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Triangulated Maximally Filtered Graph (TMFG)

Source: R/tmfg.R
tmfg_network.Rd

Builds a sparse, planar, chordal association network by greedily retaining the 3(p - 2) most informative edges (Massara et al. 2016). Equivalent in purpose to NetworkToolbox::TMFG() / bootnet's "TMFG" default, pure base R; correctness is certified structurally by tmfg_certificate().

Usage

tmfg_network(
  data = NULL,
  cor_matrix = NULL,
  n = NULL,
  cor_method = c("pearson", "spearman", "kendall", "auto"),
  na_method = c("pairwise", "listwise"),
  labels = NULL
)

Arguments

data

Numeric data frame or matrix (rows = observations). Optional if cor_matrix is supplied.

cor_matrix

Optional correlation matrix.

n

Accepted and ignored. TMFG is a structural filter and needs no sample size; the argument exists only so a uniform (cor_matrix=, n=) call shared with the other estimators does not partial-match na_method.

cor_method

Correlation when data is supplied: "pearson" (default), "spearman", "kendall", or "auto" (polychoric/polyserial; see cor_auto()).

na_method

Missing-data handling when data is supplied: "pairwise" (default) or "listwise". See ebic_glasso().

labels

Optional node labels.

Value

A psychnet object whose $weights is the filtered (signed) correlation matrix on the retained edges, with $adjacency, $cliques, $separators (the chordal decomposition used by logo_network()), and $cor_matrix.

Examples

set.seed(1)
x <- matrix(stats::rnorm(200 * 6), 200, 6)
tmfg_network(x)
#> <psychnet> tmfg network
#>   nodes: 6   edges: 12   (undirected)