Description Usage Arguments Details Author(s) See Also Examples
Given alpha
, this function generates a plot of the quality (objective) function across lambda
, which is useful to examine how was the "best lambda
" value selected.
1 2 3 
x 

alpha.index 
Integer indices to select 
xlab 
Custom xaxis label. 
ylab 
Custom yaxis label. 
cex.lab 
Axis label size. 
main 
Custom title. 
col.main 
Title color. 
cex.main 
Title size. 
log 
Log scale axis. 
type 
Plot type. 
... 
Additional plotting parameters. 
By definition, the "best lambda
" value for a given alpha
is the one that maximizes the quality function (QF) over the range of lambda
values considered. Therefore, QF vs lambda
distributions with sharp, narrow, welldefined peaks provide more confidence in the selection of the optimal lambda
value than those with lessdefined peaks. Sometimes, and particularly for the ridge (alpha
=0) solutions, QF is observed to increase or decrease monotonically with lambda
over its entire range, causing a boundary lambda
value to be selected;
we conservatively recommend to disregard alpha
models generated under such circumstances. If interested in investigating further, we suggest to rerun those alpha
models by extending the default range of lambda
values (via the argument nlambda.ext
) or its density (via the argument nlambda
). On occasion, the range of lambda
values is effectively limited by convergence issues of the underlying glmnet
model; in such scenario, we recommend to increment the maximum allowed number of iterations (via the argument mxit
, which is passed on to glmnet.control
) or to limit the complexity of the model (e.g. by filtering and reducing the number of features fed into eNetXplorer
).
Julian Candia and John S. Tsang
Maintainer: Julian Candia julian.candia@nih.gov
1 2 3 4 5  data(QuickStartEx)
fit = eNetXplorer(x=QuickStartEx$predictor,y=QuickStartEx$response,
family="gaussian",n_run=20,n_perm_null=10,seed=111)
plot(x=fit,plot.type="lambdaVsQF")
plotLambdaVsQF(x=fit,alpha.index=c(1,3),main="custom title",col.main="red")

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