Description Usage Arguments Value Author(s)
Fit a generalized linear model at grids of tuning parameter via penalized maximum likelihood. The regularization path is computed for a combination of sparse and smoothness penalty. The sparse penalty is MCP penalty and phylogeny-constraint smoothness penalty is derived from the phylogeny-induced correlation structure (C) based on patristic distance between OTU (D) in the form of C=exp(-2*pho*D). pho characterizes the evolutionary rate and performs phylogenetic grouping. Large pho groups OTUs into clusters at lower phylogenetic depth. The phylogeny-constraint smoothness penalty is in the form of beta^T*C^-1*beta. It has the advantage to encourage local smoothing by reducing the effects of distant OTUs. The estimator is called Sparse Inverse Correlation Srinkage Estimator (SICS).
1 |
X |
Input matrix; each row is an observation vector. |
Y |
Response vector. Quantitative for |
D |
patristic distance between OTU. |
family |
Either "gaussian", "binomial", depending on the response. |
pho |
A user-specified sequence of |
lambda2 |
A user-specified sequence of |
nfolds |
folds to perform cross-validation. Default value is 5. |
beta |
A vector of fitted coefficients not include intercept |
Li Chen <li.chen@auburn.edu>, Jun Chen <chen.jun2@mayo.edu>
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