dendro is an experimental package I wrote to play around with tree structures and the new (as of this writing) S7 class system. It’s not intended for serious workloads, but rather as a way for me to kick the wheels on S7 and toy with recursive operations.
You can install the development version of dendro like so:
# install.packages("remotes")
remotes::install_github("RConsortium/OOP-WG")
remotes::install_github("mikemahoney218/dendro")The core of the dendro package lives in two S7 classes, node() and
tree(). The node class has four slots: the index value of the node
within the tree, the index of the node’s parent, and the index of any
children the node has, as well as a list slot for any attributes you
want to attach to the node:
library(dendro)
#>
#> Attaching package: 'dendro'
#> The following object is masked from 'package:base':
#>
#> @
node(
index = 1L,
value = list(),
parent = 0L,
children = 2L
)
#> <dendro::node>
#> @ index : int 1
#> @ value : list()
#> @ parent : int 0
#> @ children: int 2Nodes are almost entirely unvalidated – there’s no requirement a parent knows about all its children, that a node’s parent exists, that the node’s index is unique, or that its index corresponds to its location in a tree. Node-creating code is responsible for those validations.
The tree class is slightly more interesting. Its constructor function takes a list of nodes:
tree(list(node(1L)))
#> <dendro::tree>
#> @ size : int 1
#> @ node_indices: int 1
#> @ next_idx : int 2
#> @ root : int 1
#> @ nodes :List of 1
#> .. $ : <dendro::node>
#> .. ..@ index : int 1
#> .. ..@ value : list()
#> .. ..@ parent : int(0)
#> .. ..@ children: int(0)The tree class also doesn’t do a ton of validation; it only checks to
make sure that every node (save for one, the root node) has a parent.
However, this class also comes with a few useful dynamic slots: size,
the number of nodes in the tree; node_indices, a vector of all index
values in the nodes list; next_idx, a safe position for the next node
to be inserted at, and root, the index of the root node in the nodes
list.
There’s also a handful of methods defined for tree classes. For
instance, add_node() will automatically add a node at the next
available index, for programmatic tree construction:
example_tree <- tree() |>
add_node(name = "root") |>
add_node(list(), parent = 1L) |>
add_node(list(), parent = 1L) |>
add_node(list(), parent = 2L) |>
add_node(list(), parent = 4L)
example_tree
#> <dendro::tree>
#> @ size : int 5
#> @ node_indices: Named int [1:5] 1 2 3 4 5
#> .. - attr(*, "names")= chr [1:5] "root" "" "" "" ...
#> @ next_idx : int 6
#> @ root : Named int 1
#> .. - attr(*, "names")= chr "root"
#> @ nodes :List of 5
#> .. $ root: <dendro::node>
#> .. ..@ index : int 1
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int NA
#> .. ..@ children: int [1:2] 2 3
#> .. $ : <dendro::node>
#> .. ..@ index : int 2
#> .. ..@ value : list()
#> .. ..@ parent : int 1
#> .. ..@ children: int 4
#> .. $ : <dendro::node>
#> .. ..@ index : int 3
#> .. ..@ value : list()
#> .. ..@ parent : int 1
#> .. ..@ children: int(0)
#> .. $ : <dendro::node>
#> .. ..@ index : int 4
#> .. ..@ value : list()
#> .. ..@ parent : int 2
#> .. ..@ children: int 5
#> .. $ : <dendro::node>
#> .. ..@ index : int 5
#> .. ..@ value : list()
#> .. ..@ parent : int 4
#> .. ..@ children: int(0)Note that add_node() is relatively slow, as the tree is re-validated
after each call to add_node(). To make an entirely new tree from
scratch, it’s usually faster to call tree() with a list of nodes
instead.
You can call drop_node() to drop nodes from the tree. Note that all
descendants of the node will be dropped as well, as dendro doesn’t allow
multiple roots in a tree:
example_tree |>
drop_node(1)
#> <dendro::tree>
#> @ size : int 0
#> @ node_indices: NULL
#> @ next_idx : int 1
#> @ root : int NA
#> @ nodes : Named list()# Get the depth of a node in the tree
example_tree |>
node_depth(5)
#> [1] 4
# Get the distance between two nodes in the tree
example_tree |>
distance_to_target(1, 5)
#> [1] 3
# Get the indices of the children for a node
example_tree |>
get_children(1)
#> [1] 2 3
# Get the indices of _all_ descendants for a node
example_tree |>
get_all_descendants(1)
#> [1] 1 2 3 4 5
# Get node objects from a tree
example_tree |>
get_nodes(1)
#> $root
#> <dendro::node>
#> @ index : int 1
#> @ value :'data.frame': 0 obs. of 0 variables
#> @ parent : int NA
#> @ children: int [1:2] 2 3
# Get the value slot of a node object from a tree
example_tree |>
get_node_values(1)
#> $root
#> data frame with 0 columns and 0 rowsThere’s also a function, as_tree, for converting data frames to tree
formats:
data.frame(x = letters[1:4], y = letters[25:26]) |>
as_tree(c("x", "y"), root_name = "root")
#> <dendro::tree>
#> @ size : int 9
#> @ node_indices: Named int [1:9] 1 2 3 4 5 6 7 8 9
#> .. - attr(*, "names")= chr [1:9] "root" "a" "y" "b" ...
#> @ next_idx : int 10
#> @ root : Named int 1
#> .. - attr(*, "names")= chr "root"
#> @ nodes :List of 9
#> .. $ root: <dendro::node>
#> .. ..@ index : int 1
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int NA
#> .. ..@ children: Named int [1:4] 2 4 6 8
#> .. .. .. - attr(*, "names")= chr [1:4] "a" "b" "c" "d"
#> .. $ a : <dendro::node>
#> .. ..@ index : int 2
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int 1
#> .. ..@ children: Named int 3
#> .. .. .. - attr(*, "names")= chr "y"
#> .. $ y : <dendro::node>
#> .. ..@ index : int 3
#> .. ..@ value :'data.frame': 1 obs. of 0 variables
#> .. ..@ parent : int 2
#> .. ..@ children: int(0)
#> .. $ b : <dendro::node>
#> .. ..@ index : int 4
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int 1
#> .. ..@ children: Named int 5
#> .. .. .. - attr(*, "names")= chr "z"
#> .. $ z : <dendro::node>
#> .. ..@ index : int 5
#> .. ..@ value :'data.frame': 1 obs. of 0 variables
#> .. ..@ parent : int 4
#> .. ..@ children: int(0)
#> .. $ c : <dendro::node>
#> .. ..@ index : int 6
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int 1
#> .. ..@ children: Named int 7
#> .. .. .. - attr(*, "names")= chr "y"
#> .. $ y : <dendro::node>
#> .. ..@ index : int 7
#> .. ..@ value :'data.frame': 1 obs. of 0 variables
#> .. ..@ parent : int 6
#> .. ..@ children: int(0)
#> .. $ d : <dendro::node>
#> .. ..@ index : int 8
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int 1
#> .. ..@ children: Named int 9
#> .. .. .. - attr(*, "names")= chr "z"
#> .. $ z : <dendro::node>
#> .. ..@ index : int 9
#> .. ..@ value :'data.frame': 1 obs. of 0 variables
#> .. ..@ parent : int 8
#> .. ..@ children: int(0)
data.frame(x = letters[1:4], y = letters[25:26]) |>
as_tree(c("y", "x"), root_name = "root")
#> <dendro::tree>
#> @ size : int 7
#> @ node_indices: Named int [1:7] 1 2 3 4 5 6 7
#> .. - attr(*, "names")= chr [1:7] "root" "y" "a" "c" ...
#> @ next_idx : int 8
#> @ root : Named int 1
#> .. - attr(*, "names")= chr "root"
#> @ nodes :List of 7
#> .. $ root: <dendro::node>
#> .. ..@ index : int 1
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int NA
#> .. ..@ children: Named int [1:2] 2 5
#> .. .. .. - attr(*, "names")= chr [1:2] "y" "z"
#> .. $ y : <dendro::node>
#> .. ..@ index : int 2
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int 1
#> .. ..@ children: Named int [1:2] 3 4
#> .. .. .. - attr(*, "names")= chr [1:2] "a" "c"
#> .. $ a : <dendro::node>
#> .. ..@ index : int 3
#> .. ..@ value :'data.frame': 1 obs. of 0 variables
#> .. ..@ parent : int 2
#> .. ..@ children: int(0)
#> .. $ c : <dendro::node>
#> .. ..@ index : int 4
#> .. ..@ value :'data.frame': 1 obs. of 0 variables
#> .. ..@ parent : int 2
#> .. ..@ children: int(0)
#> .. $ z : <dendro::node>
#> .. ..@ index : int 5
#> .. ..@ value :'data.frame': 0 obs. of 0 variables
#> .. ..@ parent : int 1
#> .. ..@ children: Named int [1:2] 6 7
#> .. .. .. - attr(*, "names")= chr [1:2] "b" "d"
#> .. $ b : <dendro::node>
#> .. ..@ index : int 6
#> .. ..@ value :'data.frame': 1 obs. of 0 variables
#> .. ..@ parent : int 5
#> .. ..@ children: int(0)
#> .. $ d : <dendro::node>
#> .. ..@ index : int 7
#> .. ..@ value :'data.frame': 1 obs. of 0 variables
#> .. ..@ parent : int 5
#> .. ..@ children: int(0)