[Enhancement] Remove the include.always variable from the image(obj) function

[AlexanderLyNL]

Hi Merlise,

Would it be possible to remove the variables that are "include.always" from the plotting output:

• plot(obj) [in particular, the Inclusion Probabilities plot]
• image(obj)
  I think that this might be sensible. By removing the include.always variables, there's more space to display the effects of the variables that are of interest, and it might save some space for memory as well.

Cheers,
Alexander

[merliseclyde]

Yes; there is a subset option for image to specify which variables to include, so in principle we can bootstrap off of that rather easily. plot.bas does not have that option, but a similar fix should be straightforward there.

I'll probably need to add an option to save the indices of the variables that are always included as part of the output to simplify identifying them later. (needed as well for the flat prior and shrinkage in issue #22 )

[merliseclyde]

This is added to image.bas now in the master branch, using option drop.include.always=TRUE (default). Feedback welcome!

[merliseclyde]

Update: switched drop.always.included to be FALSE by default in image.bas so that defaults agree with images in Coursera course.

added subset=NULL and drop.always.included=FALSE to plot.bas so that a subset of probabilities may be shown/dropped or variables that are always forced in may be excluded. Default settings agree with what is in Coursera course.