backbone (version 1.2.2)

universal: Compute universal threshold backbone

Description

`universal` returns a backbone graph in which edge weights are set to 1 if above the given upper parameter threshold, set to -1 if below the given lower parameter threshold, and are 0 otherwise.

Usage

universal(M, upper = NULL, lower = NULL, bipartite = NULL, narrative = FALSE)

Arguments

M

graph: Bipartite graph object of class matrix, sparse matrix, igraph, edgelist, or network object.

upper

Real, FUN, or NULL: upper threshold value or function to be applied to the edge weights. Default is NULL.

lower

Real, FUN, or NULL: lower threshold value or function to be applied to the edge weights. Default is NULL.

bipartite

Boolean: TRUE if bipartite matrix, FALSE if weighted matrix. Default is NULL.

narrative

Boolean: TRUE if suggested text for a manuscript is to be returned

Value

backbone, a list(backbone, summary). The `backbone` object is a graph object of the same class as M. The `summary` contains a data frame summary of the inputted matrix and the model used including: model name, number of rows, skew of row sums, number of columns, skew of column sums, and running time.

Details

If both `upper` and `lower` are `NULL`, a weighted projection is returned.

If `bipartite` is `NULL`, the function tries to guess at whether the data is bipartite or unipartite based on its shape.

Examples

# NOT RUN {
test <- universal(davis%*%t(davis), upper = function(x)mean(x)+sd(x), lower=function(x)mean(x))
test2 <- universal(davis, upper = function(x)mean(x)+2*sd(x), lower = 2, bipartite = TRUE)
test3 <- universal(davis, upper = 4, lower = 2, bipartite = TRUE)
# }