SpiecEasi R package, says in his package that this is "a reimplementation of SparCC algorithm (Friedman et Alm, PLoS Comp Bio, 2012)." Installation of SpiecEasi can sometimes generate errors, so I have included Dr. Huaying Fang's sparcc wrapper as one of the functions in this package for the estimation of co-abundance networks. His code was acquired from CCLasso (Fang et al, Bioinformatics, 2015), provided in GitHub (https://github.com/huayingfang/CCLasso).
sparcc(x, imax = 20, kmax = 10, alpha = 0.1, Vmin = 1e-04)This will estimate an association matrix (network) for observed OTU table.
count data matrix (OTU table)
Number of iterations in the outer loop
max iteration steps for SparCC
threshold for strong correlation
absolute value of correlations below this threshold are considered zero by the inner SparCC loop.