Validate birds

[taylorpapke]

Summary

This PR improves reproducibility, standardizes file handling, and aligns case study outputs more closely with expected results.

Changes

Initialization Script

• Updated R/scripts/0.0_initialize.R to install packages using the CRAN mirror:
  https://cloud.r-project.org

Test Updates (R/tests/test_birds_vz.R)

• Replaced here() with file.path() for more consistent and portable path handling
• Refactored beta and gamma symbols to use clearly named variables
• Fixed data preparation logic for the 2009 dataset

Case Study Update

• Updated R/case_studies/Medium_ground_finch.md to reflect revised outputs
• Results now better align with the original study benchmarks

Impact

• Improves cross-environment compatibility
• Enhances code clarity and maintainability
• Produces results that are more consistent with expected empirical outcomes

Notes

• No breaking changes expected, but downstream scripts relying on previous path handling or variable naming should be reviewed