Reformat response options similarity matrix #18

[AlexNikic]

Description

Similar to #14, I have reformatted the response options matrix to be in data frame format.
I have changed the example notebook to reflect this change.

Fixes #18

Testing

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• test-crosswalk.R
• test-match-negative-polarity.R

Since the Harmony Python package is used by the Harmony API (which is itself used by the R library and the web app), we need to avoid making any changes that break the Harmony API. Please also run the Harmony API unit tests and check that the API still runs with your changes to the Python package: https://github.com/harmonydata/harmonyapi

Test Configuration

• Library version: Version 0.2.1 (2025-03-03)
• OS: Windows 11
• Toolchain: R version 4.4.3 (2025-02-28 ucrt)

Checklist

• My PR is for one issue, rather than for multiple unrelated fixes.
• My code follows the style guidelines of this project.
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules
• I have checked my code and corrected any misspellings
• I add third party dependencies only when necessary.
• If I introduced a new feature, I documented it (e.g. making a script example in the script examples repository so that people will know how to use it.

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