fixedfill: Extract backbone using the Fixed Fill Model

View source: R/fixedfill.R

fixedfillR Documentation

Extract backbone using the Fixed Fill Model


fixedfill extracts the backbone of a bipartite projection using the Fixed Fill Model.


  alpha = 0.05, = FALSE,
  signed = FALSE,
  mtc = "none",
  class = "original",
  narrative = FALSE



An unweighted bipartite graph, as: (1) an incidence matrix in the form of a matrix or sparse Matrix; (2) an edgelist in the form of a two-column dataframe; (3) an igraph object.


real: significance level of hypothesis test(s)

boolean: should missing edges be treated as edges with zero weight and tested for significance


boolean: TRUE for a signed backbone, FALSE for a binary backbone (see details)


string: type of Multiple Test Correction to be applied; can be any method allowed by p.adjust.


string: the class of the returned backbone graph, one of c("original", "matrix", "Matrix", "igraph", "edgelist"). If "original", the backbone graph returned is of the same class as B.


boolean: TRUE if suggested text & citations should be displayed.


The fixedfill function compares an edge's observed weight in the projection B*t(B) to the distribution of weights expected in a projection obtained from a random bipartite graph where the number of edges present (i.e., the number of cells filled with a 1) is equal to the number of edges in B. When B is large, this function may be impractically slow and may return a backbone object that contains NaN values.

When signed = FALSE, a one-tailed test (is the weight stronger?) is performed for each edge. The resulting backbone contains edges whose weights are significantly stronger than expected in the null model. When signed = TRUE, a two-tailed test (is the weight stronger or weaker?) is performed for each edge. The resulting backbone contains positive edges for those whose weights are significantly stronger, and negative edges for those whose weights are significantly weaker, than expected in the null model.


If alpha != NULL: Binary or signed backbone graph of class class.

If alpha == NULL: An S3 backbone object containing (1) the weighted graph as a matrix, (2) upper-tail p-values as a matrix, (3, if signed = TRUE) lower-tail p-values as a matrix, (4, if present) node attributes as a dataframe, and (5) several properties of the original graph and backbone model, from which a backbone can subsequently be extracted using backbone.extract().


package: Neal, Z. P. (2022). backbone: An R Package to Extract Network Backbones. PLOS ONE, 17, e0269137. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1371/journal.pone.0269137")}

fixedfill: Neal, Z. P., Domagalski, R., and Sagan, B. (2021). Comparing Alternatives to the Fixed Degree Sequence Model for Extracting the Backbone of Bipartite Projections. Scientific Reports, 11, 23929. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41598-021-03238-3")}


#A binary bipartite network of 30 agents & 75 artifacts; agents form three communities
B <- rbind(cbind(matrix(rbinom(250,1,.8),10),

P <- B%*%t(B) #An ordinary weighted projection...
plot(igraph::graph_from_adjacency_matrix(P, mode = "undirected",
                                         weighted = TRUE, diag = FALSE)) a dense hairball

bb <- fixedfill(B, alpha = 0.05, narrative = TRUE, class = "igraph") #A fixedfill backbone...
plot(bb) sparse with clear communities

backbone documentation built on May 29, 2024, 8:03 a.m.