Open erfanshekarriz opened 1 year ago
Nevermind!
I seem to have found it.
ranks <- round(exp(seq(log(2), log(32), len=6)))
se.slr <- spiec.easi(phy_taxfilt, method='slr', nlambda=50,
lambda.min.ratio=1e-2, r=ranks, lambda.log=TRUE,
pulsar.params=list(ncores=32, rep.num=30))
se.slr$ebic <- sapply(se.slr, function(x)
ebic(x$refit$stars, x$est$data,
x$est$loglik[x$select$stars$opt.index]))
Please correct me if I'm wrong, but I assume the model with the lowest eBIC is the best to go with.
Thanks for the awesome package!
Erfan
That's correct. I'll add docs for this.
Dear Zachary, I hope all is well.
I wanted to inquire about your pre-print and the beta/rank penalty parameter tuning for model selection.
Specifically in your manuscript, you've written :
I understand what you mean, but can't seem to find the "rank"-path in the SE object. A reviewer has asked me to at minimum undergo the same model selection using the extended Bayesian Information Criterion (eBIC) for my final revision, and your help would be most appreciated.
Is there a piece of code you could provide to select the optimal rank?
Best,
Erfan