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FAQ

Is pyhuge 0.3 pure Python?

Yes. pyhuge 0.3 is native Python and does not require rpy2.

runtime=False in pyhuge.test() means what?

Usually at least one core dependency is missing:

  • numpy
  • scipy
  • pyhuge._native_core (native extension)

Install with:

pip install "pyhuge[runtime]"

Which method should I start with?

Use method="mb" first. Then compare with method="glasso".

Difference between fit.path and sel.refit?

  • fit.path: full path of estimated graphs
  • sel.refit: single selected graph under criterion (ric, stars, ebic)

Which selection criterion should I use?

  • ric: fast and simple
  • stars: stability-focused, slower
  • ebic: common for glasso

Why is plotting failing?

Install visualization deps:

pip install "pyhuge[viz]"

In headless environments:

export MPLBACKEND=Agg

Can input be covariance/correlation matrix?

Yes. For ct and glasso, huge(...) accepts square covariance/correlation input. For mb and tiger, use raw data matrix (n x d).

Is there a built-in dataset?

Yes:

from pyhuge import huge_stockdata
stock = huge_stockdata()
print(stock.data.shape, stock.info.shape)

Where are full function docs?