scca_compute_tree: Build recursively a scca tree

Description Usage Arguments Details

View source: R/scca_compute_tree.R

Description

See scca_compute for description

Usage

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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
)

Arguments

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

Details

Function scca_compute_tree calls itself recursively for every sub cluster found at a node until one of the stop conditions is met:


UtrechtUniversity/SCCA documentation built on April 16, 2021, 3:23 a.m.