Refactored function names in R/tree.R

[teddyCodex]

Description

Refactored specified function names in R/tree.R based on issue #7

Original	Modified	User Facing
convert_fa2tre	convertFA2Tree	✅
generate_trees	convertAlignment2Trees	✅
generate_fa2tre	createFA2Tree	✅

Fixes issue #54

What kind of change(s) are included?

• [ ] Feature (adds or updates new capabilities)
• [x] Bug fix (fixes an issue).
• [ ] Enhancement (adds functionality).
• [ ] Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

• [x] I have read and followed the CONTRIBUTING.md guidelines.
• [x] I have searched for existing content to ensure this is not a duplicate.
• [x] I have performed a self-review of these additions (including spelling, grammar, and related).
• [x] I have added comments to my code to help provide understanding.
• [x] I have added a test which covers the code changes found within this PR.
• [x] I have deleted all non-relevant text in this pull request template.
• [x] Reviewer assignment: Tag a relevant team member to review and approve the changes.