View source: R/PLNnetworkfamily-S3methods.R
extract_probs | R Documentation |
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.
extract_probs(
Robject,
penalty = NULL,
index = NULL,
crit = c("StARS", "BIC", "EBIC"),
format = c("matrix", "vector"),
tol = 1e-05
)
Robject |
an object with class |
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 |
format |
output format. Either a matrix (default) or a named vector. |
tol |
tolerance for rounding error when comparing penalties. |
Either a matrix or named vector of edge-wise probabilities. In the latter case, edge names follow igraph convention.
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)
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