This PR introduces several improvements and refactorings to increase coverage in R, as well as minor side effects.

Test coverage

• Refactor and expand test coverage in test_base.R, test_io.R, and test_stats.R, including new tests for edge cases (e.g., empty vectors/matrices, unsupported dimensions, and error conditions), and reorganize test helpers for better reuse and clarity.
• Ensure same test config constants in R and Python

Side effects

• Enforce stricter type checking in functions such as to_newick, cophenetic_distances, vcovp, and precision, requiring integer vectors instead of generic vectors, and update error messages accordingly.
• Use fully qualified names for functions from the tools, Matrix, and ape packages to avoid ambiguity and unnecessary imports (to make covr work)
• Fix a few comments here and there
• Add documentation about code coverage in the docs