Reduce usage of default argument values

[xtrojak]

The default argument values were pretty messy and used in many top and low-level functions. In #162 we decided to keep them only on top-level unsupervised and hybrid functions and eliminate all the rest.

Part of #159 and #53.
Close #162.

[hechth]

@xtrojak the CI is failing since the code for the examples also relied on the default values

> ### ** Examples
> 
> data(prof)
> this.feature<-prof.to.features(prof[[1]])

So seems like we have to pass those values now in the examples.

[xtrojak]

@xtrojak the CI is failing since the code for the examples also relied on the default values

> ### ** Examples
> 
> data(prof)
> this.feature<-prof.to.features(prof[[1]])

So seems like we have to pass those values now in the examples.

Thank you, @hechth. Actually, I noticed there is bunch of outdated .Rd files that do not correspond to any functions. Some of them also contained examples. I removed them in e25c165.

[hechth]

@xtrojak with the CI taking so long maybe it is time to implement it a bit differently in the future.