_cophenetic.R                                |  187 +++
|  R/cor_cophenetic.b                                |  187 ---
|  R/cut_lower_fun.R                                 |  104 ++
|  R/cut_lower_fun.b                                 |  104 --
|  R/cutree.dendrogram.R                             |  952 ++++++++++++++
|  R/cutree.dendrogram.b                             |  952 --------------
|  R/dendextend-package.R                            |   30 +
|  R/dendextend-package.b                            |   30 -
|  R/dendextend.R                                    |   70 +
|  R/dendextend.b                                    |   70 -
|  R/dendlist.R                                      |  222 ++++
|  R/dendlist.b                                      |  222 ----
|  R/entanglement.R                                  |  458 +++++++
|  R/entanglement.b                                  |  458 -------
|  R/imports_stats.R                                 |  285 +++++
|  R/imports_stats.b                                 |  285 -----
|  R/labels.R                                        |  369 ++++++
|  R/labels.b                                        |  369 ------
|  R/labels_colors.R                                 |  144 +++
|  R/labels_colors.b                                 |  144 ---
|  R/nleaves.R                                       |  316 +++++
|  R/nleaves.b                                       |  316 -----
|  R/rotate.R                                        |  337 +++++
|  R/rotate.b                                        |  337 -----
|  R/sample.dendrogram.R                             |  267 ++++
|  R/sample.dendrogram.b                             |  267 ----
|  R/tanglegram.R                                    |  815 ++++++++++++
|  R/tanglegram.b                                    |  815 ------------
|  R/trim.R                                          |  248 ++++
|  R/trim.b                                          |  248 ----
|  R/unbranch.R                                      |  246 ++++
|  R/unbranch.b                                      |  246 ----
|  R/untangle.R                                      | 1262 +++++++++++++++++++
|  R/untangle.b                                      | 1262 -------------------
|  R/zzz.R                                           |  360 ++++++
|  R/zzz.b                                           |  360 ------
|  demo/dendextend.R                                 |   23 +
|  demo/dendextend.b                                 |   23 -
|  .../2013-09-05_Boston-useR_01_intro.R             |  198 +++
|  .../2013-09-05_Boston-useR_01_intro.b             |  198 ---
|  .../2013-09-05_Boston-useR_02_dendextend.R        |  432 +++++++
|  .../2013-09-05_Boston-useR_02_dendextend.b        |  432 -------
|  .../2013-09-05_Boston-useR_03_untangle_iris.R     |  179 +++
|  .../2013-09-05_Boston-useR_03_untangle_iris.b     |  179 ---
|  .../2013-09-05_Boston-useR_04_tree_inference.R    |  125 ++
|  .../2013-09-05_Boston-useR_04_tree_inference.b    |  125 --
|  inst/tests/test-attr_access.R                     |  181 +++
|  inst/tests/test-attr_access.b                     |  181 ---
|  inst/tests/test-bk_method.R                       |  286 +++++
|  inst/tests/test-bk_method.b                       |  286 -----
|  inst/tests/test-cor_bakers_gamma.R                |   48 +
|  inst/tests/test-cor_bakers_gamma.b                |   48 -
|  inst/tests/test-cut_lower_fun.R                   |   95 ++
|  inst/tests/test-cut_lower_fun.b                   |   95 --
|  inst/tests/test-cutree.dendrogram.R               |  450 +++++++
|  inst/tests/test-cutree.dendrogram.b               |  450 -------
|  inst/tests/test-dendlist.R                        |   61 +
|  inst/tests/test-dendlist.b                        |   61 -
|  inst/tests/test-entanglement.R                    |  139 ++
|  inst/tests/test-entanglement.b                    |  139 --
|  inst/tests/test-labels-assign.R                   |  193 +++
|  inst/tests/test-labels-assign.b                   |  193 ---
|  inst/tests/test-labels_colors.R                   |   81 ++
|  inst/tests/test-labels_colors.b                   |   81 --
|  inst/tests/test-nleaves.R                         |   68 +
|  inst/tests/test-nleaves.b                         |   68 -
|  inst/tests/test-rotate.R                          |   91 ++
|  inst/tests/test-rotate.b                          |   91 --
|  inst/tests/test-trim.R                            |   81 ++
|  inst/tests/test-trim.b                            |   81 --
|  inst/tests/test-unbranch.R                        |   45 +
|  inst/tests/test-unbranch.b                        |   45 -
|  inst/tests/test-untangle.R                        |  162 +++
|  inst/tests/test-untangle.b                        |  162 ---
|  tests/test-all.R                                  |   13 +
|  tests/test-all.b                                  |   13 -
|  86 files changed, 12311 insertions(+), 12311 deletions(-)

* 2014-07-10(Tal Galili) rename all .r files to .b (so to allow the renaming from .r to .R on git on windows) |6145838| 
|  R/as.dendrogram.randomForest.b                    |   54 +
|  R/as.dendrogram.randomForest.r                    |   54 -
|  R/attr_access.b                                   |  814 ++++++++++++
|  R/attr_access.r                                   |  814 ------------
|  R/bk_method.b                                     | 1098 ++++++++++++++++
|  R/bk_method.r                                     | 1098 ----------------
|  R/color_branches.b                                |  482 +++++++
|  R/color_branches.r                                |  482 -------
|  R/cor_bakers_gamma.b                              |  240 ++++
|  R/cor_bakers_gamma.r                              |  240 ----
|  R/cor_cophenetic.b                                |  187 +++
|  R/cor_cophenetic.r                                |  187 ---
|  R/cut_lower_fun.b                                 |  104 ++
|  R/cut_lower_fun.r                                 |  104 --
|  R/cutree.dendrogram.b                             |  952 ++++++++++++++
|  R/cutree.dendrogram.r                             |  952 --------------
|  R/dendextend-package.b                            |   30 +
|  R/dendextend-package.r                            |   30 -
|  R/dendextend.b                                    |   70 +
|  R/dendextend.r                                    |   70 -
|  R/dendlist.R                                      |  222 ----
|  R/dendlist.b                                      |  222 ++++
|  R/entanglement.b                                  |  458 +++++++
|  R/entanglement.r                                  |  458 -------
|  R/imports_stats.b                                 |  285 +++++
|  R/imports_stats.r                                 |  285 -----
|  R/labels.b                                        |  369 ++++++
|  R/labels.r                                        |  369 ------
|  R/labels_colors.b                                 |  144 +++
|  R/labels_colors.r                                 |  144 ---
|  R/nleaves.b                                       |  316 +++++
|  R/nleaves.r                                       |  316 -----
|  R/rotate.b                                        |  337 +++++
|  R/rotate.r                                        |  337 -----
|  R/sample.dendrogram.b                             |  267 ++++
|  R/sample.dendrogram.r                             |  267 ----
|  R/tanglegram.b                                    |  815 ++++++++++++
|  R/tanglegram.r                                    |  815 ------------
|  R/trim.b                                          |  248 ++++
|  R/trim.r                                          |  248 ----
|  R/unbranch.b                                      |  246 ++++
|  R/unbranch.r                                      |  246 ----
|  R/untangle.b                                      | 1262 +++++++++++++++++++
|  R/untangle.r                                      | 1262 -------------------
|  R/zzz.b                                           |  360 ++++++
|  R/zzz.r                                           |  360 ------
|  demo/dendextend.b                                 |   23 +
|  demo/dendextend.r                                 |   23 -
|  .../2013-09-05_Boston-useR_01_intro.R             |  198 ---
|  .../2013-09-05_Boston-useR_01_intro.b             |  198 +++
|  .../2013-09-05_Boston-useR_02_dendextend.R        |  432 -------
|  .../2013-09-05_Boston-useR_02_dendextend.b        |  432 +++++++
|  .../2013-09-05_Boston-useR_03_untangle_iris.R     |  179 ---
|  .../2013-09-05_Boston-useR_03_untangle_iris.b     |  179 +++
|  .../2013-09-05_Boston-useR_04_tree_inference.R    |  125 --
|  .../2013-09-05_Boston-useR_04_tree_inference.b    |  125 ++
|  inst/tests/test-attr_access.b                     |  181 +++
|  inst/tests/test-attr_access.r                     |  181 ---
|  inst/tests/test-bk_method.b                       |  286 +++++
|  inst/tests/test-bk_method.r                       |  286 -----
|  inst/tests/test-cor_bakers_gamma.b                |   48 +
|  inst/tests/test-cor_bakers_gamma.r                |   48 -
|  inst/tests/test-cut_lower_fun.b                   |   95 ++
|  inst/tests/test-cut_lower_fun.r                   |   95 --
|  inst/tests/test-cutree.dendrogram.b               |  450 +++++++
|  inst/tests/test-cutree.dendrogram.r               |  450 -------
|  inst/tests/test-dendlist.R                        |   61 -
|  inst/tests/test-dendlist.b                        |   61 +
|  inst/tests/test-entanglement.b                    |  139 ++
|  inst/tests/test-entanglement.r                    |  139 --
|  inst/tests/test-labels-assign.b                   |  193 +++
|  inst/tests/test-labels-assign.r                   |  193 ---
|  inst/tests/test-labels_colors.b                   |   81 ++
|  inst/tests/test-labels_colors.r                   |   81 --
|  inst/tests/test-nleaves.b                         |   68 +
|  inst/tests/test-nleaves.r                         |   68 -
|  inst/tests/test-rotate.b                          |   91 ++
|  inst/tests/test-rotate.r                          |   91 --
|  inst/tests/test-trim.b                            |   81 ++
|  inst/tests/test-trim.r                            |   81 --
|  inst/tests/test-unbranch.b                        |   45 +
|  inst/tests/test-unbranch.r                        |   45 -
|  inst/tests/test-untangle.b                        |  162 +++
|  inst/tests/test-untangle.r                        |  162 ---
|  tests/test-all.b                                  |   13 +
|  tests/test-all.r                                  |   13 -
|  86 files changed, 12311 insertions(+), 12311 deletions(-)

* 2014-07-08(Tal Galili) .Rd files commit |1fdac74| 
|  man/Bk.Rd                                  |  65 ++++++------
|  man/Bk_permutations.Rd                     |  69 ++++++------
|  man/Bk_plot.Rd                             | 150 ++++++++++++---------------
|  man/FM_index.Rd                            |  85 +++++++--------
|  man/FM_index_R.Rd                          |  64 ++++++------
|  man/FM_index_permutation.Rd                |  36 +++----
|  man/FM_index_profdpm.Rd                    |  81 +++++++--------
|  man/all_couple_rotations_at_k.Rd           |  29 +++---
|  man/as_hclust_fixed.Rd                     |  18 ++--
|  man/assign_dendextend_options.Rd           |   1 +
|  man/assign_values_to_branches_edgePar.Rd   |  16 ++-
|  man/assign_values_to_leaves_nodePar.Rd     |  29 +++---
|  man/bakers_gamma_for_2_k_matrix.Rd         |  16 ++-
|  man/click_rotate.Rd                        |  10 +-
|  man/color_branches.Rd                      |  90 +++++++---------
|  man/color_labels.Rd                        |  53 ++++------
|  man/cor_bakers_gamma.Rd                    |  90 +++++++---------
|  man/cor_cophenetic.Rd                      |  63 ++++++-----
|  man/count_terminal_nodes.Rd                |  26 ++---
|  man/cut_lower_fun.Rd                       |  34 +++---
|  man/cutree-methods.Rd                      | 142 ++++++++++++-------------
|  man/cutree_1h.dendrogram.Rd                |  35 +++----
|  man/cutree_1k.dendrogram.Rd                |  59 +++++------
|  man/dendextend-package.Rd                  |   4 +-
|  man/dendextend_options.Rd                  |  16 +--
|  man/dendlist.Rd                            |  10 +-
|  man/duplicate_leaf.Rd                      |  32 +++---
|  man/entanglement.Rd                        |  93 +++++++++--------
|  man/fac2num.Rd                             |  24 ++---
|  man/fix_members_attr.dendrogram.Rd         |  12 +--
|  man/flatten.dendrogram.Rd                  |  19 ++--
|  man/flip_leaves.Rd                         |  19 ++--
|  man/get_branches_attr.Rd                   |  16 ++-
|  man/get_branches_heights.Rd                |  13 ++-
|  man/get_childrens_heights.Rd               |   5 +-
|  man/get_leaves_attr.Rd                     |  23 ++--
|  man/get_nodes_attr.Rd                      |  35 +++----
|  man/hang.dendrogram.Rd                     |  32 +++---
|  man/heights_per_k.dendrogram.Rd            |   9 +-
|  man/intersect_trees.Rd                     |  14 +--
|  man/is.dendrogram.Rd                       |   3 +-
|  man/is.hclust.Rd                           |   3 +-
|  man/is.natural.number.Rd                   |  17 ++-
|  man/is.phylo.Rd                            |   3 +-
|  man/labels-assign.Rd                       |  39 +++----
|  man/labels_colors.Rd                       |  27 +++--
|  man/leaf_Colors.Rd                         |   9 +-
|  man/lowest_common_branch.Rd                |  20 ++--
|  man/match_order_by_labels.Rd               |  25 +++--
|  man/match_order_dendrogram_by_old_order.Rd |  45 ++++----
|  man/nleaves.Rd                             |  33 +++---
|  man/nnodes.Rd                              |  16 ++-
|  man/order.dendrogram-assign.Rd             |  13 +--
|  man/plot_horiz.dendrogram.Rd               |  86 +++++++--------
|  man/prune.Rd                               |  15 ++-
|  man/prune_leaf.Rd                          |   8 +-
|  man/raise.dendrogram.Rd                    |   8 +-
|  man/rank_branches.Rd                       |  29 +++---
|  man/rank_order.dendrogram.Rd               |  11 +-
|  man/remove_branches_edgePar.Rd             |  11 +-
|  man/remove_leaves_nodePar.Rd               |  11 +-
|  man/rllply.Rd                              |  27 +++--
|  man/sample.dendrogram.Rd                   |  62 ++++++-----
|  man/shuffle.Rd                             |  34 +++---
|  man/sort_2_clusters_vectors.Rd             |  31 +++---
|  man/sort_dist_mat.Rd                       |  11 +-
|  man/sort_levels_values.Rd                  |  49 ++++-----
|  man/tanglegram.Rd                          |  23 ++--
|  man/unbranch.Rd                            |  14 ++-
|  man/unclass_dend.Rd                        |   5 +-
|  man/untangle_random_search.Rd              |  75 ++++++--------
|  man/untangle_step_rotate_1side.Rd          |  64 +++++-------
|  man/untangle_step_rotate_2side.Rd          |  57 +++++-----
|  73 files changed, 1170 insertions(+), 1351 deletions(-)

* 2014-07-08(Tal Galili) untangle_DendSer - a new untangle function (this time, only for dendlist), for leverging the serialization package for some more heuristics. |e6c4a48| 
|  ChangeLog                 | 35 ++++++++++++++++--
|  NAMESPACE                 |  7 ++++
|  NEWS                      |  1 +
|  R/untangle.r              | 87 +++++++++++++++++++++++++++++++++++++++++++--
|  man/DendSer.dendrogram.Rd | 38 ++++++++++++++++++++
|  man/as.dendlist.Rd        | 33 +++++++++++++++++
|  man/is.dendlist.Rd        | 23 ++++++++++++
|  man/is_null_list.Rd       | 38 ++++++++++++++++++++
|  man/untangle.Rd           | 84 +++++++++++++++++++++++++++++++++++++++++++
|  man/untangle_DendSer.Rd   | 42 ++++++++++++++++++++++
|  10 files changed, 382 insertions(+), 6 deletions(-)

* 2014-07-08(Tal Galili) Added tests for empty dendlist |d128b2b| 
|  inst/tests/test-dendlist.R | 38 ++++++++++++++++++++++++++++++++++++++
|  1 file changed, 38 insertions(+)

* 2014-07-08(Tal Galili) Added "untangle" - a master function to control all untangle functions (making it much easier to navigate this feature, as well as use it through %>% piping) |f276111| 
|  NEWS                       |   4 ++
|  R/untangle.r               | 100 +++++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-untangle.r |  35 +++++++++++++++
|  3 files changed, 139 insertions(+)

* 2014-07-08(Tal Galili) Make sure that the main untangle functions will return a dendlist (and also that untangle_step_rotate_2side will be able to work with the new untangle_step_rotate_1side output) |01d5312| 
|  R/untangle.r | 35 ++++++++++++++++++++---------------
|  1 file changed, 20 insertions(+), 15 deletions(-)

* 2014-07-08(Tal Galili) tanglegram - a minor fix to the doc |1470d5a| 
|  R/tanglegram.r | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2014-07-08(Tal Galili) added the functions: * is.dendlist - to check that an object is a dendlist * as.dendlist - to turn a list to a dendlist * (hidden) is_null_list |780e851| 
|  NEWS         |   2 ++
|  R/dendlist.R | 103 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 105 insertions(+)

* 2014-07-08(Tal Galili) Added a S3 dendlist method to shuffle |0af1ac2| 
|  NAMESPACE                  |  2 ++
|  R/untangle.r               | 24 ++++++++++++++++++++++++
|  inst/tests/test-untangle.r | 10 ++++++----
|  3 files changed, 32 insertions(+), 4 deletions(-)

* 2014-07-08(Tal Galili) Modify the changelog to a more compact view. |096a505| 
|  ChangeLog | 5373 +++++++++++++++++++++++++++++++++++------------------------
|  R/zzz.r   |    6 +
|  2 files changed, 3231 insertions(+), 2148 deletions(-)

* 2014-07-08(Tal Galili) Start creating "ChangeLog" file, based on my git commits :) |75ab7a8| 
|  ChangeLog | 2148 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/zzz.r   |   32 +
|  2 files changed, 2180 insertions(+)

* 2014-07-08(Tal Galili) Added credit to Dylan Beaudette for his dueling.dendrograms function (the origin of the tanglegram plot) |2ff8718| 
|  R/tanglegram.r | 5 +++++
|  1 file changed, 5 insertions(+)

* 2014-07-08(Tal Galili) Add pipes to the untangle docs |6715788| 
|  R/untangle.r | 6 ++----
|  1 file changed, 2 insertions(+), 4 deletions(-)

* 2014-07-08(Tal Galili) Add tests for entenglement on dendlist |39fef73| 
|  inst/tests/test-entanglement.r | 10 ++++++++--
|  1 file changed, 8 insertions(+), 2 deletions(-)

* 2014-07-08(Tal Galili) tanglegram - making its output be a dendlist object |d9db482| 
|  R/tanglegram.r | 16 +++++++++-------
|  1 file changed, 9 insertions(+), 7 deletions(-)

* 2014-07-07(Tal Galili) Added entanglement.dendlist function |f7f8c83| 
|  NEWS             |  2 ++
|  R/entanglement.r | 33 +++++++++++++++++++++++++++------
|  2 files changed, 29 insertions(+), 6 deletions(-)

* 2014-07-07(Tal Galili) tanglegram.dendlist - bug fix for it to work + some minor fixes to the doc |acd20bb| 
|  R/tanglegram.r | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2014-07-07(Tal Galili) Move magrittr to Depends, to make it easier to work with examples (this way it will always get the chain %>% operator to be available to all examples) |ec46e29| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2014-07-07(Tal Galili) Added horiz and continue paramters to the click_rotate function |e19f738| 
|  R/rotate.r    |  43 ++++++++++++++--------
|  man/rotate.Rd | 110 +++++++++++++++++++++++++-------------------------------
|  2 files changed, 77 insertions(+), 76 deletions(-)

* 2014-07-06(Tal Galili) Check dendlist works (new tests) |c5866a8| 
|  DESCRIPTION                |  1 +
|  NEWS                       |  4 ++++
|  inst/tests/test-dendlist.R | 23 +++++++++++++++++++++++
|  3 files changed, 28 insertions(+)

* 2014-07-06(Tal Galili) Updated DESCRIPTION and NEWS |1ce17d7| 
|  DESCRIPTION |  9 +++++----
|  NEWS        | 29 +++++++++++++++++++++++++++++
|  2 files changed, 34 insertions(+), 4 deletions(-)

* 2014-07-06(Tal Galili) Added the click_rotate function (thanks to Andrej-Nikolai Spiess) |c455d60| 
|  NAMESPACE           |  2 ++
|  R/rotate.r          | 76 +++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/click_rotate.Rd | 47 +++++++++++++++++++++++++++++++
|  3 files changed, 125 insertions(+)

* 2014-07-05(Tal Galili) Added tanglegramm.dendlist S3 method |20e4c79| 
|  NAMESPACE         |   1 +
|  R/attr_access.r   |   2 +-
|  R/tanglegram.r    |  20 +++++-
|  man/tanglegram.Rd | 179 ++++++++++++++++++++++++----------------------------
|  4 files changed, 102 insertions(+), 100 deletions(-)

* 2014-07-05(Tal Galili) Make dendlist handle hclust and phylo |c74f06a| 
|  R/dendlist.R | 21 ++++++++++++++++++---
|  1 file changed, 18 insertions(+), 3 deletions(-)

* 2014-07-04(Tal Galili) dendlist - a function which creates a list of dendrogram of the new "dendlist" class. |2dec5f9| 
|  NAMESPACE       |   3 ++
|  R/dendlist.R    | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/dendlist.Rd |  38 ++++++++++++++++++++
|  3 files changed, 145 insertions(+)

* 2014-04-26(Tal Galili) Version 0.14.3 - minor changes to DESCRIPTION |70b93f9| 
|  DESCRIPTION |  4 ++--
|  NEWS        | 12 ++++++++++++
|  2 files changed, 14 insertions(+), 2 deletions(-)

* 2014-04-26(Tal Galili) minor fixes to examples |d7d3c86| 
|  R/color_branches.r    | 1 +
|  R/cutree.dendrogram.r | 2 +-
|  2 files changed, 2 insertions(+), 1 deletion(-)

* 2014-03-18(Tal Galili) Added dendextendRcpp (>= 0.5.0) to Suggests! |acd6f98| 
|  DESCRIPTION | 16 ++++++++--------
|  1 file changed, 8 insertions(+), 8 deletions(-)

* 2014-03-18(Tal Galili) Fixing spaces |b74e3ba| 
|  README.md | 3 +++
|  1 file changed, 3 insertions(+)

* 2014-03-18(Tal Galili) Fixing "jefferis" to full name |e2f9496| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2014-03-15(Tal Galili) Added dependency for R (>= 3.0.0) |25e3103| 
|  DESCRIPTION |  6 ++++--
|  NEWS        | 11 +++++++++++
|  2 files changed, 15 insertions(+), 2 deletions(-)

* 2014-03-15(Tal Galili) Note that the package will go on CRAN |8e92afb| 
|  DESCRIPTION | 1 -
|  NEWS        | 8 +++++++-
|  2 files changed, 7 insertions(+), 2 deletions(-)

* 2014-03-15(Tal Galili) Bumped to  0.14.1 |029e5a0| 
|  DESCRIPTION |  3 +--
|  NEWS        | 18 +++++++++++++++---
|  2 files changed, 16 insertions(+), 5 deletions(-)

* 2014-03-15(Tal Galili) Fix Undocumented arguments in documentation object 'dendextend_options'   'option' 'value' |a3d3520| 
|  R/zzz.r                   | 4 ++++
|  man/dendextend_options.Rd | 7 +++++++
|  2 files changed, 11 insertions(+)

* 2014-03-15(Tal Galili) update test_rotate.r so it would make sure ape is loaded BEFORE dendextend. |067afc4| 
|  NEWS                     |  2 +-
|  inst/tests/test-rotate.r | 14 ++++++++++++++
|  2 files changed, 15 insertions(+), 1 deletion(-)

* 2014-03-15(Tal Galili) dendextend_options (actually an enviornment + a function) - added |095861c| 
|  NAMESPACE                 |  1 +
|  NEWS                      |  2 +-
|  R/zzz.r                   | 77 ++++++++++++++++++++++++++++-----------------
|  man/dendextend_options.Rd | 27 ++++++++++++++++
|  4 files changed, 77 insertions(+), 30 deletions(-)

* 2014-03-15(Tal Galili) update tests to the new names in dendextendRcpp (dendextendRcpp_cut_lower_fun, dendextend_options) |d4c03b0| 
|  NEWS                            | 2 ++
|  inst/tests/test-attr_access.r   | 2 +-
|  inst/tests/test-cut_lower_fun.r | 8 ++++----
|  3 files changed, 7 insertions(+), 5 deletions(-)

* 2014-03-15(Tal Galili) assign_dendextend_options - is now exported. |b0f1028| 
|  NAMESPACE                        |  1 +
|  NEWS                             |  5 +++--
|  R/zzz.r                          |  7 +++++++
|  man/assign_dendextend_options.Rd | 10 ++++++++++
|  4 files changed, 21 insertions(+), 2 deletions(-)

* 2014-03-15(Tal Galili) Moved to passing the functions through "dendextend_options" instead of through "options" (Thanks to suggestions by Kurt Hornik and Uwe Ligges). |ce0c91b| 
|  DESCRIPTION           |  9 +++++---
|  NEWS                  | 14 +++++++++++++
|  R/attr_access.r       |  2 +-
|  R/cut_lower_fun.r     |  2 +-
|  R/cutree.dendrogram.r |  2 +-
|  R/zzz.r               | 56 +++++++++++++++++++++++++++++++++++++++++++------
|  6 files changed, 73 insertions(+), 12 deletions(-)

* 2014-03-01(Tal Galili) Bump to version 0.13.0 |7c8c681| 
|  DESCRIPTION |  5 +++--
|  NEWS        | 26 ++++++++++++++++++++++++++
|  README.md   |  6 +++---
|  3 files changed, 32 insertions(+), 5 deletions(-)

* 2014-03-01(Tal Galili) Added a compressed version of the pdf tutorial. |68d7376| 
|  inst/doc/dendextend-tutorial.pdf | Bin 0 -> 569458 bytes
|  1 file changed, 0 insertions(+), 0 deletions(-)

* 2014-03-01(Tal Galili) assign_dendextend_options - we now pass all functions that have a Rcpp equivalent through "options". While this adds a bit of an overhead (sadly), it still gets a much faster speed gain, and without verious warnings that CRAN checks would not like. |4e47c40| 
|  NAMESPACE                       |  3 +++
|  R/attr_access.r                 | 24 +++++++++++++++++++++++-
|  R/cut_lower_fun.r               | 15 ++++++++++++++-
|  R/cutree.dendrogram.r           | 28 +++++++++++++++++++++++++---
|  R/dendextend-package.r          |  2 +-
|  R/zzz.r                         | 21 +++++++++++++++++++--
|  man/cut_lower_fun.Rd            |  1 +
|  man/dendextend-package.Rd       |  4 ++--
|  man/get_branches_heights.Rd     | 14 ++++++++++++++
|  man/heights_per_k.dendrogram.Rd | 15 +++++++++++++++
|  tests/test-all.r                | 10 ++++++++--
|  11 files changed, 125 insertions(+), 12 deletions(-)

* 2014-03-01(Tal Galili) When comparing to dendextendRcpp - added condition to not make the check if the package is not loaded and in the search path (this way I could compare the tests with and without the dendextendRcpp package). |f7bad9b| 
|  inst/tests/test-cut_lower_fun.r     | 148 +++++++++++++++++-----------------
|  inst/tests/test-cutree.dendrogram.r |   6 +-
|  2 files changed, 79 insertions(+), 75 deletions(-)

* 2014-03-01(Tal Galili) added a minor test for dendextend_get_branches_heights - checking the function directly through the options. |523e604| 
|  inst/tests/test-attr_access.r | 4 +++-
|  1 file changed, 3 insertions(+), 1 deletion(-)

* 2014-02-03(Tal Galili) dendextend 0.12.2 is intended to be shipped to CRAN. |d86832f| 
|  NEWS    | 27 ++++++++++++++++++++++++++-
|  R/zzz.r | 29 ++++++++++++++++++++++++++++-
|  2 files changed, 54 insertions(+), 2 deletions(-)

* 2014-02-03(Tal Galili) Hidden "stats" functions have been added to a new file "imports_stats.r"       with a new local copy for                            'stats:::.memberDend' 'stats:::.midDend'                            'stats:::midcache.dendrogram' 'stats:::plotNode'                            'stats:::plotNodeLimit'       with stats::: -> stats_ |62f874e| 
|  R/imports_stats.r     | 285 ++++++++++++++++++++++++++++++++++++++++++++++++
|  R/sample.dendrogram.r |   4 +-
|  R/tanglegram.r        |  16 +--
|  R/trim.r              |   2 +-
|  R/unbranch.r          |   2 +-
|  5 files changed, 297 insertions(+), 12 deletions(-)

* 2014-02-03(Tal Galili) dendextend:::cutree -> dendextend::cutree |c6db8e8| 
|  R/color_branches.r | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2014-02-03(Tal Galili) UPDATED DESCRIPTION:    * Removed VignetteBuilder: knitr (until later)    * Removed Suggests: dendextendRcpp, (until later)    * fixed mis-spelled words: extanding (14:40) |b83bb5a| 
|  DESCRIPTION | 8 +++-----
|  1 file changed, 3 insertions(+), 5 deletions(-)

* 2014-02-03(Tal Galili) stats:::cutree -> stats::cutree |72eee44| 
|  R/cutree.dendrogram.r               | 6 +++---
|  inst/tests/test-cutree.dendrogram.r | 2 +-
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2014-02-02(Tal Galili) Fix "\examples lines wider than 100 characters:" in several places. |18a2420| 
|  NEWS                        |  1 +
|  R/bk_method.r               | 24 ++++++++++++++++--------
|  R/color_branches.r          |  6 ++++--
|  R/cor_bakers_gamma.r        |  3 ++-
|  R/cutree.dendrogram.r       |  7 ++++---
|  R/nleaves.r                 | 15 ++++++++++-----
|  R/trim.r                    | 10 ++++++++--
|  man/Bk_plot.Rd              |  3 ++-
|  man/FM_index.Rd             | 15 ++++++++++-----
|  man/FM_index_profdpm.Rd     |  6 ++++--
|  man/color_branches.Rd       |  6 ++++--
|  man/cor_bakers_gamma.Rd     |  3 ++-
|  man/cutree_1k.dendrogram.Rd |  7 ++++---
|  man/intersect_trees.Rd      | 10 ++++++++--
|  man/unclass_dend.Rd         | 15 ++++++++++-----
|  15 files changed, 89 insertions(+), 42 deletions(-)

* 2014-02-02(Tal Galili) data(iris) -> data(iris, envir = environment()) |c5f56e4| 
|  NEWS                           | 2 ++
|  R/as.dendrogram.randomForest.r | 2 +-
|  R/color_branches.r             | 6 +++---
|  R/zzz.r                        | 8 ++++++++
|  man/color_branches.Rd          | 4 ++--
|  5 files changed, 16 insertions(+), 6 deletions(-)

* 2014-02-02(Tal Galili) Made sure to check dendextendRcpp is available before calling it. |c0b9bc0| 
|  DESCRIPTION                         |  6 ++---
|  NEWS                                |  7 +++--
|  inst/tests/test-bk_method.r         | 32 +++++++++++-----------
|  inst/tests/test-cor_bakers_gamma.r  |  4 +--
|  inst/tests/test-cut_lower_fun.r     | 51 ++++++++++++++++++-----------------
|  inst/tests/test-cutree.dendrogram.r | 20 ++++++++------
|  inst/tests/test-entanglement.r      |  4 +--
|  tests/test-all.r                    |  2 +-
|  8 files changed, 68 insertions(+), 58 deletions(-)

* 2014-02-02(Tal Galili) Commented out manipulations on the search path and of assignInNamespace. (to avoid NOTES/warnings) |d40fc34| 
|  NEWS                            |   9 ++-
|  R/attr_access.r                 |   4 +-
|  R/cut_lower_fun.r               |   6 +-
|  R/cutree.dendrogram.r           |   4 +-
|  R/nleaves.r                     |   3 +-
|  R/zzz.r                         | 160 +++++++++++++++++++-------------------
|  man/cut_lower_fun.Rd            |   1 -
|  man/get_branches_heights.Rd     |   1 -
|  man/heights_per_k.dendrogram.Rd |   1 -
|  9 files changed, 99 insertions(+), 90 deletions(-)

* 2014-02-01(Tal Galili) Vignettes - getting the latest version. |6e073a7| 
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|  vignettes/dendextend-tutorial-concordance.tex     |   14 +-
|  vignettes/dendextend-tutorial.log                 | 1205 +--
|  vignettes/dendextend-tutorial.pdf                 | 8003 ++++++++++---------
|  vignettes/dendextend-tutorial.rnw                 |   21 +-
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|  vignettes/dendextend-tutorial.tex                 |  331 +-
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|  .../untangle_step_rotate_2side_example1.pdf       |  Bin 6158 -> 6158 bytes
|  .../untangle_step_rotate_2side_example2.pdf       |  Bin 6137 -> 6137 bytes
|  .../untangle_step_rotate_2side_example3.pdf       |  Bin 6154 -> 6154 bytes
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|  231 files changed, 5284 insertions(+), 4290 deletions(-)

* 2014-02-01(Tal Galili) rotate - Remove the "flip" command in the example (after I noticed that "rev" does this just fine...) |4e2b110| 
|  NEWS          | 2 ++
|  R/rotate.r    | 4 ++--
|  man/rotate.Rd | 4 ++--
|  3 files changed, 6 insertions(+), 4 deletions(-)

* 2014-02-01(Tal Galili) Fixed the usage of person() in DESCRIPTION. (props goes to Uwe Ligges for his input) |28d84d8| 
|  DESCRIPTION | 15 ++++++++-------
|  NEWS        |  2 +-
|  2 files changed, 9 insertions(+), 8 deletions(-)

* 2014-02-01(Tal Galili) Fix "Argument items with no description in Rd object": 'plot_horiz.dendrogram', 'untangle_step_rotate_1side'. |6173ec9| 
|  NEWS                              | 2 +-
|  R/tanglegram.r                    | 2 +-
|  R/untangle.r                      | 2 +-
|  man/plot_horiz.dendrogram.Rd      | 3 ++-
|  man/untangle_step_rotate_1side.Rd | 4 +++-
|  5 files changed, 8 insertions(+), 5 deletions(-)

* 2014-02-01(Tal Galili) Fix "Objects in \usage without \alias in documentation object 'shuffle'":   'shuffle.dendrogram' 'shuffle.hclust' 'shuffle.phylo' |87ec513| 
|  NEWS           | 3 +++
|  R/untangle.r   | 4 +++-
|  man/shuffle.Rd | 3 +++
|  3 files changed, 9 insertions(+), 1 deletion(-)

* 2014-02-01(Tal Galili) Fix "Undocumented arguments in documentation object" for:       * 'bakers_gamma_for_2_k_matrix'       * 'cor_bakers_gamma'       * 'cut_lower_fun' |35bf958| 
|  NEWS                               | 4 ++++
|  R/cor_bakers_gamma.r               | 5 +++--
|  R/cut_lower_fun.r                  | 1 +
|  man/bakers_gamma_for_2_k_matrix.Rd | 4 ++--
|  man/cor_bakers_gamma.Rd            | 5 ++++-
|  man/cut_lower_fun.Rd               | 2 ++
|  6 files changed, 16 insertions(+), 5 deletions(-)

* 2014-02-01(Tal Galili) Fix "'library' or 'require' call not declared from: 'ape'" by commenting-off every "require(ape)" command in the code, since it is already mentioned in imports!       (see: http://stackoverflow.com/questions/15648772/how-do-i-prevent-r-library-or-require-calls-not-declared-warnings-when-dev)       The problem still persists because of .onLoad in zzz.r, but we'll look into this later... |651bd98| 
|  NEWS          | 4 +++-
|  R/nleaves.r   | 7 +++----
|  R/rotate.r    | 6 +++---
|  R/trim.r      | 2 +-
|  R/unbranch.r  | 2 +-
|  R/zzz.r       | 7 +++++--
|  man/rotate.Rd | 2 +-
|  7 files changed, 17 insertions(+), 13 deletions(-)

* 2014-02-01(Tal Galili) Fix "Argument names in code not in docs", for: edge.lwd dLeaf_left dLeaf_right main sub rank_branches hang match_order_by_labels cex_main cex_main_left cex_main_right cex_sub |1f58846| 
|  NEWS              |  1 +
|  R/tanglegram.r    | 12 ++++++++++++
|  man/tanglegram.Rd | 12 ++++++++++++
|  3 files changed, 25 insertions(+)

* 2014-02-01(Tal Galili) Fix "Mismatches in argument default values "tanglegram" |a4fe297| 
|  NEWS              | 9 ++++++++-
|  R/tanglegram.r    | 6 +++---
|  man/tanglegram.Rd | 6 +++---
|  3 files changed, 14 insertions(+), 7 deletions(-)

* 2014-02-01(Tal Galili) Fix "Codoc mismatches from documentation object 'rotate':" - by removing k and h (since I never got to implement them...) |12a24bf| 
|  NEWS          |  1 +
|  R/rotate.r    | 15 +++++++++------
|  man/rotate.Rd |  8 --------
|  3 files changed, 10 insertions(+), 14 deletions(-)

* 2014-02-01(Tal Galili) Fix Undocumented code objects: 'old_cut_lower_fun' 'old_get_branches_heights'   'old_heights_per_k.dendrogram'.  By adding them as "#' @aliases" |13c28a1| 
|  NEWS                            | 2 ++
|  R/attr_access.r                 | 2 ++
|  R/cut_lower_fun.r               | 2 ++
|  R/cutree.dendrogram.r           | 2 ++
|  man/cut_lower_fun.Rd            | 1 +
|  man/get_branches_heights.Rd     | 1 +
|  man/heights_per_k.dendrogram.Rd | 1 +
|  7 files changed, 11 insertions(+)

* 2014-02-01(Tal Galili) Fix various "Missing link or links in documentation object" |cb607c6| 
|  NEWS                                       | 8 +++++---
|  NEWS.md                                    | 2 +-
|  R/color_branches.r                         | 2 +-
|  R/cutree.dendrogram.r                      | 1 -
|  R/entanglement.r                           | 8 ++++----
|  R/tanglegram.r                             | 2 +-
|  R/unbranch.r                               | 2 +-
|  man/all_couple_rotations_at_k.Rd           | 5 ++---
|  man/cutree-methods.Rd                      | 1 -
|  man/entanglement.Rd                        | 5 ++---
|  man/flip_leaves.Rd                         | 4 ++--
|  man/leaf_Colors.Rd                         | 2 +-
|  man/match_order_by_labels.Rd               | 2 +-
|  man/match_order_dendrogram_by_old_order.Rd | 2 +-
|  man/plot_horiz.dendrogram.Rd               | 2 +-
|  man/unbranch.Rd                            | 2 +-
|  man/untangle_random_search.Rd              | 4 ++--
|  man/untangle_step_rotate_1side.Rd          | 6 +++---
|  man/untangle_step_rotate_2side.Rd          | 6 +++---
|  19 files changed, 32 insertions(+), 34 deletions(-)

* 2014-02-01(Tal Galili) remove \link{untangle} from various .Rd (I never created this function...) |0d9c368| 
|  NEWS         |  6 ++++--
|  R/untangle.r | 10 +++++-----
|  2 files changed, 9 insertions(+), 7 deletions(-)

* 2014-02-01(Tal Galili) fix "Unknown package 'dendroextra' in Rd xrefs" in color_branches docs. |52b0ff4| 
|  NEWS                  | 4 ++++
|  R/color_branches.r    | 6 +++---
|  R/tanglegram.r        | 2 +-
|  R/unbranch.r          | 2 +-
|  man/color_branches.Rd | 8 ++++----
|  5 files changed, 13 insertions(+), 9 deletions(-)

* 2014-02-01(Tal Galili) Add DESCRIPTION and NEWS to git. |e80c96f| 
|  DESCRIPTION | 40 ++++++++--------------------
|  NEWS        | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++---
|  NEWS.md     |  6 ++---
|  R/zzz.r     | 10 ++++---
|  4 files changed, 100 insertions(+), 39 deletions(-)

* 2014-02-01(Tal Galili) Return "as.phylo.dendrogram" by adding "ape" to "Imports" in DESCRIPTION and "import" to NAMESPACE. Also fixing consistancy (using x instead of object). |6706c68| 
|  NAMESPACE   |  2 ++
|  R/nleaves.r | 17 +++++++++++------
|  2 files changed, 13 insertions(+), 6 deletions(-)

* 2014-02-01(Tal Galili) Remove "as.phylo.dendrogram" so to not force the package to depend on "ape" |52f4780| 
|  NAMESPACE      |  2 --
|  R/dendextend.r | 15 +++++++++++++++
|  R/nleaves.r    | 18 +++++++++++-------
|  3 files changed, 26 insertions(+), 9 deletions(-)

* 2014-02-01(Tal Galili) Moved from ::: to :: (where possible with dendextendRcpp). |519cad5| 
|  NAMESPACE                           | 1 +
|  R/cut_lower_fun.r                   | 2 +-
|  R/cutree.dendrogram.r               | 3 +--
|  inst/tests/test-cut_lower_fun.r     | 3 ++-
|  inst/tests/test-cutree.dendrogram.r | 4 +++-
|  man/cut_lower_fun.Rd                | 2 +-
|  vignettes/dendextend-tutorial.rnw   | 8 ++++----
|  7 files changed, 13 insertions(+), 10 deletions(-)

* 2014-02-01(Tal Galili) Using 'talgalili/dendextend', in install_github |ec75abf| 
|  README.md | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2014-02-01(Tal Galili) Moved from ::: to :: (where possible). |f4cff30| 
|  R/rotate.r                        |  5 ++++-
|  R/trim.r                          | 13 +++++++++----
|  R/unbranch.r                      |  2 +-
|  R/zzz.r                           | 12 +++++++++++-
|  vignettes/dendextend-tutorial.rnw |  2 +-
|  vignettes/dendextend-tutorial.tex |  2 +-
|  6 files changed, 27 insertions(+), 9 deletions(-)

* 2014-02-01(Tal Galili) cutree.dendrogram - turned into S3 (no longer exported) |20e1dae| 
|  man/cutree.dendrogram.Rd | 118 ---------------------------------------------
|  1 file changed, 118 deletions(-)

* 2014-02-01(Tal Galili) changed functions names:       * trim -> prune       * unroot -> unbranch |9ca729c| 
|  man/prune.Rd     |  2 +-
|  man/trim.Rd      | 48 ------------------------------------------------
|  man/trim_leaf.Rd | 32 --------------------------------
|  man/unroot.Rd    | 50 --------------------------------------------------
|  4 files changed, 1 insertion(+), 131 deletions(-)

* 2014-02-01(Tal Galili) cut_lower_fun acts diffirently on dendextendRcpp vs old dendextend, so I updated the tests to reflect that. |b520e84| 
|  inst/tests/test-cut_lower_fun.r | 25 ++++++++++++++++++-------
|  1 file changed, 18 insertions(+), 7 deletions(-)

* 2014-02-01(Tal Galili) S3methods no longer seem to be exported (due to something in roxygen2), I chose to update the tests accordingly.       * cutree.hclust -> dendextend:::cutree.hclust       * cutree.dendrogram -> dendextend:::cutree.dendrogram |e8ac80b| 
|  R/nleaves.r                         |  4 ++++
|  inst/tests/test-cutree.dendrogram.r | 12 ++++++------
|  2 files changed, 10 insertions(+), 6 deletions(-)

* 2014-01-31(Tal Galili) Added to .Rbuildignore "vignettes/" (we'll deal with this later...) |4ea429e| 
|  .Rbuildignore | 3 ++-
|  1 file changed, 2 insertions(+), 1 deletion(-)

* 2014-01-31(Tal Galili) leaf_Colors - fix example (added "dend"). |0594889| 
|  R/color_branches.r | 1 +
|  man/leaf_Colors.Rd | 1 +
|  2 files changed, 2 insertions(+)

* 2014-01-31(Tal Galili) exported prune_leaf |c572359| 
|  NAMESPACE         | 1 +
|  R/trim.r          | 3 ++-
|  man/prune_leaf.Rd | 2 +-
|  man/trim_leaf.Rd  | 2 +-
|  4 files changed, 5 insertions(+), 3 deletions(-)

* 2014-01-31(Tal Galili) README.md - invitation to get credit for using dendextend. |dcc55c3| 
|  README.md | 17 +++++++++++++++++
|  1 file changed, 17 insertions(+)

* 2014-01-31(Tal Galili) Added to .Rbuildignore: (large files which are not essential)       * inst/doc/2013-09-05_Boston-useR       * vignettes/figure |a2a4684| 
|  .Rbuildignore | 4 +++-
|  1 file changed, 3 insertions(+), 1 deletion(-)

* 2014-01-31(Tal Galili) Added "ape::" to as.phylo |e7cbf41| 
|  R/nleaves.r  | 6 ++++--
|  R/unbranch.r | 3 ++-
|  2 files changed, 6 insertions(+), 3 deletions(-)

* 2014-01-31(Tal Galili) Fix S3method in NAMESPACE |738d0ed| 
|  NAMESPACE | 29 +++++++++++------------------
|  1 file changed, 11 insertions(+), 18 deletions(-)

* 2014-01-31(Tal Galili) Fixing .Rd indentation. |8c68f20| 
|  man/Bk.Rd                                  |  42 +++++-----
|  man/Bk_permutations.Rd                     |  57 +++++++-------
|  man/Bk_plot.Rd                             |  79 +++++++++----------
|  man/FM_index.Rd                            |  56 +++++++-------
|  man/FM_index_R.Rd                          |  54 +++++++------
|  man/FM_index_permutation.Rd                |  26 +++----
|  man/FM_index_profdpm.Rd                    |  70 +++++++++--------
|  man/all_couple_rotations_at_k.Rd           |  23 +++---
|  man/as_hclust_fixed.Rd                     |  14 ++--
|  man/assign_values_to_branches_edgePar.Rd   |  13 ++--
|  man/assign_values_to_leaves_nodePar.Rd     |  13 ++--
|  man/bakers_gamma_for_2_k_matrix.Rd         |   9 +--
|  man/color_branches.Rd                      |  85 ++++++++++-----------
|  man/color_labels.Rd                        |  35 +++++----
|  man/cor_bakers_gamma.Rd                    |  82 ++++++++++----------
|  man/cor_cophenetic.Rd                      |  63 ++++++++-------
|  man/count_terminal_nodes.Rd                |  29 ++++---
|  man/cut_lower_fun.Rd                       |  28 +++----
|  man/cutree-methods.Rd                      | 100 ++++++++++++------------
|  man/cutree_1h.dendrogram.Rd                |  17 ++---
|  man/cutree_1k.dendrogram.Rd                |  33 ++++----
|  man/dendextend-package.Rd                  |   6 +-
|  man/duplicate_leaf.Rd                      |  16 ++--
|  man/entanglement.Rd                        |  53 +++++++------
|  man/fac2num.Rd                             |  16 ++--
|  man/fix_members_attr.dendrogram.Rd         |  10 +--
|  man/flatten.dendrogram.Rd                  |  12 +--
|  man/flip_leaves.Rd                         |  18 ++---
|  man/get_branches_attr.Rd                   |  10 +--
|  man/get_branches_heights.Rd                |   9 +--
|  man/get_childrens_heights.Rd               |  10 +--
|  man/get_leaves_attr.Rd                     |  17 ++---
|  man/get_nodes_attr.Rd                      |  24 +++---
|  man/hang.dendrogram.Rd                     |  22 +++---
|  man/heights_per_k.dendrogram.Rd            |   9 +--
|  man/intersect_trees.Rd                     |  10 +--
|  man/is.dendrogram.Rd                       |   6 +-
|  man/is.hclust.Rd                           |   6 +-
|  man/is.natural.number.Rd                   |  20 ++---
|  man/is.phylo.Rd                            |   6 +-
|  man/labels-assign.Rd                       |  36 +++++----
|  man/labels_colors.Rd                       |  22 +++---
|  man/leaf_Colors.Rd                         |  15 ++--
|  man/lowest_common_branch.Rd                |  18 ++---
|  man/match_order_by_labels.Rd               |  22 +++---
|  man/match_order_dendrogram_by_old_order.Rd |  37 +++++----
|  man/nleaves.Rd                             |  33 ++++----
|  man/nnodes.Rd                              |  26 +++----
|  man/order.dendrogram-assign.Rd             |  12 +--
|  man/plot_horiz.dendrogram.Rd               |  39 +++++-----
|  man/prune.Rd                               |  22 +++---
|  man/prune_leaf.Rd                          |   8 +-
|  man/raise.dendrogram.Rd                    |   6 +-
|  man/rank_branches.Rd                       |  31 ++++----
|  man/rank_order.dendrogram.Rd               |  14 ++--
|  man/remove_branches_edgePar.Rd             |  13 ++--
|  man/remove_leaves_nodePar.Rd               |  12 +--
|  man/rllply.Rd                              |  20 ++---
|  man/rotate.Rd                              | 110 +++++++++++++--------------
|  man/sample.dendrogram.Rd                   |  27 +++----
|  man/shuffle.Rd                             |  37 +++++----
|  man/sort_2_clusters_vectors.Rd             |  12 +--
|  man/sort_dist_mat.Rd                       |   9 +--
|  man/sort_levels_values.Rd                  |  32 ++++----
|  man/tanglegram.Rd                          |  77 ++++++++++---------
|  man/unbranch.Rd                            |  16 ++--
|  man/unclass_dend.Rd                        |   8 +-
|  man/untangle_random_search.Rd              |  26 +++----
|  man/untangle_step_rotate_1side.Rd          |  38 ++++-----
|  man/untangle_step_rotate_2side.Rd          |  31 ++++----
|  70 files changed, 987 insertions(+), 1030 deletions(-)

* 2014-01-31(Tal Galili) Added a placeholder for "as.dendrogram.randomForest" |2172548| 
|  R/as.dendrogram.randomForest.r | 54 ++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 54 insertions(+)

* 2013-12-10(Tal Galili) heirarchical -> Hierarchical |ee796c1| 
|  vignettes/dendextend-tutorial.rnw | 14 +++++++-------
|  1 file changed, 7 insertions(+), 7 deletions(-)

* 2013-09-05(Tal Galili) Added a fix to declare the UTF-8 encoding (for non-Windows users trying to install from github) |9bd9615| 
|  vignettes/dendextend-tutorial.rnw | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-09-01(Tal Galili) NEWS.md file added. |73e0f18| 
|  .Rbuildignore |   2 +-
|  NEWS.md       | 383 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/zzz.r       |   1 +
|  README.md     |   6 +
|  4 files changed, 391 insertions(+), 1 deletion(-)

* 2013-08-31(Tal Galili) Added R code for the presentations. |e4a1fc2| 
|  .../2013-09-05_Boston-useR_01_intro.R             |   8 +-
|  .../2013-09-05_Boston-useR_01_intro.Rpres         |   2 +-
|  .../2013-09-05_Boston-useR_02_dendextend.R        |   4 +-
|  .../2013-09-05_Boston-useR_03_untangle_iris.R     | 179 ++++++++++++++++++++
|  .../2013-09-05_Boston-useR_04_tree_inference.R    | 125 ++++++++++++++
|  5 files changed, 314 insertions(+), 4 deletions(-)

* 2013-08-31(Tal Galili) Updated presentations links |3197196| 
|  README.md | 6 +++++-
|  1 file changed, 5 insertions(+), 1 deletion(-)

* 2013-08-31(Tal Galili) Finished tanglegram and untangle.  Finished statistical measures of similarity between trees. |0f265bf| 
|  DESCRIPTION                                       |    2 +-
|  NEWS                                              |    8 +-
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    3 +-
|  ...chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.RData |  Bin 3018 -> 0 bytes
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|  .../dend1_plot_1.png                              |  Bin 0 -> 3877 bytes
|  .../precip_dend5_plot_2.png                       |  Bin 0 -> 3334 bytes
|  .../tanglegram_dend12_1.png                       |  Bin 0 -> 4528 bytes
|  .../unnamed-chunk-10.png                          |  Bin 0 -> 7186 bytes
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|  .../unnamed-chunk-9.png                           |  Bin 0 -> 2000 bytes
|  ...2013-09-05_Boston-useR_04_tree_inference.Rpres |  182 ++-
|  .../2013-09-05_Boston-useR_04_tree_inference.html | 1100 +++++++++++++++++++
|  .../2013-09-05_Boston-useR_04_tree_inference.md   |  229 +++-
|  19 files changed, 1466 insertions(+), 58 deletions(-)

* 2013-08-31(Tal Galili) Vignettes tweaks |c992a7b| 
|  .gitignore                                        |    1 +
|  vignettes/.gitignore                              |    1 +
|  ...hunk-28_a920283370fb5e377c9ab52b0e8e6f00.RData |  Bin 3490 -> 0 bytes
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|  vignettes/dendextend-tutorial-concordance.tex     |    2 +-
|  vignettes/dendextend-tutorial.log                 |   22 +-
|  vignettes/dendextend-tutorial.pdf                 | 1569 ++++++++++---------
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 240665 -> 240890 bytes
|  vignettes/dendextend-tutorial.tex                 |   18 +-
|  vignettes/figure/unnamed-chunk-28.pdf             |  Bin 4694 -> 4694 bytes
|  vignettes/figure/unnamed-chunk-29.pdf             |  Bin 5655 -> 5655 bytes
|  15 files changed, 814 insertions(+), 799 deletions(-)

* 2013-08-30(Tal Galili) "trim" is now called "prune"! |e783d26| 
|  DESCRIPTION                                       |   7 +-
|  NAMESPACE                                         |  10 +-
|  NEWS                                              |   9 +-
|  R/attr_access.r                                   |  14 +-
|  R/cutree.dendrogram.r                             |   4 +-
|  R/sample.dendrogram.r                             |   6 +-
|  R/tanglegram.r                                    |   6 +-
|  R/trim.r                                          |  96 +++---
|  README.md                                         |   2 +-
|  demo/dendextend.r                                 |   2 +-
|  .../2013-09-05_Boston-useR_02_dendextend.R        |   8 +-
|  .../2013-09-05_Boston-useR_02_dendextend.Rpres    |   6 +-
|  .../2013-09-05_Boston-useR_02_dendextend.html     |   8 +-
|  .../2013-09-05_Boston-useR_02_dendextend.md       |   8 +-
|  inst/tests/test-trim.r                            |  34 +-
|  man/fix_members_attr.dendrogram.Rd                |  10 +-
|  man/intersect_trees.Rd                            |  14 +-
|  man/prune.Rd                                      |  48 +++
|  man/prune_leaf.Rd                                 |  32 ++
|  man/rank_order.dendrogram.Rd                      |   4 +-
|  man/sample.dendrogram.Rd                          |   2 +-
|  man/tanglegram.Rd                                 |   4 +-
|  man/trim.Rd                                       |  30 +-
|  man/trim_leaf.Rd                                  |  14 +-
|  vignettes/dendextend-tutorial.bib                 |   2 +-
|  vignettes/dendextend-tutorial.log                 |   4 +-
|  vignettes/dendextend-tutorial.pdf                 | 328 ++++++++++----------
|  vignettes/dendextend-tutorial.rnw                 |  18 +-
|  vignettes/dendextend-tutorial.tex                 |  22 +-
|  29 files changed, 416 insertions(+), 336 deletions(-)

* 2013-08-30(Tal Galili) Finished tanglegram and untangle. We are left with |3689f21| 
|  NEWS                                              |    3 +
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    3 +-
|  .../2013-09-05_Boston-useR_01_intro.Rpres         |    8 +-
|  .../dend_hang_tree_1.png                          |  Bin 0 -> 4731 bytes
|  .../dend_rotating_example_1.png                   |  Bin 0 -> 4759 bytes
|  .../dend_trimming_example_1.png                   |  Bin 0 -> 4139 bytes
|  .../dend_unbranching_example_1.png                |  Bin 0 -> 4748 bytes
|  .../first_tanglegram_with_code.png                |  Bin 0 -> 40772 bytes
|  .../simple_tanglegram_1.png                       |  Bin 2846 -> 3256 bytes
|  .../simple_tanglegram_1_worst_case.png            |  Bin 4124 -> 4577 bytes
|  .../simple_tanglegram_one_shuffle_1.png           |  Bin 2932 -> 3621 bytes
|  .../simple_tanglegram_random_search_1.png         |  Bin 2296 -> 2846 bytes
|  ...ple_tanglegram_step_rotate_1side_example_1.png |  Bin 0 -> 2822 bytes
|  .../tanglegram_iris_untangle_random.png           |  Bin 0 -> 42100 bytes
|  .../unnamed-chunk-15.png                          |  Bin 4731 -> 4755 bytes
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|  .../unnamed-chunk-24.png                          |  Bin 0 -> 22344 bytes
|  .../2013-09-05_Boston-useR_02_dendextend.R        |  122 +-
|  .../2013-09-05_Boston-useR_02_dendextend.Rpres    |  103 +-
|  .../2013-09-05_Boston-useR_02_dendextend.html     | 1666 +++++++++++++++++++
|  .../2013-09-05_Boston-useR_02_dendextend.md       |   95 +-
|  .../first_tanglegram_with_2side_untangle.png      |  Bin 0 -> 18166 bytes
|  .../first_tanglegram_with_2side_untangle_hang.png |  Bin 0 -> 26292 bytes
|  .../first_tanglegram_with_code.png                |  Bin 0 -> 29397 bytes
|  .../first_tanglegram_with_random_untangle.png     |  Bin 0 -> 23574 bytes
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|  .../unnamed-chunk-9.png                           |  Bin 0 -> 18112 bytes
|  .../2013-09-05_Boston-useR_03_untangle_iris.Rpres |  184 ++
|  .../2013-09-05_Boston-useR_03_untangle_iris.html  | 1058 ++++++++++++
|  .../2013-09-05_Boston-useR_03_untangle_iris.md    |  200 +++
|  .../__packages                                    |    8 +
|  ...ordered_ca9a216309a7a760068a06f608ab2ccd.RData |  Bin 0 -> 2844 bytes
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|  ...d-chunk-1_58a12d7b33c21c7d7cf3b61809b68f49.rdx |  Bin 0 -> 175 bytes
|  .../iris_tanglegram_ordered.png                   |  Bin 0 -> 18166 bytes
|  ...2013-09-05_Boston-useR_04_tree_inference.Rpres |   80 +
|  .../2013-09-05_Boston-useR_04_tree_inference.md   |   62 +
|  46 files changed, 3471 insertions(+), 121 deletions(-)

* 2013-08-30(Tal Galili)  untangle_step_rotate_2side added k_seq parameter. |b3aab6a| 
|  R/untangle.r                      | 13 ++++++++-----
|  man/untangle_step_rotate_2side.Rd |  7 ++++++-
|  2 files changed, 14 insertions(+), 6 deletions(-)

* 2013-08-30(Tal Galili) tanglegram now has "sub" and "cex_sub" parameters. |eecbd30| 
|  NEWS              | 7 +++++++
|  R/tanglegram.r    | 7 ++++++-
|  man/tanglegram.Rd | 6 +++++-
|  3 files changed, 18 insertions(+), 2 deletions(-)

* 2013-08-30(Tal Galili) Seperated 2013-09-05_Boston-useR.Rpres into two files (since RStudio is not able to handle them) |73d9714| 
|  NAMESPACE                                         |   90 +-
|  NEWS                                              |    2 +
|  R/tanglegram.r                                    |    2 +-
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    3 +-
|  .../first_tanglegram.png                          |  Bin 39575 -> 0 bytes
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|  .../2013-09-05_Boston-useR.R                      |  459 -----
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|  .../2013-09-05_Boston-useR.html                   | 1803 -------------------
|  .../2013-09-05_Boston-useR.md                     | 1161 ------------
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|  .../2013-09-05_Boston-useR_01_intro.R             |  192 ++
|  .../2013-09-05_Boston-useR_01_intro.Rpres         |  448 +++++
|  .../2013-09-05_Boston-useR_01_intro.html          | 1471 +++++++++++++++
|  .../2013-09-05_Boston-useR_01_intro.md            |  659 +++++++
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|  .../2013-09-05_Boston-useR_02_dendextend.R        |  378 ++++
|  .../2013-09-05_Boston-useR_02_dendextend.Rpres    |  671 +++++++
|  .../2013-09-05_Boston-useR_02_dendextend.md       |  853 +++++++++
|  man/leaf_Colors.Rd                                |    2 +-
|  vignettes/dendextend-tutorial.log                 |    2 +-
|  vignettes/dendextend-tutorial.pdf                 |   13 +-
|  vignettes/dendextend-tutorial.tex                 |    4 +-
|  96 files changed, 4733 insertions(+), 4344 deletions(-)

* 2013-08-29(Tal Galili) untangle_random_search - made sure the function will return the original trees if no better tree was found. |1d6d9fb| 
|  NEWS         | 2 ++
|  R/untangle.r | 2 ++
|  2 files changed, 4 insertions(+)

* 2013-08-29(Tal Galili) tanglegram now returns an invisible list with the two dendrograms (after they have been modified within the function). |d3b0f07| 
|  NEWS              | 1 +
|  R/tanglegram.r    | 5 +++--
|  man/tanglegram.Rd | 3 ++-
|  3 files changed, 6 insertions(+), 3 deletions(-)

* 2013-08-29(Tal Galili) Added "warn" parameter to: assign_values_to_leaves_nodePar, And set it to FALSE when used inside "tanglegram". |5e1abf1| 
|  NEWS                                   |  1 +
|  R/attr_access.r                        |  9 +++++++--
|  R/tanglegram.r                         | 12 ++++++------
|  man/assign_values_to_leaves_nodePar.Rd |  7 ++++++-
|  4 files changed, 20 insertions(+), 9 deletions(-)

* 2013-08-29(Tal Galili) color_labels - added a "warn" parameter. And also set the default (in case no k/h is supplied) - to just color all of the labels. |2fc659e| 
|  NEWS                |  7 +++++++
|  R/color_branches.r  | 16 ++++++++++++----
|  man/color_labels.Rd |  7 ++++++-
|  man/tanglegram.Rd   |  8 ++++++++
|  4 files changed, 33 insertions(+), 5 deletions(-)

* 2013-08-29(Tal Galili) Version bump to 0.11.0 |10d8cc3| 
|  DESCRIPTION | 14 ++++++++------
|  NEWS        | 12 ++++++++++++
|  2 files changed, 20 insertions(+), 6 deletions(-)

* 2013-08-29(Tal Galili) tangelgram - added cex_main parameter. |79ab582| 
|  R/tanglegram.r | 11 ++++++++++-
|  1 file changed, 10 insertions(+), 1 deletion(-)

* 2013-08-26(Tal Galili) Adding links to the documents, and a better "install" code sequence. |2c9b5b4| 
|  README.md | 10 ++++++++--
|  1 file changed, 8 insertions(+), 2 deletions(-)

* 2013-08-26(Tal Galili) Added auto purl for extracting the R code. |d86616c| 
|  .../2013-09-05_Boston-useR.R                      | 459 ++++++++++++++++++++
|  .../2013-09-05_Boston-useR.Rpres                  |   5 +-
|  2 files changed, 462 insertions(+), 2 deletions(-)

* 2013-08-26(Tal Galili) Boston-useR presentation |d1f14cf| 
|  inst/doc/2013-09-05_Boston-useR/.gitignore        |    1 +
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|  .../2013-09-05_Boston-useR.Rpres                  |  863 +++++++++
|  .../2013-09-05_Boston-useR.html                   | 1803 +++++++++++++++++++
|  .../2013-09-05_Boston-useR.md                     | 1161 ++++++++++++
|  48 files changed, 3828 insertions(+)

* 2013-08-24(Tal Galili) vignette - minor fixes |a286c6e| 
|  vignettes/dendextend-tutorial.bib        |   11 -
|  vignettes/dendextend-tutorial.blg        |    6 +-
|  vignettes/dendextend-tutorial.log        |  116 +-
|  vignettes/dendextend-tutorial.pdf        | 2559 ++++++++++++++--------------
|  vignettes/dendextend-tutorial.rnw        |    2 +-
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|  vignettes/dendextend-tutorial.tex        |    6 +-
|  7 files changed, 1316 insertions(+), 1384 deletions(-)

* 2013-08-22(Tal Galili) Updated the list of contributors to the package. |325c8df| 
|  DESCRIPTION | 7 ++++++-
|  1 file changed, 6 insertions(+), 1 deletion(-)

* 2013-08-21(Tal Galili) VIGNETTES: Added FM-index and Bk plot sections. |fba17c3| 
|  NEWS                                              |    2 +-
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|  vignettes/dendextend-tutorial-concordance.tex     |    6 +-
|  vignettes/dendextend-tutorial.log                 |  270 +-
|  vignettes/dendextend-tutorial.pdf                 | 4212 ++++++++++++-------
|  vignettes/dendextend-tutorial.rnw                 |  232 +-
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|  vignettes/dendextend-tutorial.tex                 |  322 +-
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|  vignettes/figure/FM_permutation_example_1.pdf     |  Bin 0 -> 10674 bytes
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|  41 files changed, 3391 insertions(+), 1653 deletions(-)

* 2013-08-21(Tal Galili) New tests for Bk methods and some minor doc changes. |35df06c| 
|  NEWS                        |  4 ++++
|  R/bk_method.r               |  5 +++-
|  inst/tests/test-bk_method.r | 56 +++++++++++++++++++++++++++++++++++++++++++
|  man/FM_index_permutation.Rd |  1 +
|  4 files changed, 65 insertions(+), 1 deletion(-)

* 2013-08-20(Tal Galili) Version bump - 0.10.0 |0079a2c| 
|  DESCRIPTION | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-08-20(Tal Galili) Vignette - cut_lower_fun PDF and extra files are updated. |c08cec1| 
|  ...wer_fun_11e6d15e4d39a2eca09990d42c1235c0.RData |  Bin 0 -> 3255 bytes
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|  vignettes/dendextend-tutorial-concordance.tex     |    4 +-
|  vignettes/dendextend-tutorial.log                 |   62 +-
|  vignettes/dendextend-tutorial.pdf                 | 1653 +++++++++----------
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 223843 -> 223345 bytes
|  vignettes/dendextend-tutorial.tex                 |   70 +-
|  8 files changed, 880 insertions(+), 909 deletions(-)

* 2013-08-20(Tal Galili) cut_lower_fun function added - it wraps the "cut" function, and is built to be masked by the function in dendextendRcpp in order to gain 4-14 speed gain. |987af61| 
|  DESCRIPTION                       |  1 +
|  NAMESPACE                         |  1 +
|  NEWS                              | 13 ++++++
|  R/cut_lower_fun.r                 | 86 +++++++++++++++++++++++++++++++++++++
|  R/cutree.dendrogram.r             |  3 +-
|  R/zzz.r                           | 15 +++++--
|  inst/tests/test-cut_lower_fun.r   | 78 +++++++++++++++++++++++++++++++++
|  man/cut_lower_fun.Rd              | 59 +++++++++++++++++++++++++
|  vignettes/dendextend-tutorial.rnw | 12 ++++++
|  9 files changed, 263 insertions(+), 5 deletions(-)

* 2013-08-20(Tal Galili) cor_bakers_gamma.hclust function added. |9bd41bf| 
|  NAMESPACE             |  1 +
|  NEWS                  | 10 ++++++++++
|  R/cor_bakers_gamma.r  | 16 +++++++++++++++-
|  R/cutree.dendrogram.r |  2 ++
|  man/cutree-methods.Rd |  4 ++--
|  5 files changed, 30 insertions(+), 3 deletions(-)

* 2013-08-20(Tal Galili) Vignettes - some Bk thoery, and Rcpp section. |c534cc0| 
|  NEWS                                              |    3 +
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|  vignettes/cache/__packages                        |    4 +
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|  vignettes/dendextend-tutorial-concordance.tex     |    6 +-
|  vignettes/dendextend-tutorial.bib                 |  110 +-
|  vignettes/dendextend-tutorial.blg                 |    2 +-
|  vignettes/dendextend-tutorial.log                 |  129 +-
|  vignettes/dendextend-tutorial.pdf                 | 3607 ++++++++++---------
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|  vignettes/dendextend-tutorial.tex                 |  153 +-
|  25 files changed, 2376 insertions(+), 1707 deletions(-)

* 2013-08-19(Tal Galili) Create hidden backups of the R functions which are replaced by the Rcpp function so that we will be able to benchmark them. |a8b17c0| 
|  DESCRIPTION | 4 ++--
|  R/zzz.r     | 8 ++++++++
|  2 files changed, 10 insertions(+), 2 deletions(-)

* 2013-08-19(Tal Galili) UPDATED FUNCTIONS:  * Bk_plot - now adds dots for the asymptotic lines in case of NA's    * Bk - now calculates cutree once for all relevant k's - and only then goes forth with FM_index. |0d4d3dd| 
|  NEWS              | 20 +++++++++++--
|  R/bk_method.r     | 85 +++++++++++++++++++++++++++++++++++++++++++++--------
|  man/Bk.Rd         | 15 ++++++++--
|  man/Bk_plot.Rd    |  1 +
|  man/FM_index_R.Rd |  5 ++++
|  5 files changed, 108 insertions(+), 18 deletions(-)

* 2013-08-19(Tal Galili) Rename the package RcppDend-> dendextendRcpp |8903084| 
|  DESCRIPTION                         |  2 +-
|  NEWS                                |  3 ++-
|  R/color_branches.r                  |  2 +-
|  R/zzz.r                             | 22 +++++++++++-----------
|  inst/tests/test-cutree.dendrogram.r |  2 +-
|  tests/test-all.r                    |  2 +-
|  6 files changed, 17 insertions(+), 16 deletions(-)

* 2013-08-19(Tal Galili) note on labels.dendrogram. |740aaf7| 
|  R/zzz.r | 12 ++++++++++++
|  1 file changed, 12 insertions(+)

* 2013-08-19(Tal Galili) color_labels - added "labels" parameter for selective coloring of labels by name. |730cf25| 
|  NEWS                |  1 +
|  R/color_branches.r  | 20 +++++++++++++++++---
|  man/color_labels.Rd |  9 ++++++++-
|  3 files changed, 26 insertions(+), 4 deletions(-)

* 2013-08-19(Tal Galili) Make RcppDend loads and override core functions in dendextend in order to make it MUCH faster :) |ffb7187| 
|  R/zzz.r          | 70 ++++++++++++++++++++++++++++++++++++++++++++----------
|  tests/test-all.r |  1 +
|  2 files changed, 59 insertions(+), 12 deletions(-)

* 2013-08-19(Tal Galili) add more explenation in the tests for how labels.dendrogram acts when there are missing labels. (in stats vs RcppDend package) |979beed| 
|  inst/tests/test-cutree.dendrogram.r | 9 ++++++++-
|  1 file changed, 8 insertions(+), 1 deletion(-)

* 2013-08-19(Tal Galili) T -> TRUE |fc3ea18| 
|  R/trim.r | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-08-19(Tal Galili) being explisit about "sort" in get_branches_heights |f532205| 
|  R/cutree.dendrogram.r | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-08-18(Tal Galili) Bk_plot function added! |814a668| 
|  NAMESPACE             |   1 +
|  NEWS                  |   3 +-
|  R/bk_method.r         | 382 ++++++++++++++++++++----------------------------
|  R/cutree.dendrogram.r |   2 +-
|  R/sample.dendrogram.r |   2 +-
|  man/Bk.Rd             |  83 -----------
|  man/Bk_plot.Rd        | 180 +++++++++++++++++++++++
|  man/cutree-methods.Rd |   4 +-
|  8 files changed, 343 insertions(+), 314 deletions(-)

* 2013-08-18(Tal Galili) Bk_permutations function added. |d5a24cd| 
|  NAMESPACE              |   1 +
|  NEWS                   |   1 +
|  R/bk_method.r          | 232 +++++++++++++++++++++++++++++++++++++++++++++++
|  man/Bk.Rd              |  83 +++++++++++++++++
|  man/Bk_permutations.Rd |  93 +++++++++++++++++++
|  5 files changed, 410 insertions(+)

* 2013-08-18(Tal Galili) Bk Function added! |bf73478| 
|  NAMESPACE     |   1 +
|  NEWS          |   1 +
|  R/bk_method.r | 207 +++++++++++++++++++++++++++++---------------------------
|  man/Bk.Rd     |  93 +++++++++++++++++++++++++
|  4 files changed, 202 insertions(+), 100 deletions(-)

* 2013-08-18(Tal Galili) Exaplin what happens to FM distribution for different values of k. |feb6432| 
|  R/bk_method.r               | 7 ++++++-
|  man/FM_index_permutation.Rd | 7 ++++++-
|  2 files changed, 12 insertions(+), 2 deletions(-)

* 2013-08-18(Tal Galili) FM_index_permutation function added |4cc208d| 
|  DESCRIPTION                 |   6 ++-
|  NAMESPACE                   |   1 +
|  NEWS                        |  25 ++++++++++-
|  R/bk_method.r               | 102 ++++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-bk_method.r |  34 ++++++++++++++
|  man/FM_index_permutation.Rd |  85 +++++++++++++++++++++++++++++++++++
|  6 files changed, 250 insertions(+), 3 deletions(-)

* 2013-08-18(Tal Galili) tests for FM_index_R and FM_index |ee50173| 
|  inst/tests/test-bk_method.r | 112 ++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 112 insertions(+)

* 2013-08-18(Tal Galili) FM_index_R and FM_index functions added. |e7a250b| 
|  NAMESPACE               |   2 +
|  R/bk_method.r           | 244 +++++++++++++++++++++++++++++++++++++++-------
|  man/FM_index.Rd         | 113 +++++++++++++++++++++
|  man/FM_index_R.Rd       |  94 ++++++++++++++++++
|  man/FM_index_profdpm.Rd |  13 ++-
|  5 files changed, 427 insertions(+), 39 deletions(-)

* 2013-08-18(Tal Galili) sort_2_clusters_vectors function added. |e4913b5| 
|  NAMESPACE                      |  1 +
|  R/bk_method.r                  | 99 +++++++++++++++++++++++++++++++---------
|  inst/tests/test-bk_method.r    | 52 +++++++++++++++------
|  man/sort_2_clusters_vectors.Rd | 59 ++++++++++++++++++++++++
|  4 files changed, 177 insertions(+), 34 deletions(-)

* 2013-08-18(Tal Galili) export lowest_common_branch. |f2dc78b| 
|  NAMESPACE            | 1 +
|  R/cor_bakers_gamma.r | 1 +
|  2 files changed, 2 insertions(+)

* 2013-08-18(Tal Galili) FM_index_profdpm function added. |35cf12d| 
|  NAMESPACE                   |   1 +
|  R/bk_method.r               | 338 +++++++++++++++++++++++++++++++++++-------
|  inst/tests/test-bk_method.r |  58 ++++++++
|  man/FM_index_profdpm.Rd     |  96 ++++++++++++
|  man/color_labels.Rd         |   3 +-
|  5 files changed, 437 insertions(+), 59 deletions(-)

* 2013-08-18(Tal Galili) Change variable names from "." to "_" |858167f| 
|  R/bk_method.r | 98 ++++++++++++++++++++++++++++++++++-----------------------
|  1 file changed, 59 insertions(+), 39 deletions(-)

* 2013-08-17(Tal Galili) Added a commented-out section which could (in the future) be the basis of an Rcpp cutree (actually cutree_1h.dendrogram) function! |cde09ff| 
|  R/cutree.dendrogram.r | 46 ++++++++++++++++++++++++++++++++++++++++++++--
|  1 file changed, 44 insertions(+), 2 deletions(-)

* 2013-08-16(Tal Galili) color_labels_by_labels - code added (now need to document, and add to color_labels). |88c8685| 
|  R/color_branches.r | 64 ++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 64 insertions(+)

* 2013-08-16(Tal Galili) color_labels - removed unused 'groupLabels' parameter. |4680820| 
|  R/color_branches.r | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-08-16(Tal Galili) copyright notice. |02c1f28| 
|  R/bk_method.r | 19 +++++++++++++++++++
|  1 file changed, 19 insertions(+)

* 2013-08-16(Tal Galili) Bk-method.r file added |5db46e6| 
|  R/bk_method.r | 260 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 260 insertions(+)

* 2013-08-15(Tal Galili) Added some ref for tanglegram problem |f5fbc66| 
|  vignettes/dendextend-tutorial.bib | 12 +++++-------
|  1 file changed, 5 insertions(+), 7 deletions(-)

* 2013-08-14(Tal Galili) Vignettes - Cophenetic correlation |8d83bee| 
|  NEWS                                              |    1 +
|  ...ample_1_49438132f802c72c76330a0c6277e5c9.RData |  Bin 0 -> 3844 bytes
|  ...example_1_49438132f802c72c76330a0c6277e5c9.rdb |  Bin 0 -> 1636 bytes
|  ...example_1_49438132f802c72c76330a0c6277e5c9.rdx |  Bin 0 -> 174 bytes
|  ...ation_2_f52d3297030e8ccb9446f2dc58662c66.RData |  Bin 0 -> 3525 bytes
|  ...ulation_2_f52d3297030e8ccb9446f2dc58662c66.rdb |  Bin 0 -> 9947 bytes
|  ...ulation_2_f52d3297030e8ccb9446f2dc58662c66.rdx |  Bin 0 -> 264 bytes
|  ...on_CI_3_3243f384d2df989a75438b63f85f44f5.RData |  Bin 0 -> 3884 bytes
|  ...tion_CI_3_3243f384d2df989a75438b63f85f44f5.rdb |  Bin 0 -> 9380 bytes
|  ...tion_CI_3_3243f384d2df989a75438b63f85f44f5.rdx |  Bin 0 -> 308 bytes
|  ...on_CI_4_dd6497988cbed58310cbeaaabb6163b2.RData |  Bin 0 -> 3904 bytes
|  ...tion_CI_4_dd6497988cbed58310cbeaaabb6163b2.rdb |  Bin 0 -> 8389 bytes
|  ...tion_CI_4_dd6497988cbed58310cbeaaabb6163b2.rdx |  Bin 0 -> 308 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    3 +-
|  vignettes/dendextend-tutorial.bib                 |   16 +
|  vignettes/dendextend-tutorial.blg                 |    6 +-
|  vignettes/dendextend-tutorial.log                 |  152 +-
|  vignettes/dendextend-tutorial.pdf                 | 2769 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |  213 ++
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 182727 -> 203406 bytes
|  vignettes/dendextend-tutorial.tex                 |  299 ++
|  vignettes/figure/cor_cophenetic_simulation_2.pdf  |  Bin 0 -> 7663 bytes
|  .../figure/cor_cophenetic_simulation_CI_3.pdf     |  Bin 0 -> 7152 bytes
|  .../figure/cor_cophenetic_simulation_CI_4.pdf     |  Bin 0 -> 7524 bytes
|  24 files changed, 2315 insertions(+), 1144 deletions(-)

* 2013-08-14(Tal Galili) cor_cophenetic function added (also sort_dist_mat) |cecaa2a| 
|  DESCRIPTION             |   1 +
|  NAMESPACE               |   3 +
|  NEWS                    |   6 +-
|  R/cor_bakers_gamma.r    |   4 +-
|  R/cor_cophenetic.r      | 187 ++++++++++++++++++++++++++++++++++++++++++++++
|  man/cor_bakers_gamma.Rd |   7 +-
|  man/cor_cophenetic.Rd   | 112 +++++++++++++++++++++++++++
|  man/sort_dist_mat.Rd    |  28 +++++++
|  8 files changed, 341 insertions(+), 7 deletions(-)

* 2013-08-14(Tal Galili) Adding copyright notice |87bce54| 
|  R/sample.dendrogram.r | 20 ++++++++++++++++++++
|  1 file changed, 20 insertions(+)

* 2013-08-14(Tal Galili) VIGNETTES: Added a bootstrap and permutation examples for inference on Baker's Gamma. |08fb0c3| 
|  NEWS                                              |    1 +
|  R/sample.dendrogram.r                             |    2 +-
|  ...ation_1_80285bbfbf4a8a4612444b6a03b5bfa2.RData |  Bin 3496 -> 0 bytes
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|  ...ation_1_dd930ca5c4802d808d8e1ff37bc0edef.RData |  Bin 0 -> 3502 bytes
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|  ...ulation_1_dd930ca5c4802d808d8e1ff37bc0edef.rdx |  Bin 0 -> 257 bytes
|  ...ation_2_a386542ebf46e61430ae6d546755ef8a.RData |  Bin 0 -> 3513 bytes
|  ...ulation_2_a386542ebf46e61430ae6d546755ef8a.rdb |  Bin 0 -> 8768 bytes
|  ...ulation_2_a386542ebf46e61430ae6d546755ef8a.rdx |  Bin 0 -> 259 bytes
|  ...ation_2_faf7c50fae3d6d1cf2dedf6718056d8a.RData |  Bin 3503 -> 0 bytes
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|  ...ation_3_a2067a06e2dadc01a424503feeb67ad9.RData |  Bin 0 -> 3527 bytes
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|  ...ulation_3_a2067a06e2dadc01a424503feeb67ad9.rdx |  Bin 0 -> 269 bytes
|  ...on_CI_4_a4452373b91f83c32fa8ad187e0fa475.RData |  Bin 0 -> 3914 bytes
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|  ...tion_CI_4_a4452373b91f83c32fa8ad187e0fa475.rdx |  Bin 0 -> 310 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    4 +-
|  vignettes/dendextend-tutorial.log                 |  110 +-
|  vignettes/dendextend-tutorial.pdf                 | 1667 ++++++++++++-------
|  vignettes/dendextend-tutorial.rnw                 |   71 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 175961 -> 182727 bytes
|  vignettes/dendextend-tutorial.tex                 |  107 +-
|  .../figure/cor_bakers_gamma_simulation_1.pdf      |  Bin 7148 -> 7148 bytes
|  .../figure/cor_bakers_gamma_simulation_2.pdf      |  Bin 7609 -> 7609 bytes
|  .../figure/cor_bakers_gamma_simulation_3.pdf      |  Bin 7596 -> 7596 bytes
|  .../figure/cor_bakers_gamma_simulation_CI_41.pdf  |  Bin 0 -> 5047 bytes
|  .../figure/cor_bakers_gamma_simulation_CI_42.pdf  |  Bin 0 -> 4848 bytes
|  .../figure/cor_bakers_gamma_simulation_CI_43.pdf  |  Bin 0 -> 7496 bytes
|  35 files changed, 1307 insertions(+), 655 deletions(-)

* 2013-08-14(Tal Galili) Added a "warn" parameter to cor_bakers_gamma |f6f62b2| 
|  R/cor_bakers_gamma.r    | 8 +++++---
|  man/cor_bakers_gamma.Rd | 4 ++++
|  2 files changed, 9 insertions(+), 3 deletions(-)

* 2013-08-14(Tal Galili) sample.dendrogram function added - it allows for permutation and bootstrap tests for comparing two trees. |e02436f| 
|  NAMESPACE                |   1 +
|  NEWS                     |   7 +-
|  R/sample.dendrogram.r    | 229 +++++++++++++++++++++++++++++++++++++++++++--
|  man/duplicate_leaf.Rd    |  53 +++++++++++
|  man/sample.dendrogram.Rd |  77 +++++++++++++++
|  5 files changed, 355 insertions(+), 12 deletions(-)

* 2013-08-14(Tal Galili) Fix cor_bakers_gamma to work in case if trees with only leaves. |e264773| 
|  R/cor_bakers_gamma.r | 6 +++++-
|  1 file changed, 5 insertions(+), 1 deletion(-)

* 2013-08-14(Tal Galili) nleaves - fix doc. |8735d55| 
|  R/nleaves.r    | 2 +-
|  man/nleaves.Rd | 4 ++--
|  2 files changed, 3 insertions(+), 3 deletions(-)

* 2013-08-14(Tal Galili) More protection for cutree by forcing nleaves to use method order. |aa129cd| 
|  R/cutree.dendrogram.r | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2013-08-14(Tal Galili) fix_members_attr.dendrogram - fixed a bug introduced by the new "members" method in nleaves. (test added) |6ba6295| 
|  DESCRIPTION                   |  2 +-
|  NEWS                          |  2 ++
|  R/attr_access.r               |  2 +-
|  inst/tests/test-attr_access.r | 15 +++++++++++++++
|  4 files changed, 19 insertions(+), 2 deletions(-)

* 2013-08-14(Tal Galili) sample.dendrogram function added. Only works for replace = FALSE |c213ffc| 
|  DESCRIPTION           |  5 +++--
|  NAMESPACE             |  1 +
|  NEWS                  |  5 +++++
|  R/sample.dendrogram.r | 38 ++++++++++++++++++++++++++++++++++++++
|  4 files changed, 47 insertions(+), 2 deletions(-)

* 2013-08-14(Tal Galili) rank_order.dendrogram function added. |39a5237| 
|  NAMESPACE                    |  2 +
|  R/attr_access.r              | 95 ++++++++++++++++++++++++++++++++++++++++++
|  R/trim.r                     | 49 ----------------------
|  man/rank_order.dendrogram.Rd | 33 +++++++++++++++
|  4 files changed, 130 insertions(+), 49 deletions(-)

* 2013-08-14(Tal Galili) added ref to Baker 1974 |33390db| 
|  man/cor_bakers_gamma.Rd | 6 ++++++
|  1 file changed, 6 insertions(+)

* 2013-08-14(Tal Galili) Vignettes: adding a third simulation |bfef209| 
|  ...ation_3_1728f5856aa0b70528c40164da84c605.RData |  Bin 0 -> 3522 bytes
|  ...ulation_3_1728f5856aa0b70528c40164da84c605.rdb |  Bin 0 -> 9119 bytes
|  ...ulation_3_1728f5856aa0b70528c40164da84c605.rdx |  Bin 0 -> 268 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    4 +-
|  vignettes/dendextend-tutorial.log                 |   67 +-
|  vignettes/dendextend-tutorial.pdf                 | 1024 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |   34 +
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 172701 -> 175961 bytes
|  vignettes/dendextend-tutorial.tex                 |   58 +-
|  .../figure/cor_bakers_gamma_simulation_3.pdf      |  Bin 0 -> 7596 bytes
|  10 files changed, 730 insertions(+), 457 deletions(-)

* 2013-08-14(Tal Galili) VIGNETTES - Added the Baker's Gamma Index section. |9dd5cdd| 
|  NEWS                                              |    3 +
|  ...ample_1_a6f852561e8ce9d553b9d2b27b424b22.RData |  Bin 0 -> 3823 bytes
|  ...example_1_a6f852561e8ce9d553b9d2b27b424b22.rdb |  Bin 0 -> 2409 bytes
|  ...example_1_a6f852561e8ce9d553b9d2b27b424b22.rdx |  Bin 0 -> 204 bytes
|  ...ation_1_80285bbfbf4a8a4612444b6a03b5bfa2.RData |  Bin 0 -> 3496 bytes
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|  ...ation_2_faf7c50fae3d6d1cf2dedf6718056d8a.RData |  Bin 0 -> 3503 bytes
|  ...ulation_2_faf7c50fae3d6d1cf2dedf6718056d8a.rdb |  Bin 0 -> 8761 bytes
|  ...ulation_2_faf7c50fae3d6d1cf2dedf6718056d8a.rdx |  Bin 0 -> 259 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    3 +-
|  vignettes/dendextend-tutorial.log                 |  175 +-
|  vignettes/dendextend-tutorial.pdf                 | 3073 ++++++++++++-------
|  vignettes/dendextend-tutorial.rnw                 |  153 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 154731 -> 172701 bytes
|  vignettes/dendextend-tutorial.tex                 |  283 +-
|  vignettes/figure/cor_bakers_gamma_example_11.pdf  |  Bin 0 -> 5053 bytes
|  vignettes/figure/cor_bakers_gamma_example_12.pdf  |  Bin 0 -> 5082 bytes
|  vignettes/figure/cor_bakers_gamma_example_13.pdf  |  Bin 0 -> 5053 bytes
|  vignettes/figure/cor_bakers_gamma_example_14.pdf  |  Bin 0 -> 5056 bytes
|  .../figure/cor_bakers_gamma_simulation_1.pdf      |  Bin 0 -> 7148 bytes
|  .../figure/cor_bakers_gamma_simulation_2.pdf      |  Bin 0 -> 7609 bytes
|  22 files changed, 2500 insertions(+), 1190 deletions(-)

* 2013-08-14(Tal Galili) Adding reference to Baker's paper from 1974. |5a0209d| 
|  R/cor_bakers_gamma.r              |  7 +++++++
|  vignettes/dendextend-tutorial.bib | 36 ++++++++++++++++++++++++++++++++++++
|  2 files changed, 43 insertions(+)

* 2013-08-14(Tal Galili) cor_bakers_gamma function added. |8857952| 
|  DESCRIPTION                        |   2 +-
|  NAMESPACE                          |   3 +
|  NEWS                               |   9 ++
|  R/cor_bakers_gamma.r               | 210 +++++++++++++++++++++++++++++++++++
|  inst/tests/test-cor_bakers_gamma.r |  48 ++++++++
|  man/bakers_gamma_for_2_k_matrix.Rd |  31 ++++++
|  man/cor_bakers_gamma.Rd            |  99 +++++++++++++++++
|  man/lowest_common_branch.Rd        |  35 ++++++
|  8 files changed, 436 insertions(+), 1 deletion(-)

* 2013-08-14(Tal Galili) Added {} |da980a9| 
|  R/trim.r | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-08-14(Tal Galili) tanglegram - added the match_order_by_labels parameter. |646329a| 
|  R/tanglegram.r    | 9 ++++++++-
|  man/tanglegram.Rd | 7 +++++++
|  2 files changed, 15 insertions(+), 1 deletion(-)

* 2013-08-14(Tal Galili) Added test for cutree's use_labels_not_values parameter. |733f127| 
|  inst/tests/test-cutree.dendrogram.r | 11 +++++++++++
|  1 file changed, 11 insertions(+)

* 2013-08-14(Tal Galili) tanglegram - added the hang parameter. |82b3bd2| 
|  NEWS                                              |    1 +
|  R/tanglegram.r                                    |   11 +-
|  man/tanglegram.Rd                                 |    6 +-
|  ...example_802a64d3a4c0dd3e9bb0e2a4dee353da.RData |  Bin 0 -> 3699 bytes
|  ...e_example_802a64d3a4c0dd3e9bb0e2a4dee353da.rdb |  Bin 0 -> 6426 bytes
|  ...e_example_802a64d3a4c0dd3e9bb0e2a4dee353da.rdx |  Bin 0 -> 205 bytes
|  ...example_bb4ceb1d930b3bb07d6747839ba48794.RData |  Bin 3657 -> 0 bytes
|  ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdb |  Bin 6426 -> 0 bytes
|  ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdx |  Bin 205 -> 0 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    2 +-
|  vignettes/dendextend-tutorial.log                 |   59 +-
|  vignettes/dendextend-tutorial.pdf                 | 1103 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |   11 +
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 153993 -> 154731 bytes
|  vignettes/dendextend-tutorial.tex                 |   14 +
|  .../untangle_step_rotate_2side_example1.pdf       |  Bin 6158 -> 6158 bytes
|  .../untangle_step_rotate_2side_example2.pdf       |  Bin 6137 -> 6137 bytes
|  .../untangle_step_rotate_2side_example3.pdf       |  Bin 6154 -> 6154 bytes
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|  .../untangle_step_rotate_2side_example5.pdf       |  Bin 5714 -> 5714 bytes
|  .../untangle_step_rotate_2side_example6.pdf       |  Bin 0 -> 6163 bytes
|  21 files changed, 694 insertions(+), 513 deletions(-)

* 2013-08-14(Tal Galili) Version bump 0.7.3 |2bb5655| 
|  DESCRIPTION                                       |    4 +-
|  NEWS                                              |   41 +-
|  ...hunk-40_9f83c05b11ed630ecb319c8a28110b35.RData |  Bin 3466 -> 0 bytes
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|  ...-chunk-40_b48b442cc366777991b02835121a00b7.rdx |  Bin 0 -> 205 bytes
|  ...example_bb4ceb1d930b3bb07d6747839ba48794.RData |  Bin 0 -> 3657 bytes
|  ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdb |  Bin 0 -> 6426 bytes
|  ...e_example_bb4ceb1d930b3bb07d6747839ba48794.rdx |  Bin 0 -> 205 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    2 +-
|  vignettes/dendextend-tutorial.log                 |  259 +--
|  vignettes/dendextend-tutorial.pdf                 | 2039 +++++++------------
|  vignettes/dendextend-tutorial.rnw                 |   11 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 153579 -> 153993 bytes
|  vignettes/dendextend-tutorial.tex                 |   36 +-
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|  .../untangle_step_rotate_2side_example1.pdf       |  Bin 0 -> 6158 bytes
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|  .../untangle_step_rotate_2side_example5.pdf       |  Bin 0 -> 5714 bytes
|  32 files changed, 946 insertions(+), 1446 deletions(-)

* 2013-08-14(Tal Galili) tanglegram - fixed the right tree's labels position relative to the leaves tips. (they were too far away because of a combination of text_adj with dLeaf) |5c0f75e| 
|  R/tanglegram.r               | 15 +++++++++++----
|  man/plot_horiz.dendrogram.Rd |  6 ++----
|  man/tanglegram.Rd            |  4 ++++
|  3 files changed, 17 insertions(+), 8 deletions(-)

* 2013-08-14(Tal Galili) rank_branches function added. |f56a9d8| 
|  NAMESPACE                     |   2 +
|  R/attr_access.r               | 104 ++++++++++++++++++++++++++++++++++++++--
|  R/tanglegram.r                |  12 +++--
|  inst/tests/test-attr_access.r |  11 +++++
|  man/get_childrens_heights.Rd  |  27 +++++++++++
|  man/rank_branches.Rd          |  48 +++++++++++++++++++
|  man/tanglegram.Rd             |   8 +++-
|  7 files changed, 204 insertions(+), 8 deletions(-)

* 2013-08-14(Tal Galili) sort_levels_values now deals with vectors haing NA values (just returning the vector as is) |62631fa| 
|  R/cutree.dendrogram.r         | 17 ++++++++++++-----
|  man/get_heights.dendrogram.Rd | 26 --------------------------
|  man/sort_levels_values.Rd     | 13 ++++++++-----
|  3 files changed, 20 insertions(+), 36 deletions(-)

* 2013-08-13(Tal Galili) Version bump to 0.7.2 |7d8ae64| 
|  DESCRIPTION |  5 +++--
|  NEWS        | 17 ++++++++++++++++-
|  2 files changed, 19 insertions(+), 3 deletions(-)

* 2013-08-13(Tal Galili) tanglegram - labels are now alligned to the leaves tips in the right dendrogram. |e153fd2| 
|  R/tanglegram.r               | 384 +++++++++++++++++++++++++++++++++++------
|  man/cutree-methods.Rd        |  10 +-
|  man/plot_horiz.dendrogram.Rd |  53 ++++--
|  man/tanglegram.Rd            |  27 ++-
|  4 files changed, 406 insertions(+), 68 deletions(-)

* 2013-08-13(Tal Galili) Set sort_cluster_numbers = TRUE for cutree, in order to make it compatible with stats:::cutree |e7a0dcb| 
|  NEWS                                |  3 +-
|  R/cutree.dendrogram.r               | 60 +++++++++++++++++++++++++++++++----
|  inst/tests/test-cutree.dendrogram.r | 13 ++++++--
|  3 files changed, 66 insertions(+), 10 deletions(-)

* 2013-08-13(Tal Galili) Fix untangle_step_rotate_1side to work with non-missing dend_heights_per_k |3ed6210| 
|  NEWS         | 8 ++++++++
|  R/untangle.r | 8 +++-----
|  2 files changed, 11 insertions(+), 5 deletions(-)

* 2013-08-13(Tal Galili) Fix some names in untangle_step_rotate_2side test |889c0e8| 
|  inst/tests/test-untangle.r | 9 ++++++---
|  1 file changed, 6 insertions(+), 3 deletions(-)

* 2013-08-13(Tal Galili) Make a quicker test for untangle_step_rotate_2side |0d4b138| 
|  inst/tests/test-untangle.r | 69 ++++++++++++++++++++++++++++----------------
|  1 file changed, 44 insertions(+), 25 deletions(-)

* 2013-08-12(Tal Galili) Set print_times=FALSE for tests. |b36c95d| 
|  inst/tests/test-untangle.r | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-08-12(Tal Galili) Version bump to 0.7.1 |3109111| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 2 ++
|  2 files changed, 4 insertions(+), 2 deletions(-)

* 2013-08-12(Tal Galili) Vignettes - untangle_step_rotate_2side |1026419| 
|  vignettes/cache/__packages                        |    1 +
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|  vignettes/dendextend-tutorial-concordance.tex     |    7 +-
|  vignettes/dendextend-tutorial.log                 |  673 ++-
|  vignettes/dendextend-tutorial.pdf                 | 5274 ++++++++++++-------
|  vignettes/dendextend-tutorial.rnw                 |   65 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 133707 -> 153579 bytes
|  vignettes/dendextend-tutorial.tex                 |  357 +-
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|  41 files changed, 4214 insertions(+), 2163 deletions(-)

* 2013-08-12(Tal Galili) untangle_step_rotate_2side - added tests |af6c7bf| 
|  inst/tests/test-untangle.r | 35 ++++++++++++++++++++++++++++++++++-
|  1 file changed, 34 insertions(+), 1 deletion(-)

* 2013-08-12(Tal Galili) Moving old code done (maybe I will document it in the future, and maybe not...) |08ba75f| 
|  R/untangle.r | 169 +++++++++++++++++++++++++++++++--------------------------
|  1 file changed, 92 insertions(+), 77 deletions(-)

* 2013-08-12(Tal Galili) untangle_step_rotate_2side function added. |07e1fb0| 
|  NAMESPACE                         |   1 +
|  NEWS                              |   9 +++
|  R/untangle.r                      | 123 ++++++++++++++++++++++++++++++------
|  man/untangle_step_rotate_1side.Rd |   7 +-
|  man/untangle_step_rotate_2side.Rd |  85 +++++++++++++++++++++++++
|  5 files changed, 203 insertions(+), 22 deletions(-)

* 2013-08-12(Tal Galili) Version bump to 0.7 |ddd2552| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 3 +++
|  2 files changed, 5 insertions(+), 2 deletions(-)

* 2013-08-12(Tal Galili) Vignettes doc for untangaling trees. |e208ba3| 
|  vignettes/dendextend-tutorial.rnw | 103 ++++++++++++++++++++++++++++++++++++
|  1 file changed, 103 insertions(+)

* 2013-08-12(Tal Galili) Added k_seq and dend_heights_per_k to untangle_step_rotate_1side. |581245c| 
|  R/untangle.r                      | 26 ++++++++++++++++++--------
|  man/untangle_step_rotate_1side.Rd | 13 +++++++++++--
|  2 files changed, 29 insertions(+), 10 deletions(-)

* 2013-08-12(Tal Galili) Rename: untangle_forward_rotate_1side -> untangle_step_rotate_1side |43178f5| 
|  NAMESPACE                            |  2 +-
|  R/untangle.r                         | 68 ++++++++++++++++------------------
|  inst/tests/test-untangle.r           |  7 +++-
|  man/untangle_forward_rotate_1side.Rd | 59 -----------------------------
|  man/untangle_step_rotate_1side.Rd    | 65 ++++++++++++++++++++++++++++++++
|  5 files changed, 103 insertions(+), 98 deletions(-)

* 2013-08-11(Tal Galili) untangle_forward_rotate_1side function added! |f721906| 
|  NAMESPACE                            |  1 +
|  NEWS                                 |  1 +
|  R/untangle.r                         | 84 +++++++++++++++++++++++++---------
|  inst/tests/test-untangle.r           | 18 ++++++++
|  man/all_couple_rotations_at_k.Rd     |  2 +-
|  man/untangle_forward_rotate_1side.Rd | 59 ++++++++++++++++++++++++
|  6 files changed, 142 insertions(+), 23 deletions(-)

* 2013-08-11(Tal Galili) There is some problem with match_order_dendrogram_by_old_order - might need to revisit this in the future... |88175b6| 
|  R/entanglement.r               |  2 ++
|  inst/tests/test-entanglement.r | 31 ++++++++++++++++++++++++++++---
|  2 files changed, 30 insertions(+), 3 deletions(-)

* 2013-08-11(Tal Galili) Added shuffle to the namespace. |a85ad68| 
|  NAMESPACE                        |  3 ++
|  R/untangle.r                     | 66 ++++++++++++++++----------------------
|  man/all_couple_rotations_at_k.Rd |  8 +++++
|  man/shuffle.Rd                   |  6 ++++
|  4 files changed, 45 insertions(+), 38 deletions(-)

* 2013-08-11(Tal Galili) all_couple_rotations_at_k function added. |6acc7e7| 
|  NAMESPACE                        |   1 +
|  NEWS                             |   1 +
|  R/untangle.r                     | 105 +++++++++++++++++++++----------------
|  inst/tests/test-attr_access.r    |   2 +-
|  inst/tests/test-untangle.r       |  13 ++++-
|  man/all_couple_rotations_at_k.Rd |  47 +++++++++++++++++
|  6 files changed, 123 insertions(+), 46 deletions(-)

* 2013-08-11(Tal Galili) scaler -> scalar |01b489e| 
|  R/attr_access.r        | 4 ++--
|  man/get_leaves_attr.Rd | 2 +-
|  man/get_nodes_attr.Rd  | 2 +-
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2013-08-11(Tal Galili) donotrun  -> dontrun |2b65ab3| 
|  R/cutree.dendrogram.r           | 2 +-
|  man/heights_per_k.dendrogram.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2013-08-11(Tal Galili) flip_leaves function added |3d9fda5| 
|  NAMESPACE                  |   1 +
|  NEWS                       |   1 +
|  R/untangle.r               | 111 ++++++++++++++++++++++++-------------------
|  inst/tests/test-untangle.r |  19 ++++++--
|  man/flip_leaves.Rd         |  42 ++++++++++++++++
|  5 files changed, 121 insertions(+), 53 deletions(-)

* 2013-08-11(Tal Galili) move some code down the file. |7e840b5| 
|  R/untangle.r | 126 ++++++++++++++++++++++++++++++---------------------------
|  1 file changed, 66 insertions(+), 60 deletions(-)

* 2013-08-11(Tal Galili) untangle_random_search function added - random search for two trees with low entanglement. |4fe24f9| 
|  NAMESPACE                     |   1 +
|  NEWS                          |   2 +-
|  R/untangle.r                  |  92 +++++++++++++++++++++++----
|  man/shuffle.Rd                | 137 +++++++---------------------------------
|  man/untangle_random_search.Rd |  84 ++++++++++++++++++++++++
|  5 files changed, 190 insertions(+), 126 deletions(-)

* 2013-08-11(Tal Galili) shuffle function added. |79ec35e| 
|  NAMESPACE                      |   1 +
|  NEWS                           |   4 ++
|  R/untangle.r                   |  71 +++++++++++++++-----
|  inst/tests/test-entanglement.r |   2 +-
|  inst/tests/test-untangle.r     |  23 +++++++
|  man/shuffle.Rd                 | 137 +++++++++++++++++++++++++++++++++++++++
|  6 files changed, 222 insertions(+), 16 deletions(-)

* 2013-08-11(Tal Galili) rotate - minor code and doc improvements. |270ae47| 
|  NAMESPACE     |  1 -
|  NEWS          |  8 ++++++++
|  R/rotate.r    | 18 ++++++++++--------
|  man/rotate.Rd |  6 ++++--
|  4 files changed, 22 insertions(+), 11 deletions(-)

* 2013-08-11(Tal Galili) Bump version to 0.6 |b483d57| 
|  DESCRIPTION | 2 +-
|  NEWS        | 7 ++++++-
|  2 files changed, 7 insertions(+), 2 deletions(-)

* 2013-08-11(Tal Galili) Vignettes - added tanglegram and entanglement. |4e258d0| 
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|  vignettes/dendextend-tutorial-concordance.tex     |   11 +-
|  vignettes/dendextend-tutorial.log                 |  639 +--
|  vignettes/dendextend-tutorial.pdf                 | 4052 +++++++++++--------
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|  233 files changed, 3207 insertions(+), 2367 deletions(-)

* 2013-08-11(Tal Galili) entanglement - added .Rd example |1cf03a8| 
|  R/entanglement.r    |  3 ++-
|  man/entanglement.Rd | 43 +++++++++++++++++++++++++++++++++++++++----
|  2 files changed, 41 insertions(+), 5 deletions(-)

* 2013-08-11(Tal Galili) tanglegram  - added a "main" parameter. |af21484| 
|  R/tanglegram.r    | 4 +++-
|  man/tanglegram.Rd | 2 ++
|  2 files changed, 5 insertions(+), 1 deletion(-)

* 2013-08-10(Tal Galili) entanglement function added! |df51acb| 
|  DESCRIPTION                    |   1 -
|  NAMESPACE                      |   4 +
|  NEWS                           |   1 +
|  R/entanglement.r               | 238 +++++++++++++++++++++++++++++----------
|  R/nleaves.r                    |   6 +-
|  inst/tests/test-entanglement.r |  44 ++++++++
|  man/entanglement.Rd            |  83 ++++++++++++++
|  man/nleaves.Rd                 |   2 +-
|  8 files changed, 313 insertions(+), 66 deletions(-)

* 2013-08-10(Tal Galili) moved code from entanglement.r. -> to -> untangle.r |a10f2bd| 
|  DESCRIPTION      |   1 +
|  R/entanglement.r | 760 ----------------------------------------------------
|  R/untangle.r     | 772 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 773 insertions(+), 760 deletions(-)

* 2013-08-10(Tal Galili) Rename: 'untangle.r' -> 'entanglement.r' |83e7293| 
|  DESCRIPTION                    |    3 +-
|  R/entanglement.r               | 1080 +++++++++++++++++++++++++++++++++++++
|  R/untangle.r                   | 1082 --------------------------------------
|  inst/tests/test-entanglement.r |   64 +++
|  inst/tests/test-untangle.r     |   64 ---
|  5 files changed, 1146 insertions(+), 1147 deletions(-)

* 2013-08-10(Tal Galili) match_order_dendrogram_by_old_order function added. |3a1c4e2| 
|  NAMESPACE                                  |   1 +
|  NEWS                                       |   1 +
|  R/tanglegram.r                             |   4 +
|  R/untangle.r                               | 158 +++++++++++++++++----------
|  inst/tests/test-untangle.r                 |  34 ++++++
|  man/match_order_by_labels.Rd               |   6 +-
|  man/match_order_dendrogram_by_old_order.Rd |  76 +++++++++++++
|  7 files changed, 219 insertions(+), 61 deletions(-)

* 2013-08-10(Tal Galili) nleaves - now allow the use of the "members" attr of a dendrogram for telling us the size of the tree. |52e15fe| 
|  NEWS                      |  1 +
|  R/nleaves.r               | 42 ++++++++++++++++++++++++++++++++----------
|  inst/tests/test-nleaves.r |  6 ++++++
|  man/nleaves.Rd            | 10 +++++++++-
|  4 files changed, 48 insertions(+), 11 deletions(-)

* 2013-08-10(Tal Galili) length(order.dendrogram(object)) -> nleaves(object) |9c65dd8| 
|  R/untangle.r | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2013-08-10(Tal Galili) abels_order_labels -> labels |d8932be| 
|  R/untangle.r               | 15 +++++++--------
|  inst/tests/test-untangle.r |  3 +++
|  2 files changed, 10 insertions(+), 8 deletions(-)

* 2013-08-10(Tal Galili) match_order_by_labels function added. |c11b0ee| 
|  NAMESPACE                    |   1 +
|  NEWS                         |   2 +
|  R/untangle.r                 | 243 +++++++++++++++++++++++------------------
|  inst/tests/test-untangle.r   |  34 ++++--
|  man/match_order_by_labels.Rd |  51 +++++++++
|  5 files changed, 215 insertions(+), 116 deletions(-)

* 2013-08-10(Tal Galili) dendo -> dend |4080be6| 
|  R/untangle.r | 625 +++++++++++++++++++++++++++++----------------------------
|  1 file changed, 322 insertions(+), 303 deletions(-)

* 2013-08-10(Tal Galili) leaves.values -> order.dendrogram |38073ca| 
|  R/untangle.r | 80 ++++++++++++++++++++++++++++++----------------------------
|  1 file changed, 42 insertions(+), 38 deletions(-)

* 2013-08-10(Tal Galili) Old code added (it now requires modifications) |022419b| 
|  R/untangle.r | 955 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 955 insertions(+)

* 2013-08-10(Tal Galili) untangle.r file added |1f6319a| 
|  DESCRIPTION                |  1 +
|  NEWS                       |  3 +++
|  R/untangle.r               | 28 ++++++++++++++++++++++++++++
|  inst/tests/test-rotate.r   |  2 +-
|  inst/tests/test-untangle.r | 17 +++++++++++++++++
|  5 files changed, 50 insertions(+), 1 deletion(-)

* 2013-08-10(Tal Galili) vignettes - added an example of the tanglegram. |13b84b9| 
|  vignettes/dendextend-tutorial.rnw | 27 +++++++++++++++++++++++++++
|  1 file changed, 27 insertions(+)

* 2013-08-10(Tal Galili) tanglegram function officially added! |48ea0d0| 
|  NAMESPACE         |   9 +-
|  NEWS              |   1 +
|  R/tanglegram.r    | 312 +++++++++++++++++++++++++++-------------------------
|  man/tanglegram.Rd | 152 +++++++++++++++++++++++++
|  4 files changed, 324 insertions(+), 150 deletions(-)

* 2013-08-10(Tal Galili) nleaves - changed some export rules. |90c8b95| 
|  R/nleaves.r | 3 +--
|  1 file changed, 1 insertion(+), 2 deletions(-)

* 2013-08-10(Tal Galili) fix tests for the automatic addition of pch=NA. |da98bde| 
|  inst/tests/test-attr_access.r | 7 ++++---
|  1 file changed, 4 insertions(+), 3 deletions(-)

* 2013-08-10(Tal Galili) Makes sure pch==NA if we are modifying a nodePar value which is other than pch (and pch did not exist before) - in assign_values_to_leaves_nodePar |307f0b0| 
|  NEWS                                   |  3 +++
|  R/attr_access.r                        | 18 +++++++++++++++++-
|  man/assign_values_to_leaves_nodePar.Rd |  4 ++++
|  3 files changed, 24 insertions(+), 1 deletion(-)

* 2013-08-10(Tal Galili) assign_values_to_branches_edgePar function added |d11873b| 
|  NEWS                                     |  2 +
|  R/attr_access.r                          | 80 ++++++++++++++++++++++++++++++
|  man/assign_values_to_branches_edgePar.Rd | 43 ++++++++++++++++
|  man/remove_branches_edgePar.Rd           | 35 +++++++++++++
|  4 files changed, 160 insertions(+)

* 2013-08-10(Tal Galili) remove_leaves_nodePar function added. |d15f8d6| 
|  NEWS                          |  2 +-
|  R/attr_access.r               | 48 +++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-attr_access.r | 15 +++++++++++++
|  man/get_leaves_attr.Rd        |  2 ++
|  man/remove_leaves_nodePar.Rd  | 40 ++++++++++++++++++++++++++++++++++
|  5 files changed, 106 insertions(+), 1 deletion(-)

* 2013-08-10(Tal Galili) plot_horiz.dendrogram function added |0badd90| 
|  DESCRIPTION                  |   4 +-
|  NAMESPACE                    |   1 +
|  NEWS                         |   6 +
|  R/tanglegram.r               | 321 +++++++++++++++++++++++++++++++++++++----
|  man/plot_horiz.dendrogram.Rd |  84 +++++++++++
|  5 files changed, 389 insertions(+), 27 deletions(-)

* 2013-08-10(Tal Galili) fix donotrun ->dontrun |8ad570c| 
|  R/attr_access.r                        | 4 ++--
|  man/assign_values_to_leaves_nodePar.Rd | 2 +-
|  man/get_nodes_attr.Rd                  | 2 +-
|  3 files changed, 4 insertions(+), 4 deletions(-)

* 2013-08-05(Tal Galili) intersect_trees - added the "warn" parameter. |fed9f78| 
|  NEWS                   |  1 +
|  R/trim.r               | 16 +++++++++++-----
|  man/intersect_trees.Rd |  5 ++++-
|  3 files changed, 16 insertions(+), 6 deletions(-)

* 2013-08-05(Tal Galili) Changed "dend1" -> "tree1", and added methods for hclust/phylo (by simply turning them into dendrograms) |055fad9| 
|  R/tanglegram.r | 42 ++++++++++++++++++++++++------------------
|  1 file changed, 24 insertions(+), 18 deletions(-)

* 2013-08-05(Tal Galili) fac2num - updated doc |980e0c5| 
|  R/rotate.r     | 24 ++++++++++++++++++++++++
|  man/fac2num.Rd |  9 ++++++---
|  man/rotate.Rd  |  8 ++++++++
|  3 files changed, 38 insertions(+), 3 deletions(-)

* 2013-08-05(Tal Galili) tanglegram- remove un-needed comments |11ffb1f| 
|  R/tanglegram.r | 69 +++++++++++---------------------------------------------
|  1 file changed, 13 insertions(+), 56 deletions(-)

* 2013-08-05(Tal Galili) tanglegram - more parameters. Made it so that the labels will be handled by plot.dendrogram (instead of by me) |4edbc4d| 
|  R/tanglegram.r | 107 +++++++++++++++++++++++++++++++++++--------------------
|  1 file changed, 69 insertions(+), 38 deletions(-)

* 2013-08-05(Tal Galili) tanglegram file/function added! |61b7f11| 
|  DESCRIPTION    |   1 +
|  NEWS           |   2 +
|  R/tanglegram.r | 162 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 165 insertions(+)

* 2013-08-05(Tal Galili) order.dendrogram - added tests and made the function a bit more optimized. |3468f62| 
|  R/labels.r                      | 22 +++++++++++++++-------
|  inst/tests/test-labels-assign.r | 25 +++++++++++++++++++++++++
|  2 files changed, 40 insertions(+), 7 deletions(-)

* 2013-08-05(Tal Galili) fac2num - added tests and a keep_names parameter |cdde4d4| 
|  NEWS                                |  4 ++++
|  R/cutree.dendrogram.r               |  8 +++++---
|  inst/tests/test-cutree.dendrogram.r | 13 ++++++++++++-
|  3 files changed, 21 insertions(+), 4 deletions(-)

* 2013-08-05(Tal Galili) rotate - fixes calling the same functions more than once (minor improvements) |28e6de1| 
|  NEWS                     |  9 +++++++++
|  R/labels.r               |  4 ++--
|  R/rotate.r               | 19 +++++++++++++------
|  inst/tests/test-rotate.r |  3 +++
|  4 files changed, 27 insertions(+), 8 deletions(-)

* 2013-08-04(Tal Galili) Change title |b9a64d9| 
|  vignettes/dendextend-tutorial.rnw | 6 +++---
|  1 file changed, 3 insertions(+), 3 deletions(-)

* 2013-08-02(Tal Galili) bump date, and added a link to where I'll publish posts about the package. |f7e66bc| 
|  DESCRIPTION | 5 +++--
|  1 file changed, 3 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) Vignettes - added Coloring branches example! |89e6431| 
|  NEWS                                              |    5 +-
|  man/leaf_Colors.Rd                                |   35 +
|  vignettes/cache/__packages                        |    1 +
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|  vignettes/dendextend-tutorial-concordance.tex     |   12 +-
|  vignettes/dendextend-tutorial.log                 |  463 +--
|  vignettes/dendextend-tutorial.pdf                 | 3359 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |  105 +-
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|  129 files changed, 2543 insertions(+), 1715 deletions(-)

* 2013-08-02(Tal Galili) Added an example to color_branches |b34b15b| 
|  R/color_branches.r            | 39 ++++++++++++++++++++++++++++++++++++---
|  inst/tests/test-attr_access.r | 25 +++++++++++++++++++++++++
|  man/color_branches.Rd         | 38 +++++++++++++++++++++++++++++++++++---
|  3 files changed, 96 insertions(+), 6 deletions(-)

* 2013-08-02(Tal Galili) "labels_colors<-" - fix the classes of the tree's branches. |7e97f68| 
|  R/labels_colors.r | 11 +++++++++--
|  1 file changed, 9 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) Function added: assign_values_to_leaves_nodePar - allows for complex manipulation of dendrogram's leaves parameters. |b9c5d91| 
|  NAMESPACE                              |  1 +
|  NEWS                                   |  4 +-
|  R/attr_access.r                        | 88 ++++++++++++++++++++++++++++++--
|  man/assign_values_to_leaves_nodePar.Rd | 55 ++++++++++++++++++++
|  man/get_leaves_attr.Rd                 | 14 +++--
|  5 files changed, 154 insertions(+), 8 deletions(-)

* 2013-08-02(Tal Galili) test to show that labels with integer values are VERY possible. |94f1aa7| 
|  inst/tests/test-labels-assign.r | 10 ++++++++++
|  1 file changed, 10 insertions(+)

* 2013-08-02(Tal Galili) test-unroot.r -> test-unbranch.r |cefa337| 
|  inst/tests/test-unbranch.r | 45 ++++++++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-unroot.r   | 45 --------------------------------------------
|  2 files changed, 45 insertions(+), 45 deletions(-)

* 2013-08-02(Tal Galili) as.phylo.dendrogram function added |ff0b4bc| 
|  NAMESPACE   | 1 +
|  NEWS        | 3 ++-
|  R/nleaves.r | 4 +++-
|  3 files changed, 6 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) Renaming the file: unroot.r -> unbranch.r |d467113| 
|  DESCRIPTION  |   2 +-
|  R/unbranch.r | 245 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  R/unroot.r   | 237 -------------------------------------------------------
|  3 files changed, 246 insertions(+), 238 deletions(-)

* 2013-08-02(Tal Galili) unroot -> unbranch: modify .Rd files |a05d617| 
|  NAMESPACE                       | 10 ++++----
|  NEWS                            |  2 +-
|  man/color_branches.Rd           |  2 +-
|  man/cutree-methods.Rd           | 22 ++++++++---------
|  man/heights_per_k.dendrogram.Rd |  6 ++---
|  man/unbranch.Rd                 | 50 +++++++++++++++++++++++++++++++++++++++
|  6 files changed, 71 insertions(+), 21 deletions(-)

* 2013-08-02(Tal Galili) Renaming the unroot function -> to -> unbranch |938a300| 
|  R/color_branches.r                  |  2 +-
|  R/cutree.dendrogram.r               | 28 ++++++++++----------
|  R/unroot.r                          | 50 +++++++++++++++++------------------
|  R/zzz.r                             |  2 +-
|  inst/tests/test-attr_access.r       | 16 +++++------
|  inst/tests/test-cutree.dendrogram.r | 46 ++++++++++++++++----------------
|  inst/tests/test-trim.r              | 22 +++++++--------
|  inst/tests/test-unroot.r            | 20 +++++++-------
|  8 files changed, 93 insertions(+), 93 deletions(-)

* 2013-08-02(Tal Galili) cutree.dendogram - Prevent R from crashing when using cutree on a subset tree (e.g: dend[[1]]) |1cd0014| 
|  NEWS                                |  5 ++
|  R/cutree.dendrogram.r               | 36 ++++++++++++-
|  inst/tests/test-cutree.dendrogram.r | 96 ++++++++++++++++++++++++-----------
|  man/cutree-methods.Rd               |  2 +-
|  4 files changed, 106 insertions(+), 33 deletions(-)

* 2013-08-02(Tal Galili) "order.dendrogram<-" - now returns an integer (instead of numeric) |cc0d038| 
|  R/labels.r                      | 33 +++++++++++++++++++++++++++++++--
|  inst/tests/test-labels-assign.r | 22 ++++++++++++++++++++++
|  man/order.dendrogram-assign.Rd  | 13 +++++++++++++
|  3 files changed, 66 insertions(+), 2 deletions(-)

* 2013-08-02(Tal Galili) making sure labels.hclust is exported! |af9751e| 
|  NAMESPACE  |  5 +++++
|  R/labels.r | 12 ++++++------
|  2 files changed, 11 insertions(+), 6 deletions(-)

* 2013-08-02(Tal Galili) Fixed a bug in color_branches when the tree's labels are integers! |32e2a42| 
|  NEWS                                |  4 +--
|  R/color_branches.r                  | 51 ++++++++++++++++++++++++++++++++---
|  inst/tests/test-cutree.dendrogram.r | 41 ++++++++++++++++++++++++++++
|  man/color_branches.Rd               | 46 ++++++++++++++++++++++++++++++-
|  4 files changed, 136 insertions(+), 6 deletions(-)

* 2013-08-02(Tal Galili) Extend color_branches to allow REPEATED cluster color assignments to branches on to the same tree. Something which the original function was not able to handle. |479ca6f| 
|  NEWS                  |  4 ++--
|  R/color_branches.r    | 53 ++++++++++++++++++++++++++++++++++++++++---------
|  man/color_branches.Rd | 24 +++++++++++++++++++++-
|  man/color_labels.Rd   |  3 +++
|  4 files changed, 72 insertions(+), 12 deletions(-)

* 2013-08-01(Tal Galili) "labels_colors<-" - fixed it so that by default it would not add phc=1 to the leaves. |7d8d9d0| 
|  NEWS              |  2 +-
|  R/labels_colors.r | 20 +++++++++++++++++++-
|  2 files changed, 20 insertions(+), 2 deletions(-)

* 2013-08-01(Tal Galili) color_labels function added. |c17a1d1| 
|  NAMESPACE             |   1 +
|  NEWS                  |   2 +
|  R/color_branches.r    | 111 +++++++++++++++++++++++++++++++++++++++++++++---
|  man/color_branches.Rd |   5 ++-
|  man/color_labels.Rd   |  70 ++++++++++++++++++++++++++++++
|  5 files changed, 182 insertions(+), 7 deletions(-)

* 2013-08-01(Tal Galili) Fix cutree.dendrogram for the case of using hclust - so it will respect sort_cluster_numbers! |f4bd3ce| 
|  R/cutree.dendrogram.r | 4 +++-
|  1 file changed, 3 insertions(+), 1 deletion(-)

* 2013-08-01(Tal Galili) fix missed \code{ and added "..." |21b2009| 
|  man/color_branches.Rd | 8 +++++---
|  1 file changed, 5 insertions(+), 3 deletions(-)

* 2013-08-01(Tal Galili) Another test for intersect_trees |c5b15e4| 
|  inst/tests/test-trim.r | 13 +++++++++++++
|  1 file changed, 13 insertions(+)

* 2013-08-01(Tal Galili) color_branches function added. |243a91b| 
|  NAMESPACE             |   4 ++
|  NEWS                  |   1 +
|  R/color_branches.r    | 125 ++++++++++++++++++++++++++++++++----------------
|  man/color_branches.Rd |  77 +++++++++++++++++++++++++++++
|  4 files changed, 167 insertions(+), 40 deletions(-)

* 2013-08-01(Tal Galili) Fixed typo |af1128d| 
|  R/labels_colors.r | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-08-01(Tal Galili) Updated the is.X functions docs |606044e| 
|  NEWS                 | 10 +++++++++-
|  man/is.dendrogram.Rd |  6 ++++++
|  man/is.hclust.Rd     |  6 ++++++
|  man/is.phylo.Rd      |  6 ++++++
|  4 files changed, 27 insertions(+), 1 deletion(-)

* 2013-08-01(Tal Galili) sort_levels_values function added. |d591a2d| 
|  R/cutree.dendrogram.r               | 126 ++++++++++++++++++++++++++++++++++
|  inst/tests/test-cutree.dendrogram.r |  96 ++++++++++++++++++++++++++
|  man/cutree-methods.Rd               |  20 +++++-
|  man/fac2num.Rd                      |  31 +++++++++
|  man/sort_levels_values.Rd           |  67 ++++++++++++++++++
|  5 files changed, 337 insertions(+), 3 deletions(-)

* 2013-08-01(Tal Galili) color_branches.r file added - it includes the original "colour_clusters" and "leaf_colours" from the {dendroextras} package. |a0d3281| 
|  DESCRIPTION        |   1 +
|  R/color_branches.r | 133 +++++++++++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 134 insertions(+)

* 2013-08-01(Tal Galili) Fix license reference (now pointing to http://www.r-project.org/Licenses/) |5330e51| 
|  DESCRIPTION            |  2 +-
|  R/attr_access.r        | 20 +++++++++++++++++---
|  R/cutree.dendrogram.r  | 19 +++++++++++++++++++
|  R/dendextend-package.r |  5 +++--
|  R/dendextend.r         |  5 +++--
|  R/labels.r             |  5 +++--
|  R/labels_colors.r      |  5 +++--
|  R/nleaves.r            |  5 +++--
|  R/rotate.r             |  5 +++--
|  R/trim.r               |  5 +++--
|  R/unroot.r             |  5 +++--
|  R/zzz.r                |  5 +++--
|  12 files changed, 64 insertions(+), 22 deletions(-)

* 2013-07-31(Tal Galili) vignettes - adding examples for cutree.dendrogram and hang.dendrogram. |1d9844d| 
|  vignettes/cache/__packages                        |    8 +-
|  ...hunk-30_cc171774502992645f046bd982a86244.RData |  Bin 0 -> 4206 bytes
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|  ...-chunk-31_79bbada7960ab7612f76987dabda2a1b.rdx |  Bin 0 -> 156 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    4 +-
|  vignettes/dendextend-tutorial.log                 |  265 ++-
|  vignettes/dendextend-tutorial.pdf                 | 2322 ++++++++++---------
|  vignettes/dendextend-tutorial.rnw                 |   85 +
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 92717 -> 110745 bytes
|  vignettes/dendextend-tutorial.tex                 |  234 +-
|  vignettes/figure/unnamed-chunk-19.pdf             |  Bin 4578 -> 4578 bytes
|  vignettes/figure/unnamed-chunk-23.pdf             |  Bin 4921 -> 4921 bytes
|  vignettes/figure/unnamed-chunk-24.pdf             |  Bin 4576 -> 4576 bytes
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|  vignettes/figure/unnamed-chunk-30.pdf             |  Bin 0 -> 6361 bytes
|  vignettes/figure/unnamed-chunk-4.pdf              |  Bin 4198 -> 4198 bytes
|  23 files changed, 1769 insertions(+), 1149 deletions(-)

* 2013-07-31(Tal Galili) cutree.dendrogram function added. With many docs and tests! |715711a| 
|  NAMESPACE                           |   6 +
|  NEWS                                |   8 +
|  R/cutree.dendrogram.r               | 305 +++++++++++++++++++++++++++++-----
|  inst/tests/test-attr_access.r       |   2 +-
|  inst/tests/test-cutree.dendrogram.r | 114 ++++++++++++-
|  man/cutree-methods.Rd               | 167 +++++++++++++++++++
|  man/cutree.dendrogram.Rd            | 118 +++++++++++++
|  man/cutree_1h.dendrogram.Rd         |   5 +-
|  man/cutree_1k.dendrogram.Rd         |   6 +-
|  man/is.dendrogram.Rd                |  10 ++
|  man/is.hclust.Rd                    |  10 ++
|  man/is.phylo.Rd                     |  10 ++
|  12 files changed, 714 insertions(+), 47 deletions(-)

* 2013-07-31(Tal Galili) cutree_1k.dendrogram - added tests |e58929f| 
|  R/cutree.dendrogram.r               | 33 +++++++++++++++++++-----
|  inst/tests/test-cutree.dendrogram.r | 48 +++++++++++++++++++++++++++++++++++
|  2 files changed, 75 insertions(+), 6 deletions(-)

* 2013-07-31(Tal Galili) dendrogram_heights_per_k -> dend_heights_per_k |2e971e2| 
|  R/cutree.dendrogram.r               | 36 +++++++++++++++++++----------------
|  inst/tests/test-cutree.dendrogram.r |  9 ++-------
|  man/cutree_1k.dendrogram.Rd         | 28 +++++++++++++++------------
|  3 files changed, 38 insertions(+), 35 deletions(-)

* 2013-07-31(Tal Galili) cutree_1k.dendrogram function added. |7c5fff9| 
|  NAMESPACE                   |   1 +
|  NEWS                        |   4 +-
|  R/cutree.dendrogram.r       | 126 ++++++++++++++++++++++++++++++------------
|  man/cutree_1h.dendrogram.Rd |  21 ++++---
|  man/cutree_1k.dendrogram.Rd |  88 +++++++++++++++++++++++++++++
|  man/is.natural.number.Rd    |   2 +-
|  6 files changed, 197 insertions(+), 45 deletions(-)

* 2013-07-31(Tal Galili) Moving hang.dendrogram from cutree.dendrogram.r to attr_access.r |4dc03d9| 
|  R/attr_access.r                     | 97 +++++++++++++++++++++++++++++++++++
|  R/cutree.dendrogram.r               | 89 --------------------------------
|  inst/tests/test-attr_access.r       | 31 +++++++++++
|  inst/tests/test-cutree.dendrogram.r | 32 ------------
|  4 files changed, 128 insertions(+), 121 deletions(-)

* 2013-07-31(Tal Galili) Make cutree_1h.dendrogram identical to cutree when height is above ALL clusters |0395b13| 
|  R/cutree.dendrogram.r               | 10 ++++++++--
|  inst/tests/test-cutree.dendrogram.r | 12 ++++++------
|  2 files changed, 14 insertions(+), 8 deletions(-)

* 2013-07-31(Tal Galili) Fix a major bug in cutree_1h.dendrogram due to some line getting erased at some point (not clear when that bug was introduced). |981a6a3| 
|  NEWS                                |  2 ++
|  R/cutree.dendrogram.r               | 16 ++++++++++++----
|  inst/tests/test-cutree.dendrogram.r | 30 ++++++++++++++++++++++++++++++
|  man/heights_per_k.dendrogram.Rd     |  7 +++++++
|  4 files changed, 51 insertions(+), 4 deletions(-)

* 2013-07-31(Tal Galili) vignettes - added some attr extraction examples. |6779acf| 
|  vignettes/dendextend-tutorial-concordance.tex |    8 +-
|  vignettes/dendextend-tutorial.log             |  509 +++--
|  vignettes/dendextend-tutorial.pdf             | 2724 ++++++++++++-----------
|  vignettes/dendextend-tutorial.rnw             |   81 +-
|  vignettes/dendextend-tutorial.synctex.gz      |  Bin 82110 -> 92717 bytes
|  vignettes/dendextend-tutorial.tex             |  243 +-
|  vignettes/figure/unnamed-chunk-19.pdf         |  Bin 4578 -> 4578 bytes
|  vignettes/figure/unnamed-chunk-22.pdf         |  Bin 4925 -> 4921 bytes
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|  vignettes/figure/unnamed-chunk-27.pdf         |  Bin 0 -> 5132 bytes
|  vignettes/figure/unnamed-chunk-28.pdf         |  Bin 0 -> 6930 bytes
|  vignettes/figure/unnamed-chunk-29.pdf         |  Bin 0 -> 6361 bytes
|  vignettes/figure/unnamed-chunk-4.pdf          |  Bin 4198 -> 4198 bytes
|  16 files changed, 2013 insertions(+), 1552 deletions(-)

* 2013-07-31(Tal Galili) test when get_nodes_attr doesn't get an attribute |b333ba4| 
|  inst/tests/test-attr_access.r | 3 +++
|  1 file changed, 3 insertions(+)

* 2013-07-31(Tal Galili) hang.dendrogram - added a test, and source ref for the function |7fa3d0e| 
|  inst/tests/test-cutree.dendrogram.r | 22 +++++++++++++++++++---
|  man/hang.dendrogram.Rd              |  5 +++++
|  2 files changed, 24 insertions(+), 3 deletions(-)

* 2013-07-31(Tal Galili) fix_members_attr.dendrogram function added. |b471984| 
|  NEWS       |  1 +
|  R/labels.r |  1 +
|  R/trim.r   | 56 +++++++++++++++++++++++++++++++++++++++++++++++++++++---
|  3 files changed, 55 insertions(+), 3 deletions(-)

* 2013-07-31(Tal Galili) bumping version to 0.4 (we'll stay here for a while...) |8a55104| 
|  DESCRIPTION | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-07-31(Tal Galili) fix .bib (commas were missing) |fb394a7| 
|  vignettes/dendextend-tutorial.bib | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2013-07-31(Tal Galili) get_nodes_attr function added |01613a2| 
|  NAMESPACE                     |   3 +-
|  NEWS                          |   4 +-
|  R/attr_access.r               | 218 +++++++++++++++++++++++++++++++++++++++-
|  R/cutree.dendrogram.r         |  92 +++--------------
|  inst/tests/test-attr_access.r |  78 ++++++++++++++
|  man/get_branches_heights.Rd   |  30 ++++++
|  man/get_leaves_attr.Rd        |  12 ++-
|  man/get_nodes_attr.Rd         |  84 ++++++++++++++++
|  8 files changed, 436 insertions(+), 85 deletions(-)

* 2013-07-31(Tal Galili) nnodes function added - count the number of nodes in a tree |1187719| 
|  NAMESPACE                 |  8 ++++
|  NEWS                      |  6 +++
|  R/nleaves.r               | 89 ++++++++++++++++++++++++++++++++++++++++++++-
|  inst/tests/test-nleaves.r | 16 +++++++-
|  man/nleaves.Rd            |  7 ++++
|  man/nnodes.Rd             | 47 ++++++++++++++++++++++++
|  6 files changed, 170 insertions(+), 3 deletions(-)

* 2013-07-30(Tal Galili) vignettes - expended the abstract a bit. |f8491a5| 
|  vignettes/dendextend-tutorial.bib | 69 +++++++++++++++++++++++++++++++++++++
|  vignettes/dendextend-tutorial.rnw | 13 ++++---
|  2 files changed, 77 insertions(+), 5 deletions(-)

* 2013-07-30(Tal Galili) hang.dendrogram function added, including tests and doc. |82846ea| 
|  NAMESPACE                           |   8 ++
|  NEWS                                |   5 +-
|  R/cutree.dendrogram.r               | 262 +++++++++++++++++++++++++++++-----
|  inst/tests/test-cutree.dendrogram.r |  17 +++
|  man/fix_members_attr.dendrogram.Rd  |  38 +++++
|  man/get_heights.dendrogram.Rd       |  26 ++++
|  man/hang.dendrogram.Rd              |  53 +++++++
|  man/heights_per_k.dendrogram.Rd     |  31 ++++
|  man/rllply.Rd                       |  50 +++++++
|  9 files changed, 452 insertions(+), 38 deletions(-)

* 2013-07-28(Tal Galili) cutree_1h.dendrogram function added (with doc and tests) - like cutree, but only for 1 height |4754ba0| 
|  NAMESPACE                           |   3 +
|  NEWS                                |   6 +-
|  R/cutree.dendrogram.r               | 119 +++++++++++++++++++++++-----------
|  inst/tests/test-cutree.dendrogram.r |  39 +++++++++--
|  man/cutree_1h.dendrogram.Rd         |  63 ++++++++++++++++++
|  man/get_leaves_attr.Rd              |  10 +--
|  man/is.natural.number.Rd            |  40 ++++++++++++
|  7 files changed, 225 insertions(+), 55 deletions(-)

* 2013-07-28(Tal Galili) Changed functions names to be more S3 like. |2d125d0| 
|  R/cutree.dendrogram.r | 99 +++++++++++++++++--------------------------------
|  1 file changed, 33 insertions(+), 66 deletions(-)

* 2013-07-28(Tal Galili) is.natural.number function added (with tests and documentation) |58922db| 
|  NEWS                                |  3 +++
|  R/cutree.dendrogram.r               | 43 ++++++++++++++++++++++++-----------
|  inst/tests/test-cutree.dendrogram.r | 22 ++++++++++++++----
|  3 files changed, 51 insertions(+), 17 deletions(-)

* 2013-07-28(Tal Galili) cutree.dendrogram.r - added first version of the file (with the old functions which will now be revised to newer naming conventions and documentation) |55598e4| 
|  DESCRIPTION                         |   1 +
|  NEWS                                |  12 +-
|  R/attr_access.r                     |  12 +-
|  R/cutree.dendrogram.r               | 265 ++++++++++++++++++++++++++++++++++
|  inst/tests/test-cutree.dendrogram.r |  14 ++
|  vignettes/dendextend-tutorial.rnw   |   2 +-
|  6 files changed, 295 insertions(+), 11 deletions(-)

* 2013-07-27(Tal Galili) Vignettes - updated noisense files. |6793d20| 
|  vignettes/dendextend-tutorial-concordance.tex |   5 +-
|  vignettes/dendextend-tutorial.blg             |   2 +
|  vignettes/dendextend-tutorial.log             | 356 ++++++++++++------------
|  vignettes/dendextend-tutorial.synctex.gz      | Bin 65670 -> 82110 bytes
|  vignettes/dendextend-tutorial.tex             | 102 ++++++-
|  vignettes/figure/unnamed-chunk-19.pdf         | Bin 4578 -> 4578 bytes
|  vignettes/figure/unnamed-chunk-20.pdf         | Bin 4921 -> 4921 bytes
|  vignettes/figure/unnamed-chunk-21.pdf         | Bin 4576 -> 4576 bytes
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|  vignettes/figure/unnamed-chunk-24.pdf         | Bin 5126 -> 5132 bytes
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|  vignettes/figure/unnamed-chunk-26.pdf         | Bin 0 -> 6361 bytes
|  vignettes/figure/unnamed-chunk-4.pdf          | Bin 4198 -> 4198 bytes
|  14 files changed, 274 insertions(+), 191 deletions(-)

* 2013-07-27(Tal Galili) Various changes to rotate - adding documentation and testing! |74ece8d| 
|  NAMESPACE                         |    3 +-
|  NEWS                              |    7 +-
|  R/rotate.r                        |   52 +-
|  inst/tests/test-rotate.r          |   74 ++
|  man/as_hclust_fixed.Rd            |    3 +-
|  man/get_leaves_attr.Rd            |   42 +
|  man/rotate.Rd                     |   40 +-
|  vignettes/dendextend-tutorial.pdf | 1754 +++++++++++++++++++----------------
|  vignettes/dendextend-tutorial.rnw |   53 +-
|  9 files changed, 1198 insertions(+), 830 deletions(-)

* 2013-07-27(Tal Galili) Some work on attr_access.r (not sure if this would be used later or not...). |5d6414e| 
|  DESCRIPTION     |  1 +
|  R/attr_access.r | 43 +++++++++++++++++++++++++++++++++++++++++++
|  2 files changed, 44 insertions(+)

* 2013-07-27(Tal Galili) as_hclust_fixed - now works just as as.hclust when hc is missing. |a613071| 
|  R/dendextend.r | 22 ++++++++++++++--------
|  1 file changed, 14 insertions(+), 8 deletions(-)

* 2013-07-27(Tal Galili) Bump release date for DESCRIPTION (although it will keep moving until a specific stage is released...) |a74140f| 
|  DESCRIPTION | 4 ++--
|  NEWS        | 4 ++--
|  2 files changed, 4 insertions(+), 4 deletions(-)

* 2013-07-27(Tal Galili) Move from length(order.dendrogram(x)) to nleaves(x) |1e0501a| 
|  R/labels.r | 8 ++++----
|  1 file changed, 4 insertions(+), 4 deletions(-)

* 2013-07-27(Tal Galili) Vignettes - adding references to other packages. |8b105cd| 
|  vignettes/dendextend-tutorial-concordance.tex |    6 +-
|  vignettes/dendextend-tutorial.bib             |   78 +
|  vignettes/dendextend-tutorial.pdf             | 2740 +++++++++++++----------
|  vignettes/dendextend-tutorial.rnw             |   20 +-
|  vignettes/dendextend.bib                      |  636 ------
|  5 files changed, 1633 insertions(+), 1847 deletions(-)

* 2013-07-27(Tal Galili) Forcing {ape} to load before {dendextend}, thus allowing for both rotate and unroot to work for BOTH packages. It does add extra noise when loading the package, but it is the best solution I can think of at this point. |ae741d8| 
|  R/zzz.r | 22 ++++++++++++++++++++--
|  1 file changed, 20 insertions(+), 2 deletions(-)

* 2013-07-27(Tal Galili) labels_colors - added checks for "dendrogram" class |fb6dad9| 
|  R/labels_colors.r                 |  4 ++++
|  inst/tests/test-labels_colors.r   |  9 +++++++++
|  vignettes/dendextend-tutorial.rnw | 27 +++++++++++++++++++--------
|  3 files changed, 32 insertions(+), 8 deletions(-)

* 2013-07-27(Tal Galili) Fix a wrong variable name. |1c96d06| 
|  inst/tests/test-trim.r | 4 ++--
|  1 file changed, 2 insertions(+), 2 deletions(-)

* 2013-07-27(Tal Galili) Testing for partial assignment. |197370e| 
|  inst/tests/test-labels-assign.r | 11 +++++++++++
|  1 file changed, 11 insertions(+)

* 2013-07-27(Tal Galili) Adding credit. |634a7a7| 
|  R/labels.r | 6 +++++-
|  1 file changed, 5 insertions(+), 1 deletion(-)

* 2013-07-27(Tal Galili) labels_colors - adding leaves labels as names to the color vector. Giving credit to Gregory Jefferis. |0d61899| 
|  R/labels_colors.r               | 19 ++++++++++----
|  inst/tests/test-labels_colors.r | 53 ++++++++++++++++++++++++++++++++++++---
|  man/labels-assign.Rd            |  2 ++
|  man/labels_colors.Rd            | 16 +++++++++---
|  4 files changed, 78 insertions(+), 12 deletions(-)

* 2013-07-26(Tal Galili) Vignettes PDF - updated |e74fe57| 
|  vignettes/dendextend-tutorial-concordance.tex |    6 +-
|  vignettes/dendextend-tutorial.log             |  607 +++++-
|  vignettes/dendextend-tutorial.pdf             | 2378 ++++++++++++++++-------
|  vignettes/dendextend-tutorial.synctex.gz      |  Bin 44992 -> 65670 bytes
|  vignettes/dendextend-tutorial.tex             |  400 +++-
|  vignettes/dendextend-tutorial.toc             |    0
|  vignettes/figure/unnamed-chunk-19.pdf         |  Bin 4626 -> 4578 bytes
|  vignettes/figure/unnamed-chunk-20.pdf         |  Bin 0 -> 4921 bytes
|  vignettes/figure/unnamed-chunk-21.pdf         |  Bin 0 -> 4576 bytes
|  vignettes/figure/unnamed-chunk-22.pdf         |  Bin 0 -> 4925 bytes
|  vignettes/figure/unnamed-chunk-23.pdf         |  Bin 0 -> 4897 bytes
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|  vignettes/figure/unnamed-chunk-25.pdf         |  Bin 0 -> 6930 bytes
|  vignettes/figure/unnamed-chunk-4.pdf          |  Bin 4198 -> 4198 bytes
|  14 files changed, 2570 insertions(+), 821 deletions(-)

* 2013-07-26(Tal Galili) Updated NEWS/DESCRIPTION (still not done with V0.3) |e389f99| 
|  DESCRIPTION                       |  2 ++
|  NEWS                              | 13 +++++++++----
|  vignettes/dendextend-tutorial.rnw |  6 +++---
|  3 files changed, 14 insertions(+), 7 deletions(-)

* 2013-07-26(Tal Galili) Vignettes - added a section on labels_colors |9a558ea| 
|  vignettes/dendextend-tutorial.rnw | 62 ++++++++++++++++++++++++++++---------
|  1 file changed, 47 insertions(+), 15 deletions(-)

* 2013-07-26(Tal Galili) labels_colors - moved to their own file, Also added new tests. |68eba04| 
|  R/dendextend.r                  |  84 ------------------------------
|  R/labels_colors.r               | 105 ++++++++++++++++++++++++++++++++++++++
|  inst/tests/test-labels_colors.r |  25 +++++++++
|  man/labels_colors.Rd            |   4 ++
|  4 files changed, 134 insertions(+), 84 deletions(-)

* 2013-07-26(Tal Galili) Trimming by labels. |2ea1933| 
|  R/trim.r                          | 10 +++--
|  inst/tests/test-trim.r            | 68 +++++++++++++++++++++++++++++++++
|  vignettes/dendextend-tutorial.rnw | 75 ++++++++++++++++++++++++++++++++++++-
|  3 files changed, 148 insertions(+), 5 deletions(-)

* 2013-07-26(Tal Galili) Vignettes - unroot, raise.dendrogram |d7402e7| 
|  vignettes/dendextend-tutorial.rnw | 89 +++++++++++++++++++++++++++++++++++++
|  1 file changed, 89 insertions(+)

* 2013-07-26(Tal Galili) Fixes and extensions to unroot |9085f8d| 
|  R/unroot.r                  | 117 +++++++++++++++++++++++++-----------------
|  inst/tests/test-unroot.r    |  45 ++++++++++++++++
|  man/count_terminal_nodes.Rd |   8 ++-
|  man/flatten.dendrogram.Rd   |   4 +-
|  man/get_branches_attr.Rd    |   9 +++-
|  man/unclass_dend.Rd         |   4 +-
|  man/unroot.Rd               |   3 +-
|  7 files changed, 134 insertions(+), 56 deletions(-)

* 2013-07-25(Tal Galili) vignettes - spell checked. |7d6cb65| 
|  vignettes/dendextend-tutorial.rnw | 28 ++++++++++++++--------------
|  1 file changed, 14 insertions(+), 14 deletions(-)

* 2013-07-25(Tal Galili) Added tests for tree size :) |f95c928| 
|  DESCRIPTION               |  7 ++++---
|  NEWS                      |  4 +++-
|  inst/tests/test-nleaves.r | 50 +++++++++++++++++++++++++++++++++++++++++++++
|  3 files changed, 57 insertions(+), 4 deletions(-)

* 2013-07-25(Tal Galili) Vignettes - assignment recycling and tree sizes |da05752| 
|  vignettes/cache/__packages                        |   10 +
|  ...hunk-18_d9d3a2e4138d97442a69288b169de349.RData |  Bin 0 -> 3121 bytes
|  ...-chunk-18_d9d3a2e4138d97442a69288b169de349.rdb |    0
|  ...-chunk-18_d9d3a2e4138d97442a69288b169de349.rdx |  Bin 0 -> 113 bytes
|  vignettes/dendextend-tutorial-concordance.tex     |    7 +-
|  vignettes/dendextend-tutorial.log                 |  297 +++-
|  vignettes/dendextend-tutorial.pdf                 | 1743 +++++++++++--------
|  vignettes/dendextend-tutorial.rnw                 |  102 +-
|  vignettes/dendextend-tutorial.synctex.gz          |  Bin 30645 -> 44992 bytes
|  vignettes/dendextend-tutorial.tex                 |  357 +++-
|  vignettes/figure/unnamed-chunk-19.pdf             |  Bin 0 -> 4626 bytes
|  vignettes/figure/unnamed-chunk-4.pdf              |  Bin 4198 -> 4198 bytes
|  12 files changed, 1582 insertions(+), 934 deletions(-)

* 2013-07-25(Tal Galili) fix labeels-assign.Rd |14a1e5e| 
|  R/labels.r           | 2 +-
|  man/labels-assign.Rd | 2 +-
|  2 files changed, 2 insertions(+), 2 deletions(-)

* 2013-07-25(Tal Galili) unclass_dend now uses dendrapply |6e287f4| 
|  R/nleaves.r | 29 ++++++++++++++++++-----------
|  1 file changed, 18 insertions(+), 11 deletions(-)

* 2013-07-25(Tal Galili) Vignettes: a section on dendrapply |cea57f9| 
|  vignettes/dendextend-tutorial-concordance.tex |    6 +-
|  vignettes/dendextend-tutorial.log             |  421 +++---
|  vignettes/dendextend-tutorial.pdf             | 1379 ++++++++++---------
|  vignettes/dendextend-tutorial.rnw             |   59 +-
|  vignettes/dendextend-tutorial.synctex.gz      |  Bin 27918 -> 30645 bytes
|  vignettes/dendextend-tutorial.tex             |  109 +-
|  vignettes/dendextend.bib                      |  636 +++++++++
|  vignettes/figure/unnamed-chunk-4.pdf          |  Bin 4198 -> 4198 bytes
|  vignettes/jss.bst                             | 1631 +++++++++++++++++++++++
|  vignettes/jss.cls                             |  487 +++++++
|  vignettes/jsslogo.jpg                         |  Bin 0 -> 22731 bytes
|  11 files changed, 3907 insertions(+), 821 deletions(-)

* 2013-07-25(Tal Galili) Fix assignment recycling And also class of nodes are no longer "dendrogram" after label assignment |fec015c| 
|  NEWS                            |  1 +
|  R/labels.r                      | 40 ++++++++++++++++++++---
|  inst/tests/test-labels-assign.r | 68 +++++++++++++++++++++++++++++++++------
|  3 files changed, 95 insertions(+), 14 deletions(-)

* 2013-07-25(Tal Galili) Vignettes: switched from markdown to LaTeX (to make it easier to submit to a journal later on) |15d1492| 
|  .Rbuildignore                                 |    8 +-
|  NEWS                                          |    4 +-
|  dendextend.Rproj                              |    2 +-
|  vignettes/dendextend-tutorial-concordance.tex |    4 +
|  vignettes/dendextend-tutorial.Rmd             |  169 ---
|  vignettes/dendextend-tutorial.bib             |  636 +++++++++
|  vignettes/dendextend-tutorial.blg             |    3 +
|  vignettes/dendextend-tutorial.html            |  482 -------
|  vignettes/dendextend-tutorial.log             |  896 +++++++++++++
|  vignettes/dendextend-tutorial.md              |  382 ------
|  vignettes/dendextend-tutorial.pdf             | 1576 +++++++++++++++++++++++
|  vignettes/dendextend-tutorial.rnw             |  400 ++++++
|  vignettes/dendextend-tutorial.synctex.gz      |  Bin 0 -> 27918 bytes
|  vignettes/dendextend-tutorial.tex             |  664 ++++++++++
|  vignettes/figure/unnamed-chunk-11.png         |  Bin 9139 -> 0 bytes
|  vignettes/figure/unnamed-chunk-3.png          |  Bin 2766 -> 0 bytes
|  vignettes/figure/unnamed-chunk-4.pdf          |  Bin 0 -> 4198 bytes
|  vignettes/figure/unnamed-chunk-8.png          |  Bin 9139 -> 0 bytes
|  vignettes/figure/unnamed-chunk-9.png          |  Bin 9139 -> 0 bytes
|  19 files changed, 4189 insertions(+), 1037 deletions(-)

* 2013-07-25(Tal Galili) Added a clear GPL-2 copyright notice on each r file. |aebbbc0| 
|  NEWS                   |  6 ++++--
|  R/dendextend-package.r | 21 +++++++++++++++++++++
|  R/dendextend.r         | 23 +++++++++++++++++++++++
|  R/labels.r             | 26 ++++++++++++++++++++++++++
|  R/nleaves.r            | 24 ++++++++++++++++++++++++
|  R/rotate.r             | 16 ++++++++++++++++
|  R/trim.r               | 24 ++++++++++++++++++++++++
|  R/unroot.r             | 20 ++++++++++++++++++++
|  R/zzz.r                | 18 ++++++++++++++++++
|  9 files changed, 176 insertions(+), 2 deletions(-)

* 2013-07-24(Tal Galili) Updated NEWS and DESCRIPTION |35db6ed| 
|  DESCRIPTION | 17 ++++++++++++-----
|  NEWS        | 31 +++++++++++++++++++++++++++++++
|  2 files changed, 43 insertions(+), 5 deletions(-)

* 2013-07-24(Tal Galili) vingettes - labels assignment for vectors. |5a20227| 
|  inst/tests/test-labels-assign.r    |   2 +-
|  vignettes/dendextend-tutorial.Rmd  |  49 +++++++++++++++--
|  vignettes/dendextend-tutorial.html |  73 ++++++++++++++++++++++++-
|  vignettes/dendextend-tutorial.md   | 100 +++++++++++++++++++++++++++++++++--
|  4 files changed, 215 insertions(+), 9 deletions(-)

* 2013-07-24(Tal Galili) "labels.hclust" and "labels.hclust<-" - now both use order=TRUE as default. this makes them consistent with labels.dendrogram. Proper tests have been implemented. |34151cb| 
|  R/labels.r                      |  4 ++--
|  inst/tests/test-labels-assign.r | 28 ++++++++++++++++++++++++----
|  2 files changed, 26 insertions(+), 6 deletions(-)

* 2013-07-24(Tal Galili) tests - changed names, and added quick way for checking the code while developing the package. |7b1d8f9| 
|  inst/tests/test-labels-assign.r | 2 +-
|  tests/test-all.r                | 2 ++
|  2 files changed, 3 insertions(+), 1 deletion(-)

* 2013-07-24(Tal Galili) vignettes - first part of the introduction written (it is a very rough draft, but readable). |6304231| 
|  .Rbuildignore                         |   4 +-
|  vignettes/dendextend-tutorial.Rmd     | 123 ++++++++-------
|  vignettes/dendextend-tutorial.html    | 223 ++++++++++++++++++++-------
|  vignettes/dendextend-tutorial.md      | 257 +++++++++++++++++++++++++-------
|  vignettes/figure/unnamed-chunk-11.png | Bin 0 -> 9139 bytes
|  vignettes/figure/unnamed-chunk-3.png  | Bin 9139 -> 2766 bytes
|  vignettes/figure/unnamed-chunk-8.png  | Bin 0 -> 9139 bytes
|  vignettes/figure/unnamed-chunk-9.png  | Bin 0 -> 9139 bytes
|  8 files changed, 441 insertions(+), 166 deletions(-)

* 2013-07-24(Tal Galili) Added tests for labels assignment |10e9885| 
|  inst/tests/test-labels-assign.r | 55 +++++++++++++++++++++++++++++++++++++++
|  1 file changed, 55 insertions(+)

* 2013-07-24(Tal Galili) Fixes for CMD CHECK |5ee9655| 
|  R/labels.r                     |   7 +--
|  demo/00Index                   |   2 +-
|  man/labels-assign.Rd           | 108 +++++++++++++++++++++++++++++++++++++++
|  man/labels-set.Rd              | 108 ---------------------------------------
|  man/order.dendrogram-assign.Rd |  39 ++++++++++++++
|  man/order.dendrogram-set.Rd    |  39 --------------
|  tests/test-all.r               |   2 +-
|  7 files changed, 153 insertions(+), 152 deletions(-)

* 2013-07-24(Tal Galili) New: demo, vignettes (knitr), tests (testthat) - |857e081| 
|  .Rbuildignore                        |   3 +
|  demo/00Index                         |   1 +
|  demo/dendextend.r                    |  23 +++
|  dendextend.Rproj                     |   2 +-
|  tests/test-all.r                     |   4 +
|  vignettes/dendextend-tutorial.Rmd    | 109 ++++++++++++
|  vignettes/dendextend-tutorial.html   | 298 +++++++++++++++++++++++++++++++++
|  vignettes/dendextend-tutorial.md     | 147 ++++++++++++++++
|  vignettes/figure/unnamed-chunk-3.png | Bin 0 -> 9139 bytes
|  9 files changed, 586 insertions(+), 1 deletion(-)

* 2013-07-24(Tal Galili) labels.hclust - added the 'order' parameter |3f515a1| 
|  R/labels.r | 41 ++++++++++++++++++++++++++++++++++++-----
|  1 file changed, 36 insertions(+), 5 deletions(-)

* 2013-07-24(Tal Galili) Updated doc - |b3eed86| 
|  R/dendextend-package.r    |  8 ++++++
|  R/rotate.r                | 65 +++++++++++++++++++++++++++++++++++---------
|  R/unroot.r                |  1 +
|  R/zzz.r                   | 66 +++++++++++++++++++++++++++++++++++++++++++++
|  man/dendextend-package.Rd | 15 +++++++++++
|  man/get_branches_attr.Rd  |  1 +
|  man/intersect_trees.Rd    |  6 ++---
|  man/labels-set.Rd         | 15 +++++++++--
|  man/rotate.Rd             | 25 ++++++++++-------
|  9 files changed, 176 insertions(+), 26 deletions(-)

* 2013-04-10(Tal Galili) intersect_trees function added |988374d| 
|  NAMESPACE              |  1 +
|  NEWS                   |  3 ++-
|  R/trim.r               | 50 +++++++++++++++++++++++++++++++++++++++++++++++-
|  README.md              |  3 ++-
|  man/intersect_trees.Rd | 37 +++++++++++++++++++++++++++++++++++
|  5 files changed, 91 insertions(+), 3 deletions(-)

* 2013-04-06(Tal Galili) order.dendrogram<- function added. |cf1c863| 
|  NAMESPACE                   |  1 +
|  NEWS                        |  1 +
|  R/labels.r                  | 55 +++++++++++++++++++++++++++++++++++++++++++
|  README.md                   |  1 +
|  man/order.dendrogram-set.Rd | 39 ++++++++++++++++++++++++++++++
|  5 files changed, 97 insertions(+)

* 2013-04-06(Tal Galili) Notes on rotate and {ape} masking it. |ca4edad| 
|  NEWS          | 3 ++-
|  R/rotate.r    | 1 +
|  README.md     | 4 ++--
|  man/rotate.Rd | 6 ++++++
|  4 files changed, 11 insertions(+), 3 deletions(-)

* 2013-04-06(Tal Galili) updated README |0549266| 
|  README.md | 23 +++++++----------------
|  1 file changed, 7 insertions(+), 16 deletions(-)

* 2013-04-06(Tal Galili) unroot (S3'd), raise.dendrogram, flatten.dendrogram |a765a29| 
|  DESCRIPTION               |   1 +
|  NAMESPACE                 |   8 ++
|  NEWS                      |   5 +-
|  R/nleaves.r               |   3 -
|  R/rotate.r                |   6 +-
|  R/trim.r                  |   4 +-
|  R/unroot.r                | 194 ++++++++++++++++++++++++++++++++++++++++++++
|  man/flatten.dendrogram.Rd |  36 ++++++++
|  man/get_branches_attr.Rd  |  31 +++++++
|  man/raise.dendrogram.Rd   |  29 +++++++
|  man/rotate.Rd             |   6 +-
|  man/unroot.Rd             |  49 +++++++++++
|  12 files changed, 365 insertions(+), 7 deletions(-)

* 2013-04-06(Tal Galili) as_hclust_fixed function added (and implemented in trim and rotate) |67b220e| 
|  NAMESPACE              |  1 +
|  NEWS                   |  2 ++
|  R/dendextend.r         | 25 ++++++++++++++++++++++++-
|  R/rotate.r             |  7 +------
|  R/trim.r               | 16 +++++++++-------
|  man/as_hclust_fixed.Rd | 34 ++++++++++++++++++++++++++++++++++
|  man/trim.Rd            |  2 +-
|  man/trim_leaf.Rd       |  2 +-
|  8 files changed, 73 insertions(+), 16 deletions(-)

* 2013-04-06(Tal Galili) trim (leaves by labels) function added :) |0fcde8e| 
|  DESCRIPTION      |   1 +
|  NAMESPACE        |   5 ++
|  NEWS             |   1 +
|  R/nleaves.r      |   9 +++-
|  R/trim.r         | 148 +++++++++++++++++++++++++++++++++++++++++++++++++++++
|  man/rotate.Rd    |   9 +++-
|  man/trim.Rd      |  48 +++++++++++++++++
|  man/trim_leaf.Rd |  32 ++++++++++++
|  8 files changed, 250 insertions(+), 3 deletions(-)

* 2013-04-06(Tal Galili) rotate.phylo S3 method (and doc) added. |7228393| 
|  DESCRIPTION   |  2 ++
|  NAMESPACE     |  1 +
|  NEWS          |  2 +-
|  R/rotate.r    | 12 ++++++++++--
|  README.md     |  2 +-
|  man/rotate.Rd | 13 +++++++++++--
|  6 files changed, 26 insertions(+), 6 deletions(-)

* 2013-04-06(Tal Galili) rotate, sort, flip, nleaves functions were added! |84ccfd6| 
|  DESCRIPTION                 |   2 +
|  NAMESPACE                   |  11 ++++
|  NEWS                        |   7 +-
|  R/dendextend.r              | 102 -----------------------------
|  R/nleaves.r                 | 148 ++++++++++++++++++++++++++++++++++++++++++
|  R/rotate.r                  | 113 ++++++++++++++++++++++++++++++++
|  README.md                   |   5 ++
|  man/count_terminal_nodes.Rd |  14 ++--
|  man/nleaves.Rd              |  44 +++++++++++++
|  man/rotate.Rd               |  86 ++++++++++++++++++++++++
|  man/unclass_dend.Rd         |   3 +
|  11 files changed, 426 insertions(+), 109 deletions(-)

* 2013-04-06(Tal Galili) head.dendrogram S3 method to head |fe4dbbb| 
|  DESCRIPTION    |  2 ++
|  NAMESPACE      |  2 ++
|  NEWS           |  1 +
|  R/dendextend.r | 13 +++++++++++++
|  4 files changed, 18 insertions(+)

* 2013-04-06(Tal Galili) unclass_dend function added |b37a26b| 
|  NAMESPACE           |  1 +
|  NEWS                |  1 +
|  R/dendextend.r      | 36 ++++++++++++++++++++++++++++++++++++
|  README.md           |  5 +++--
|  man/unclass_dend.Rd | 29 +++++++++++++++++++++++++++++
|  5 files changed, 70 insertions(+), 2 deletions(-)

* 2013-04-06(Tal Galili) labels_colors function added |718899f| 
|  NAMESPACE                   |   4 +-
|  NEWS                        |   5 ++-
|  R/dendextend.r              | 102 +++++++++++++++++++++++++++++++++++++++---
|  man/count.terminal.nodes.Rd |  48 --------------------
|  man/count_terminal_nodes.Rd |  48 ++++++++++++++++++++
|  man/labels_colors.Rd        |  49 ++++++++++++++++++++
|  6 files changed, 200 insertions(+), 56 deletions(-)

* 2013-04-06(Tal Galili) "labels<-.dendrogram" updated - to allow duplicate labels, and shorter labels than the size of the tree. |f82ed9b| 
|  NEWS              |  2 ++
|  R/dendextend.r    |  2 +-
|  R/labels.r        | 47 +++++++++++++++++++----------------------------
|  man/labels-set.Rd |  4 ++++
|  4 files changed, 26 insertions(+), 29 deletions(-)

* 2013-04-06(Tal Galili) count.terminal.nodes function added |cbcab99| 
|  DESCRIPTION                 |  8 +++----
|  NAMESPACE                   |  1 +
|  NEWS                        |  6 ++++++
|  R/dendextend.r              | 50 +++++++++++++++++++++++++++++++++++++++++--
|  R/labels.r                  | 36 -------------------------------
|  README.md                   |  5 +++--
|  man/count.terminal.nodes.Rd | 48 +++++++++++++++++++++++++++++++++++++++++
|  7 files changed, 110 insertions(+), 44 deletions(-)

* 2013-04-06(Tal Galili) Merged "labels<-" help files |8a55439| 
|  DESCRIPTION          |   2 +-
|  NAMESPACE            |  10 ++--
|  NEWS                 |   3 +-
|  R/labels.r           | 126 +++++++++++++++++++++++++++----------------------
|  man/labels-set.Rd    |  48 ++++++++++++++++---
|  man/labels.matrix.Rd |  47 ------------------
|  6 files changed, 119 insertions(+), 117 deletions(-)

* 2013-04-05(Tal Galili) NEWS and README.md files added |0a117ae| 
|  NAMESPACE  |  8 +++++++-
|  NEWS       | 18 ++++++++++++++++++
|  R/labels.r |  4 ++--
|  README.md  | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  4 files changed, 86 insertions(+), 3 deletions(-)

* 2013-04-05(Tal Galili) labels assignment operators for matrix added |25d9c1c| 
|  DESCRIPTION          |  8 +++--
|  R/dendextend.r       |  3 ++
|  R/labels.r           | 96 +++++++++++++++++++++++++++++++++++++++++++++++++-
|  dendextend.Rproj     |  1 +
|  man/labels-set.Rd    | 57 ++++++++++++++++++++++++++++++
|  man/labels.matrix.Rd | 47 ++++++++++++++++++++++++
|  6 files changed, 209 insertions(+), 3 deletions(-)

* 2013-04-05(Tal Galili) labels.r added |2e4a497| 
|  R/labels.r | 120 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|  1 file changed, 120 insertions(+)

* 2013-04-05(Tal Galili) minor edit to DESCRIPTION |8479c64| 
|  DESCRIPTION | 2 +-
|  1 file changed, 1 insertion(+), 1 deletion(-)

* 2013-04-05(Tal Galili) Package shell |05eb3f9  
   .Rbuildignore    |  2 ++
   .gitignore       |  3 +++
   DESCRIPTION      |  9 +++++++++
   NAMESPACE        |  1 +
   R/dendextend.r   |  0
   dendextend.Rproj | 16 ++++++++++++++++
   6 files changed, 31 insertions(+)
