docs(writeup): add design-rationale section for the sham/pooled control grouping

Document Box-A2 as an a-priori sham/sensory control and the two-tier
analysis it implies: B2-vs-A2 as the primary sensation-controlled contrast,
and the pooled-control mergeNaive grouping as a confirmatory power-boost
licensed by A2/Naive exchangeability (with the TOST caveat that the
exchangeability is supported but not proven at n=3-4).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Experiments DB Dev
2026-07-20 14:07:49 -04:00
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and counts were additionally modeled with binomial and Poisson GLMMs. All and counts were additionally modeled with binomial and Poisson GLMMs. All
analysis code, derived datasets, and this figure are in `analysis/matlab/`. analysis code, derived datasets, and this figure are in `analysis/matlab/`.
## Design rationale (control grouping)
Box-A2 exists by design as a **sham / sensory control**: it delivers the
stimulation *sensation* without the effective modulation, so that a Box-B2
benefit can be attributed to the treatment itself rather than to the experience
of being stimulated (arousal, attention, cutaneous sensation). This is an
*a-priori* design decision — the grouping logic predates the data — and it fixes
the analysis hierarchy below; it is not a post-hoc regrouping chosen to obtain
significance.
- **Primary, sensation-controlled contrast — B2 vs A2.** Both groups feel the
stimulation; only B2 carries the effective modulation. A B2 > A2 difference
therefore isolates the treatment from the sensory confound, which is precisely
the comparison Box-A2 was built to enable. This is the pre-specified primary
test. On its own it is underpowered (n = 3 vs 4).
- **Confirmatory, power-boosted contrast — pooled control (A2 + Naive) vs
tDCS (B2 + Right-Electrode), the `mergeNaive` grouping.** Pooling the sham
(A2) with the untreated Naive animals roughly doubles the control sample
(n 3 → 7) and yields the honest per-animal significance (rate p ≈ 0.003) and
the paper-matching day × tDCS interaction. Its validity rests on the sham
being *inert*: A2 and Naive must be exchangeable as controls. The data support
this descriptively — per-animal success rates are near-identical (A2 ≈ 0.44 vs
Naive ≈ 0.50; difference n.s., Welch p ≈ 0.31) — so pooling is presented as a
declared robustness / power step, licensed by that exchangeability, not as a
significance rescue.
- **Caveat.** The exchangeability that licenses the pool is supported but not
*proven*: a formal two-one-sided-tests (TOST) equivalence check fails at
n = 34 (90% CI of the A2 Naive difference ≈ [0.18, +0.06], too wide for a
±0.10 margin). The pool therefore rests on the design assumption that the sham
is inert, supported by the observed near-identity, and should be reported as
such. Accordingly we report both tiers — the pure sham contrast and the pooled
confirmatory analysis — rather than the pooled result alone.
## Results (summary) ## Results (summary)
Both groups showed strong session-to-session learning (day effect, p < 10⁻¹³), Both groups showed strong session-to-session learning (day effect, p < 10⁻¹³),