%>%                     Pipe an object forward into a function
                        call/expression.
Bk                      Bk - Calculating Fowlkes-Mallows Index for two
                        dendrogram
Bk_permutations         Bk permutation - Calculating Fowlkes-Mallows
                        Index for two dendrogram
Bk_plot                 Bk plot - ploting the Fowlkes-Mallows Index of
                        two dendrogram for various k's
DendSer.dendrogram      Tries to run DendSer on a dendrogram
FM_index                Calculating Fowlkes-Mallows Index
FM_index_R              Calculating Fowlkes-Mallows index in R
FM_index_permutation    Calculating Fowlkes-Mallows Index under H0
FM_index_profdpm        Calculating Fowlkes-Mallows index using the
                        profdpm R package
all.equal.dendrogram    Global Comparison of two (or more) dendrograms
all_couple_rotations_at_k
                        Rotate tree branches for k
all_unique              Check if all the elements in a vector are
                        unique
as.dendlist             Try to coerce something into a dendlist
as.phylo.dendrogram     Convert a dendrogram into phylo
as_hclust_fixed         Convert dendrogram Objects to Class hclust
assign_dendextend_options
                        Populates dendextend functions into
                        dendextend_options
assign_values_to_branches_edgePar
                        Assign values to edgePar of dendrogram's
                        branches
assign_values_to_leaves_edgePar
                        Assign values to edgePar of dendrogram's leaves
assign_values_to_leaves_nodePar
                        Assign values to nodePar of dendrogram's leaves
assign_values_to_nodes_nodePar
                        Assign values to nodePar of dendrogram's nodes
bakers_gamma_for_2_k_matrix
                        Bakers Gamma for two k matrices
branches_attr_by_clusters
                        Change col/lwd/lty of branches based on
                        clusters
branches_attr_by_labels
                        Change col/lwd/lty of branches matching labels
                        condition
circlize_dendrogram     Plot a circlized dendrograms
click_rotate            Interactively rotate a tree object
collapse_branch         Collapse branches under a tolerance level
color_branches          Color tree's branches according to sub-clusters
color_labels            Color dend's labels according to sub-clusters
colored_bars            Add colored bars to a dendrogram
common_subtrees_clusters
                        Find clusters of common subtrees
cor.dendlist            Correlation matrix between a list of trees.
cor_FM_index            Correlation of FM_index for some k
cor_bakers_gamma        Baker's Gamma correlation coefficient
cor_common_nodes        Proportion of commong nodes between two trees
cor_cophenetic          Cophenetic correlation between two trees
count_terminal_nodes    Counts the number of terminal nodes (merging 0
                        nodes!)
cut_lower_fun           Cut a dendrogram - and run a function on the
                        output
cutree                  Cut a Tree (Dendrogram/hclust/phylo) into
                        Groups of Data
cutree_1h.dendrogram    cutree for dendrogram (by 1 height only!)
cutree_1k.dendrogram    cutree for dendrogram (by 1 k value only!)
d3dendro_options        Get or set current defaults for d3dendrogram
d3dendrogram            Plot dendrogram to webpage and view.
dend_diff               Plots two trees side by side, highlighting
                        edges unique to each tree in red.
dendextend-package      Functions for extending dendrogram objects
dendextend_labels.dendrogram
                        Labels of the Leaves in a Dendrogram
dendextend_options      Access to dendextend_options
dendlist                Creating a dendlist object from several
                        dendrograms
dist.dendlist           Topological Distances Between Two dendrograms
dist_long               Turns a dist object to a "long" table
distinct_edges          Finds the edges present in the first tree but
                        not in the second
duplicate_leaf          Duplicate a leaf X times
entanglement            Measures entanglement between two trees
fac2num                 Turns a factor into a number
fix_members_attr.dendrogram
                        Fix members attr in a dendrogram
flatten.dendrogram      Flatten the branches of a dendrogram's root
flip_leaves             Flip leaves
get_branches_heights    Get height attributes from a dendrogram
get_childrens_heights   Get height attributes from a dendrogram's
                        children
get_leaves_attr         Get/set attributes 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
get_leaves_edgePar      Get edgePar of dendrogram's leaves
get_leaves_nodePar      Get nodePar of dendrogram's leaves
get_nodes_attr          Get attributes of dendrogram's nodes
get_nodes_xy            Get the x-y coordiantes of a dendrogram's nodes
get_root_branches_attr
                        get attributes from the dendrogram's root(!)
                        branches
ggdend                  Creates dendrogram plot using ggplot.
hang.dendrogram         Hang dendrogram leaves
heights_per_k.dendrogram
                        Which height will result in which k for a
                        dendrogram
highlight_distinct_edges
                        Highlight distint edges in a tree (compared to
                        another one)
identify.dendrogram     Identify Clusters in a Dendrogram (not hclust)
intersect_trees         Intersect trees
is.dendlist             Checks if an object is of class dendlist
is.dendrogram           Is the object of class dendrogram
is.hclust               Is the object of class hclust
is.natural.number       Check if numbers are natural
is.phylo                Is the object of class phylo
is_null_list            Checks if the value is and empty list()
khan                    Microarray gene expression dataset from Khan et
                        al., 2001. Subset of 306 genes.
labels<-                "label" assignment operator
labels_cex              Retrieve/assign cex to the labels of a
                        dendrogram
labels_colors           Retrieve/assign colors to the labels of a
                        dendrogram
ladderize               Ladderize a Tree
leaf_Colors             Return the leaf Colors of a dendrogram
lowest_common_branch    Find lowest common branch were the two items
                        are shared
match_order_by_labels   Adjust the order of one dendrogram based on
                        another (using labels)
match_order_dendrogram_by_old_order
                        Adjust the order of one dendrogram based on
                        another (using order)
na_locf                 Last Observation Carried Forward
nleaves                 Counts the number of leaves in a tree
nnodes                  Counts the number of nodes (Vertices) in a tree
noded_with_condition    Find which nodes satisfies a condition
order.dendrogram<-      order.dendrogram<- assignment operator
order.hclust            Ordering of the Leaves in a hclust Dendrogram
partition_leaves        A list with labels for each subtree (edge)
plot_horiz.dendrogram   Plotting a left-tip-adjusted horizontal
                        dendrogram
prune                   Prunes a tree (using leaves' labels)
prune_common_subtrees.dendlist
                        Prune trees to their common subtrees
prune_leaf              Trimms one leaf from a dendrogram
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
raise.dendrogram        Raise the height of a dendrogram tree
rank_branches           Rank branches' heights
rank_order.dendrogram   Fix rank of leaves order values in a dendrogram
rank_values_with_clusters
                        Rank a vector based on clusters
rect.dendrogram         Draw Rectangles Around a Dendrogram's Clusters
remove_branches_edgePar
                        Remove all edgePar values from a dendrogram's
                        branches
remove_leaves_nodePar   Remove all nodePar values from a dendrogram's
                        leaves
remove_nodes_nodePar    Remove all nodePar values from a dendrogram's
                        nodes
rllply                  recursivly apply a function on a list
rotate                  Rotate a tree object
rotate_DendSer          Rotates dend based on DendSer
sample.dendrogram       Sample a tree
set                     Set (/update) features to a dendrogram
shuffle                 Random rotation of trees
sort_2_clusters_vectors
                        Sorts two clusters vector by their names
sort_dist_mat           Sorts a distance matrix by rows and columns
sort_levels_values      Sort the values level in a vector
tanglegram              Tanglegram plot
theme_dendro            Creates completely blank theme in ggplot
unbranch                unbranch trees
unclass_dend            unclass an entire dendrogram tree
untangle                untangle dendrograms
untangle_DendSer        Tries to run DendSer on a dendrogram
untangle_random_search
                        Untangle - random search
untangle_step_rotate_1side
                        Stepwise untangle one tree compared to another
untangle_step_rotate_2side
                        Stepwise untangle two trees one at a time
which_leaf              Which node is a leaf?
which_node              Which node id is common to a group of labels
