GQTSOM: Train a Growing Quadtree Self-Organizing Map

Description

Train a Growing Quadtree Self-Organizing Map

Usage

GQTSOM(
  data,
  init.dim = c(3, 3),
  target_codes = 100,
  rlen = 10,
  radius = c(sqrt(sum(init.dim^2)), 0.5),
  epochRadii = seq(radius[1], radius[2], length.out = rlen),
  coords = NULL,
  codes = NULL,
  coordsFn = NULL,
  importance = NULL,
  distf = 2,
  nhbr.distf = 2,
  noMapping = F,
  parallel = F,
  threads = if (parallel) 0 else 1
)

Arguments

data: Input data matrix
init.dim: Initial size of the SOM, default c(3,3)
target_codes: Make the SOM grow linearly to at most this amount of nodes (default 100)
rlen: Number of training iterations
radius: Start and end training radius, as in SOM()
epochRadii: Precise radii for each epoch (must be of length rlen)
coords: Quadtree coordinates of the initial SOM nodes.
codes: Initial codebook
coordsFn: Function to generate/transform grid coordinates (e.g. tSNECoords()). If NULL (default), the grid is the grid is the 2D coordinates of GQTSOM map.
importance: Weights of input data dimensions
distf: Distance measure to use in input data space (1=manhattan, 2=euclidean, 3=chebyshev, 4=cosine)
nhbr.distf: Distance measure to use in output space (as in distf)
noMapping: If TRUE, do not compute the assignment of input data to SOM nodes
parallel: Parallelize the training by setting appropriate threads. Defaults to FALSE.
threads: Number of threads to use for training. Defaults to 0 (chooses maximum available hardware threads) if parallel=TRUE or 1 (single thread) if parallel=FALSE.