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results/ralph23_variance_decomposition_summary.txt

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+================================================================================
+Ralph23 Task 5: Partial R-squared Variance Decomposition
+Date: 2026-02-12
+Script: ralph23_t05_variance_decomposition_20260212_000354.py
+Runtime: 1.0 seconds
+================================================================================
+
+Method: OLS linear regression with per-fold standardization
+CV scheme: 9-fold spatial CV (from ralph23_spatial_cv_folds.npz)
+Bio-valid samples: 1151 / 1810
+
+
+────────────────────────────────────────────────────────────
+PFAM Dimensionality: pfam20
+────────────────────────────────────────────────────────────
+
+  Chl-a:
+    R²_env (mean ± sd):      -48.5449 ± 134.3695
+    R²_pfam (mean):           -11.5829
+    R²_env+pfam (mean ± sd):  -48.5299 ± 134.7549
+    Unique PFAM (mean ± sd):  +0.0150 ± 0.7285
+    Unique Env (mean):        -36.9470
+    Shared (mean):            -11.5979
+    ΔR² (both - env):         +0.0150
+    Paired t-test:            t=0.062, p=0.9522
+    Wilcoxon signed-rank:     p=0.9102
+    Cohen's d:                0.0206
+    95% CI for ΔR²:           [-0.5450, +0.5750]
+    Folds +/-/0:              4+/5-/0=
+
+  POC:
+    R²_env (mean ± sd):      -6.1351 ± 10.7978
+    R²_pfam (mean):           -5.2632
+    R²_env+pfam (mean ± sd):  -6.1092 ± 10.3026
+    Unique PFAM (mean ± sd):  +0.0259 ± 0.5680
+    Unique Env (mean):        -0.8460
+    Shared (mean):            -5.2891
+    ΔR² (both - env):         +0.0259
+    Paired t-test:            t=0.137, p=0.8947
+    Wilcoxon signed-rank:     p=0.1289
+    Cohen's d:                0.0455
+    95% CI for ΔR²:           [-0.4108, +0.4625]
+    Folds +/-/0:              1+/8-/0=
+
+  NFLH:
+    R²_env (mean ± sd):      0.9556 ± 0.0426
+    R²_pfam (mean):           -0.2838
+    R²_env+pfam (mean ± sd):  0.9550 ± 0.0426
+    Unique PFAM (mean ± sd):  -0.0006 ± 0.0063
+    Unique Env (mean):        +1.2388
+    Shared (mean):            -0.2832
+    ΔR² (both - env):         -0.0006
+    Paired t-test:            t=-0.296, p=0.7750
+    Wilcoxon signed-rank:     p=0.4258
+    Cohen's d:                -0.0986
+    95% CI for ΔR²:           [-0.0055, +0.0043]
+    Folds +/-/0:              3+/6-/0=
+
+────────────────────────────────────────────────────────────
+PFAM Dimensionality: pfam32
+────────────────────────────────────────────────────────────
+
+  Chl-a:
+    R²_env (mean ± sd):      -48.5449 ± 134.3695
+    R²_pfam (mean):           -16.0561
+    R²_env+pfam (mean ± sd):  -38.7935 ± 101.8234
+    Unique PFAM (mean ± sd):  +9.7514 ± 32.6850
+    Unique Env (mean):        -22.7374
+    Shared (mean):            -25.8075
+    ΔR² (both - env):         +9.7514
+    Paired t-test:            t=0.895, p=0.3969
+    Wilcoxon signed-rank:     p=0.3008
+    Cohen's d:                0.2983
+    95% CI for ΔR²:           [-15.3725, +34.8753]
+    Folds +/-/0:              2+/7-/0=
+
+  POC:
+    R²_env (mean ± sd):      -6.1351 ± 10.7978
+    R²_pfam (mean):           -6.6967
+    R²_env+pfam (mean ± sd):  -9.1903 ± 16.1200
+    Unique PFAM (mean ± sd):  -3.0553 ± 5.4701
+    Unique Env (mean):        -2.4937
+    Shared (mean):            -3.6414
+    ΔR² (both - env):         -3.0553
+    Paired t-test:            t=-1.676, p=0.1323
+    Wilcoxon signed-rank:     p=0.0039
+    Cohen's d:                -0.5585
+    95% CI for ΔR²:           [-7.2600, +1.1495]
+    Folds +/-/0:              0+/9-/0=
+
+  NFLH:
+    R²_env (mean ± sd):      0.9556 ± 0.0426
+    R²_pfam (mean):           -0.3600
+    R²_env+pfam (mean ± sd):  0.9573 ± 0.0371
+    Unique PFAM (mean ± sd):  +0.0017 ± 0.0082
+    Unique Env (mean):        +1.3173
+    Shared (mean):            -0.3617
+    ΔR² (both - env):         +0.0017
+    Paired t-test:            t=0.633, p=0.5445
+    Wilcoxon signed-rank:     p=0.9102
+    Cohen's d:                0.2109
+    95% CI for ΔR²:           [-0.0046, +0.0080]
+    Folds +/-/0:              4+/5-/0=
+
+────────────────────────────────────────────────────────────
+PFAM Dimensionality: pfam64
+────────────────────────────────────────────────────────────
+
+  Chl-a:
+    R²_env (mean ± sd):      -48.5449 ± 134.3695
+    R²_pfam (mean):           -21.2594
+    R²_env+pfam (mean ± sd):  -41.8854 ± 107.5039
+    Unique PFAM (mean ± sd):  +6.6595 ± 27.3695
+    Unique Env (mean):        -20.6260
+    Shared (mean):            -27.9189
+    ΔR² (both - env):         +6.6595
+    Paired t-test:            t=0.730, p=0.4862
+    Wilcoxon signed-rank:     p=0.1289
+    Cohen's d:                0.2433
+    95% CI for ΔR²:           [-14.3786, +27.6975]
+    Folds +/-/0:              1+/8-/0=
+
+  POC:
+    R²_env (mean ± sd):      -6.1351 ± 10.7978
+    R²_pfam (mean):           -9.2675
+    R²_env+pfam (mean ± sd):  -9.7802 ± 13.1164
+    Unique PFAM (mean ± sd):  -3.6451 ± 4.2615
+    Unique Env (mean):        -0.5127
+    Shared (mean):            -5.6224
+    ΔR² (both - env):         -3.6451
+    Paired t-test:            t=-2.566, p=0.0333
+    Wilcoxon signed-rank:     p=0.0039
+    Cohen's d:                -0.8553
+    95% CI for ΔR²:           [-6.9208, -0.3694]
+    Folds +/-/0:              0+/9-/0=
+
+  NFLH:
+    R²_env (mean ± sd):      0.9556 ± 0.0426
+    R²_pfam (mean):           -0.6591
+    R²_env+pfam (mean ± sd):  0.9546 ± 0.0356
+    Unique PFAM (mean ± sd):  -0.0010 ± 0.0108
+    Unique Env (mean):        +1.6137
+    Shared (mean):            -0.6581
+    ΔR² (both - env):         -0.0010
+    Paired t-test:            t=-0.266, p=0.7970
+    Wilcoxon signed-rank:     p=0.5703
+    Cohen's d:                -0.0886
+    95% CI for ΔR²:           [-0.0093, +0.0074]
+    Folds +/-/0:              3+/6-/0=
+
+
+================================================================================
+INTERPRETATION
+================================================================================
+
+POC (primary target) across PFAM dimensionalities:
+  pfam20: ΔR² = +0.0259, p = 0.8947 (ns), d = 0.046, CI = [-0.4108, +0.4625]
+  pfam32: ΔR² = -3.0553, p = 0.1323 (ns), d = -0.559, CI = [-7.2600, +1.1495]
+  pfam64: ΔR² = -3.6451, p = 0.0333 (*), d = -0.855, CI = [-6.9208, -0.3694]
+
+  RESULT: Adding PFAM features significantly HURTS POC prediction (negative direction).
+  The additional features introduce noise that degrades OLS generalization across spatial folds.
+
+Note: This is a model-agnostic analysis using simple OLS regression.
+Nonlinear PFAM-env interactions would not be captured by this method.
+The signal must be linearly detectable in the feature space for this test to detect it.