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[portfolio] Repair pkgdown deployment

agent:cursorAssigned repair providerAssigned repair provider

gate:pkgdownFailing portfolio gateFailing portfolio gate

portfolio:repairManaged portfolio repairManaged portfolio repair

Status: Open.

#245 In bbuchsbaum/fmrireg;

· bbuchsbaum-r-package-portfolio opened on Sep 29, 2026

noise_spec(voxelwise=TRUE) silently ignored under joint estimation; shared AR uses undocumented row-mean residual pooling

Status: Open.

#216 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Aug 22, 2026

mask issue: _compute_statistical_volumes

Status: Open.

#210 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Aug 19, 2026

RFE: public covariance support for joint multi-contrast GLH/F tests

Status: Open.

#203 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Aug 5, 2026

First-level run-manifest helper: validate events/confounds against dataset run lengths

Status: Open.

#199 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Jun 17, 2026

glm_qa(manifest): one per-subject QA report (runs kept/dropped, vols, trims, collinearity, efficiency)

Status: Open.

#197 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Jun 16, 2026

Add a 'ragged dataset' vignette (legacy delimiter, short run, eventless run, out-of-frame trials, confounds!=BOLD)

Status: Open.

#198 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Jun 16, 2026

Surface trimmed trials/runs in the fit object (fit$exclusions) for QA + second-level

Status: Open.

#196 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Jun 16, 2026

Interaction-term contrasts silently dropped in prepare_fmri_lm_contrasts (term-key ':' vs '_' mismatch; see fmridesign#9)

Status: Open.

#192 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Jun 12, 2026

lowrank_control()/latent_sketch: roxygen omits key behavior (m & iters defaults, parcels needs ar_options$by_cluster, parcels=NULL mode, invocation, accuracy guidance)

Status: Open.

#191 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Jun 5, 2026

rrr_gls engine: subscript out of bounds when per-run nuisance pruning yields unequal column counts (.meta_betas_impl assumes uniform run width)

Status: Open.

#190 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Jun 5, 2026

soft_subspace_options (rrr_gls engine): functional options undocumented (incl. se_mode='bootstrap'); naming sprawl (soft_subspace/rrr_gls/latent_sketch/lowrank); no examples

Status: Open.

#189 In bbuchsbaum/fmrireg;

· bbuchsbaum opened on Jun 5, 2026