Scenario and analysis strategy | permanovaFL | adonis2 | LDM |
---|---|---|---|
(1) Matched-pair data | |||
Proposed | 0.0491 | 0.0450 | 0.0479 |
Not adjusting for ID | 0.0491 | 0.0441 | 0.0479 |
Unrestricted permutation | 0.0024 | 0.0855 | 0.0169 |
(2) Unbalanced data | |||
Proposed | 0.0471 | 0.0434 | 0.0505 |
Not adjusting for ID | 0.0501 | 0.0456 | 0.0500 |
Unrestricted permutation | 0.0039 | 0.0732 | 0.0280 |
(3) Matched-pair data with a sample-level confounder Xsam | |||
Proposed | 0.0452 | 0.0429 | 0.0476 |
Not adjusting for Xsam | 0.0688 | 0.0631 | 0.0800 |
Not adjusting for ID | 0.0713 | 0.0328 | 0.0872 |
Unrestricted permutation | 0.0016 | 0.0810 | 0.0163 |
(4) Matched-pair data with a set-level covariate Xset | |||
Proposed | 0.0510 | 0.0433 | 0.0481 |
Not adjusting for ID | 0.0510 | 0.0451 | 0.0481 |
Not adjusting for ID, adjusting for Xset | 0.0510 | 0.0450 | 0.0481 |
Unrestricted permutation | 0.0021 | 0.0874 | 0.0162 |
(5) Unbalanced data with a set-level covariate Xset | |||
Proposed | 0.0479 | 0.0444 | 0.0480 |
Not adjusting for ID | 0.0496 | 0.0446 | 0.0483 |
Not adjusting for ID, adjusting for Xset | 0.0489 | 0.0445 | 0.0489 |
Unrestricted permutation | 0.0048 | 0.0736 | 0.0257 |
(6) Matched-pair data with a continuous trait | |||
Proposed | 0.0505 | 0.044 | 0.0461 |
Not adjusting for ID | 0.0677 | 0.0612 | 0.0881 |
Unrestricted permutation | 0.190 | 0.906 | 0.994 |
(7) Matched-pair data with an interaction effect | |||
Proposed | 0.0524 | 0.0295 | 0.0536 |
Unrestricted permutation | 0 | 0.0977 | 0 |