PLNmodels (version 0.9.5)

stability_selection: Compute the stability path by stability selection

Description

This function computes the StARS stability criteria over a path of penalties. If a path has already been computed, the functions stops with a message unless force = TRUE has been specified.

Usage

stability_selection(
  Robject,
  subsamples = NULL,
  control = list(),
  mc.cores = 1,
  force = FALSE
)

Arguments

Robject

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

subsamples

a list of vectors describing the subsamples. The number of vectors (or list length) determines th number of subsamples used in the stability selection. Automatically set to 20 subsamples with size 10*sqrt(n) if n >= 144 and 0.8*n otherwise following Liu et al. (2010) recommandations.

control

a list controling the main optimization process in each call to PLNnetwork. See PLNnetwork for details.

mc.cores

the number of cores to used. Default is 1.

force

force computation of the stability path, even if a previous one has been detected.

Value

the list of subsamples. The estimated probabilities of selection of the edges are stored in the fields stability_path of the initial Robject with class PLNnetworkfamily

Examples

# NOT RUN {
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
# }
# NOT RUN {
n <- nrow(trichoptera)
subs <- replicate(10, sample.int(n, size = n/2), simplify = FALSE)
stability_selection(nets, subsamples = subs)
# }