Tables of a simplicial complex

Usage

# S3 method for class 'simplicial_complex'
hg_get(
  x,
  what = c("simplices", "f_vector", "betti", "degree", "validation"),
  ...,
  dimension = NULL,
  normalized = FALSE,
  top = NULL
)

Arguments

x: A simplicial_complex object from simplicial().
what: "simplices" (default) for one row per simplex, "f_vector" for the face counts by dimension, "betti" for the Betti numbers by dimension, "degree" for the simplicial degree of every node (the table of hg_degree()), or "validation" for the tests of a window complex built with validate = TRUE.
...: Additional arguments (ignored).
dimension: Integer or NULL. For what = "simplices": keep only simplices of this dimension (0 vertices, 1 edges, 2 triangles). For what = "validation": keep only the sets of dimension + 1 actions.
normalized: Logical. Only for what = "degree": divide each count by its largest possible value. Default FALSE.
top: Integer or NULL. Return only the first top rows, applied after any filter and after sort_by, so sort_by and top compose. Default NULL returns every row.

Value

A data.frame. For what = "simplices", one row per simplex: simplex (its number), dimension, size, members (the node names, comma separated). For what = "f_vector", one row per dimension: dimension, count. For what = "betti", one row per dimension: dimension, betti (the number of connected parts, loops, voids, ...). For what = "degree", one row per node, most connected first: node, d0, d1, ... and total. For what = "validation", one row per tested set of actions, by size, then p-value, then z: members (the actions, comma separated), size, count (windows with exactly these actions), n_windows (windows with this many distinct actions), expected (the mean count under the null model), z (the count minus expected, in null standard deviations), p_value, p_adj (Benjamini-Hochberg over n_tests possible sets), n_tests, significant.

Examples

adj <- matrix(c(0, 1, 1, 0,
                1, 0, 1, 1,
                1, 1, 0, 1,
                0, 1, 1, 0), 4, 4, dimnames = list(letters[1:4], letters[1:4]))
sc <- simplicial(adj, type = "clique")
hg_get(sc)
#>    simplex dimension size members
#> 1        1         0    1       c
#> 2        2         0    1       b
#> 3        3         1    2    b, c
#> 4        4         0    1       d
#> 5        5         1    2    b, d
#> 6        6         2    3 b, c, d
#> 7        7         1    2    c, d
#> 8        8         0    1       a
#> 9        9         1    2    a, b
#> 10      10         2    3 a, b, c
#> 11      11         1    2    a, c
hg_get(sc, what = "f_vector")
#>   dimension count
#> 1         0     4
#> 2         1     5
#> 3         2     2