getOptInd: get StARS-optimal network

In zdk123/SpiecEasi: Sparse Inverse Covariance for Ecological Statistical Inference

get StARS-optimal network

Description

Get the optimal network, and related structures, when StARS is run.

Usage

getOptInd(est)

getOptLambda(est)

getOptMerge(est)

getStability(est)

getOptNet(est)

getRefit(est)

getOptBeta(est)

getOptCov(est)

getOptiCov(est)

Arguments

est	output from spiec.easi

Details

Use the getter functions to parse spiec.easi output:

• getOptLambda: penalty parameter from provided lambda path

• getOptInd: index of the selected lambda from provided lambda path

• getOptNet / getRefit: the optimal (StARS-refit) network

• getStability: average stability at the selected sparsity

• getOptMerge: symmetric matrix with edge-wise stability

• getOptiCov: the optimal inverse covariance matrix (glasso only)

• getOptCov: the optimal covariance matrix associated with the selected network (glasso only)

• getOptBeta: the optimal coefficient matrix (mb only)

Value

numeric or matrix associated with a StARS solution.

zdk123/SpiecEasi documentation built on Oct. 20, 2023, 6:49 a.m.