tests/README.md

In GeometricMorphometricsMix: Heterogeneous Methods for Shape and Other Multidimensional Data

Tests for GeometricMorphometricsMix Package

This directory contains comprehensive unit tests for the disparity_resample() function using the testthat framework.

Test Structure

testthat.R

Main test runner file that sets up the testing environment.

Test Files

1. test-disparity_resample.R - Main comprehensive test suite
2. Input validation tests
3. Data type handling (matrix, data frame, vector, 3D array)
4. All statistical methods (multivariate variance, mean pairwise distance, etc.)
5. Bootstrap vs rarefaction methods
6. Confidence interval calculations
7. Missing data handling

8. Edge cases and error conditions

9. test-disparity_resample_helpers.R - Internal function tests

10. Tests for helper functions like muvar(), meanpairwiseEuclideanD()
11. Validation function tests
12. Data preparation function tests

13. Sample size resolution tests

14. test-disparity_resample_methods.R - S3 method tests

15. print.disparity_resample() method tests
16. plot.disparity_resample() method tests
17. Output formatting and display tests

18. Confidence interval overlap assessment tests

19. test-disparity_resample_integration.R - Integration and edge case tests

20. Tests with package datasets
21. Large dataset performance tests
22. Extreme value handling
23. Memory efficiency tests
24. Cross-platform compatibility tests

Test Coverage

The test suite covers:

Core Functionality

• ✅ All input data types (matrix, data.frame, vector, 3D array)
• ✅ All statistical methods
• ✅ Bootstrap and rarefaction resampling
• ✅ Single and multiple group analyses
• ✅ Custom sample sizes
• ✅ Confidence interval calculations

Input Validation

• ✅ Parameter validation (CI, n_resamples, statistic, etc.)
• ✅ Data validation (missing data, empty datasets, etc.)
• ✅ Group validation (minimum sizes, matching lengths, etc.)
• ✅ Rarefaction-specific validation

Statistical Accuracy

• ✅ Numerical correctness verification
• ✅ Reproducibility with set.seed()
• ✅ Edge cases (constant data, extreme values, etc.)

S3 Methods

• ✅ Print method formatting and content
• ✅ Plot method ggplot2 integration
• ✅ Confidence interval overlap assessment
• ✅ Range vs confidence interval display

Dependencies

• ✅ Optional package handling (geometry, nlshrink, Morpho, etc.)
• ✅ Graceful degradation when packages unavailable

Running the Tests

To run all tests:

library(testthat)
library(GeometricMorphometricsMix)
test_check("GeometricMorphometricsMix")

To run specific test files:

test_file("tests/testthat/test-disparity_resample.R")

Test Dependencies

The tests require: - testthat (>= 3.0.0) - Core testing framework - GeometricMorphometricsMix - The package being tested

Optional packages (tests will skip if not available): - MASS - For multivariate normal data generation - geometry - For convex hull volume tests - nlshrink - For Claramunt proper variance tests - Morpho - For 3D array handling tests - ggplot2 - For plot method tests

Notes

• Tests use skip_if_not_installed() to gracefully handle missing optional packages
• Performance tests are marked with skip_on_cran() to avoid CI timeouts
• All tests use reproducible random seeds for consistency
• Error messages are tested to ensure they are informative

Test Statistics

Total test count: ~100+ individual test cases across 4 test files Coverage: All major functions and edge cases of disparity_resample()

GeometricMorphometricsMix documentation built on April 18, 2026, 1:06 a.m.