PLNmodels (version 0.11.7)

extract_probs: Extract edge selection frequency in bootstrap subsamples

Description

Extracts edge selection frequency in networks reconstructed from bootstrap subsamples during the stars stability selection procedure, as either a matrix or a named vector. In the latter case, edge names follow igraph naming convention.

Usage

extract_probs(
  Robject,
  penalty = NULL,
  index = NULL,
  crit = c("StARS", "BIC", "EBIC"),
  format = c("matrix", "vector"),
  tol = 1e-05
)

Value

Either a matrix or named vector of edge-wise probabilities. In the latter case, edge names follow igraph convention.

Arguments

Robject

an object with class PLNnetworkfamily, i.e. an output from PLNnetwork()

penalty

penalty used for the bootstrap subsamples

index

Integer index of the model to be returned. Only the first value is taken into account.

crit

a character for the criterion used to performed the selection. Either "BIC", "ICL", "EBIC", "StARS", "R_squared". Default is ICL for PLNPCA, and BIC for PLNnetwork. If StARS (Stability Approach to Regularization Selection) is chosen and stability selection was not yet performed, the function will call the method stability_selection() with default argument.

format

output format. Either a matrix (default) or a named vector.

tol

tolerance for rounding error when comparing penalties.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
nets <- PLNnetwork(Abundance ~ 1 + offset(log(Offset)), data = trichoptera)
if (FALSE) {
stability_selection(nets)
probs <- extract_probs(nets, crit = "StARS", format = "vector")
probs
}

if (FALSE) {
## Add edge attributes to graph using igraph
net_stars <- getBestModel(nets, "StARS")
g <- plot(net_stars, type = "partial_cor", plot=F)
library(igraph)
E(g)$prob <- probs[as_ids(E(g))]
g
}