Description Usage Arguments Details
View source: R/scca_compute_tree.R
See scca_compute
for description
1 2 3 4 5 6 7 8 9 10 11 12 13 | scca_compute_tree(
labels,
m,
child,
depth,
max_depth,
n_node,
iter.max = 10,
nstart = 50,
max_eigenvalues = max_eigenvalues,
decomp = "svd",
heuristic = eigengap_heuristic
)
|
labels |
The labels (character vector) defining the (sub-)set of data set m to be analyzed |
m |
A matrix representing a bi-partite network. The matrix must have row names and column names. |
child |
The child number of this node within its siblings (= nodes with same parent) |
depth |
The depth (integer) of this node in the tree. |
max_depth |
The maximum allowed depth of the analysis proces. If Inf (default) the analysis goes on untill a stop condition has been met. |
n_node |
Number of the node in the tree. This is a depth-first, pre-order numbering, starting with 1 at the top node (a.k.a. root) |
iter.max |
The maximum number of iterations kmeans is allowed to make. Default is 10. |
nstart |
Number of random cluster sets kmeans may choose to start with. Default is 25. |
max_eigenvalues |
Restrict the number of computed eigenvalues to max_eigenvalues. The default is 25. |
decomp |
The decomposition function to use. Choices are svd (default) and svd |
heuristic |
The function to use for calculating the number of clusters. The default is eigengap_heuristic |
Function scca_compute_tree calls itself recursively for every sub cluster found at a node until one of the stop conditions is met:
The heuristic finds only one prominent eigenvalue (k = 1)
The maximum depth in a branch has been reached. k will be set to 0
The number of observations in the subset is too small to perform svd(s). This will raise a warning and k will be set to -1
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