R: Compute the stability path by stability selection

stability_selection {PLNmodels}

R Documentation

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(),
  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 `10sqrt(n)` if `n >= 144` and `0.8n` otherwise following Liu et al. (2010) recommendations.
`control`	a list controlling the main optimization process in each call to PLNnetwork. See `PLNnetwork()` for details.
`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

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)

## End(Not run)

[Package PLNmodels version 0.11.4 Index]