Discussion: cleaning up master branch

[Xinqiu Yao]

Following files are subject to deletion or moving. Let me know what you think:

1. unlist2.R -> delete. Find alternative way to do the same task.
2. dccm.mean.R -> merge to filter.dccm.R

[Lars Skjærven]

atom2ele is in use in atom2mass. usage is:

> atom.names <- c("CA", "O", "N", "OXT")
> atom2ele(atom.names)
[1] "C" "O" "N" "O"

We could in principle to try to hide it under atom2mass, but I would rather have it open and available

[Xinqiu Yao]

Okay, we should keep it.

[Barry Grant]

unlist2() can be removed - see comment although not yet tested/committed.

atom2ele() should be kept.

cmap.filter() can probably just be kept for now - I am agnostic about this.

[Xinqiu Yao]

Right. I misunderstood the purpose of cmap.filter. We can probably merge dccm.mean with filter.dccm, which basically do very similar task. The contents of this issue will be updated

[Barry Grant]

Sounds good, should we call it dccm.filter() then to math the others? I know you don't like [dots] and we have S3 concerns but this does make sense to me.

[Xinqiu Yao]

I have no problem to change the name but I concern it will affect the CNA vignette we just submitted. Is it better to change the name at some later stage?

[Barry Grant]

Good point, lets keep the name from the vignette and mark for later re-naming.

[Xinqiu Yao]

Resolved with recent commits. Function renaming is added to the to-do list.