Set or get options for FCnet

optionsFCnet(...)

Arguments

family

Defaults to "gaussian." Experimental support for "binomial" on the way.

cv.type.measure

The measure to minimize in crossvalidation inner loops. The deafult is the mean squared error.

cv.criterion

Whether crossvalidated models are chosen on the basis of their error or - relevant when different number of components are compared - AIC or BIC criteria.

intercept

whether to fit (TRUE) or not (FALSE) an intercept to the model. Useful if y is not scaled and centered.

standardize

Whether x must be standardized internally to glmnet::glmnet().

whichLambda

During crossvalidation, either selects "lambda.min" - which chooses the value of lambda which best minimizes the mean crossvalidation error - or "lambda.1se" - which "which gives the most regularized model such that error is within one standard error of the minimum". The latter would be preferable for stability.

thresh

Threshold for glmnet to stop converging to the solution. This parameter can be adapted (e.g. for speed / accuracy tradeoff).

consensus_function

which function is used to create consensus between coefficients from different models.

nested

Whether crossvalidation is to be performed in a nested fashion.

colorPaletteDefault

The default color palette for plotting matrices (a vector of colors).

colorNuances

Number of nuances along the provided colorPalette.