#### Instructions for Covariate Correlation Analysis

1. Basic Settings
   - Correlation Method:
     - Pearson: For linear relationships between continuous variables
     - Spearman: For monotonic relationships, robust to outliers
     - Kendall: For ordinal relationships, good for small sample sizes
   - Correlation Threshold:
     - Set minimum correlation value to highlight (0-1)
     - Default 0.7 is commonly used
     - Lower values (e.g., 0.5) for stricter multicollinearity control
     - Higher values (e.g., 0.8) for more relaxed variable inclusion
   - Non-numeric Variables:
     - Option to exclude non-numeric covariates
     - Categorical variables are automatically excluded if enabled
2. Visualization Options
   - Plot Type:
     - Correlation matrix: Compact view of all correlations
     - Scatter plot matrix: Detailed view of relationships
   - Display Method:
     - Color: Simple color-coded squares
     - Circle/Square: Size indicates correlation strength
     - Ellipse: Shape shows correlation direction and strength
     - Shade: Uses color intensity
     - Pie: Fills circles with pie charts
   - Ordering Method:
     - Original: Keep input order
     - AOE/FPC: Order by eigenvectors or first principal component
     - Hclust: Group similar variables
     - Alphabet: Sort alphabetically
3. Output Components
   - Correlation Plot:
     - Blue indicates positive correlations
     - Red indicates negative correlations
     - Color intensity shows correlation strength
     - Values display exact correlation coefficients
   - Highly Correlated Pairs:
     - Table shows pairs exceeding threshold
     - Lists exact correlation values
     - Helps identify potential multicollinearity issues

#### Notes:

- Large correlations suggest redundant information between variables
- Consider removing one variable from highly correlated pairs before modeling
- Choice of which variable to remove should be based on ecological relevance and data quality
- Remember that correlation does not imply causation
- Missing values are handled pairwise in correlation calculations