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(),
      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) recommendations.
`control` | a list controlling 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

    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 0.10.6 Index]