R: Extract edge selection frequency in bootstrap subsamples

extract_probs {PLNmodels} | R Documentation

## 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
    )

### 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.

### Value

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

### Examples

    data(trichoptera)
    trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
    nets <- PLNnetwork(Abundance ~ 1 + offset(log(Offset)), data = trichoptera)
    ## Not run:
    stability_selection(nets)
    probs <- extract_probs(nets, crit = "StARS", format = "vector")
    probs

    ## End(Not run)

    ## Not run:
    ## 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

    ## End(Not run)

[Package PLNmodels version 0.11.4 Index]