[R-package] refactor and improvements to lgb.convert() functions (fixes #2678, #2681)

[jameslamb]

This PR fixes #2678 and #2681 by adding the following improvements to lgb.convert() functions:

• lgb.convert():
  • now fills in missing values in factor and character columns with 0
• lgb.convert_with_rules():
  • rules no longer contains rules where the "name" in the rule is a missing value
• both:
  • now converts logical columns to integer, filling in missing values with -1
  • now warns if any columns remain which are not numeric or integer
  • moved code for getting column classes into shared internal function to reduce duplication
  • changed from inherits(data, "data.table") to data.table::is.data.table()
  • moved error handling up to the beginning of the functions
  • clarified documentation

Question for reviewers

@Laurae2 @guolinke could we remove lgb.convert() and just offer lgb.convert_with_rules()? Using lgb.convert_with_rules() without passing your own rules (the default), has identical behavior to lgb.convert() and is better because it returns the rules on how columns were changed, which improves reproducibility. Since we're considering a 3.0.0 release in #3071 right now, I think this is the right time for such a breaking change.

[guolinke]

Yeah, i think it is great

[jameslamb]

Yeah, i think it is great

ok thanks! I can do that

[jameslamb]

I just removed lgb.convert() in db27920. I also removed the demo specific to that function from demo/.

[jameslamb]

@guolinke I'll merge master into this, fix the conflicts, and merge it once CI passes. Hopefully should be quick.

[github-actions]

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