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stefpeschel / NetCoMi

Network construction, analysis, and comparison for microbial compositional data
GNU General Public License v3.0
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stability values using spieceasi #108

Closed lixiaopi1985 closed 7 months ago

lixiaopi1985 commented 10 months ago

Hi Stef,

Thank you for the package. I have a quick question.

One of the reviewers inquired about the stability values using the spieceasi algorithm. I wondered if these values were stored in the netConstruct outputs?

The code involved:

 NetCoMi::netConstruct(data, 
                                   normMethod = "clr", 
                                   zeroMethod = "multRepl", 
                                   sparsMethod = "none", 
                                   filtTax = "highestFreq",
                                   filtTaxPar = list(highestFreq=150),
                                   measure = "spieceasi",
                                   measurePar = list(pulsar.params = list(rep.num=50), nlambda = 50, lambda.min.ratio=1e-2),
                                   # thresh = cor_thresh, 
                                   verbose = 3)

Best, Xiaoping

stefpeschel commented 8 months ago

Hi, Sorry for the late reply. No, the SpiecEasi output is currently not stored and returned by netConstruct(). But I will consider including it into the output in a future version.