psyclaw 0.27.22 → 0.28.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1048) hide show
  1. package/README.md +11 -5
  2. package/dist/apps/panel/index.html +2 -2
  3. package/dist/src/adapters/pi/extension.js +225 -92
  4. package/dist/src/adapters/pi/extension.js.map +1 -1
  5. package/dist/src/agents/import.js +44 -32
  6. package/dist/src/agents/import.js.map +1 -1
  7. package/dist/src/analysis/hooks.d.ts +1 -0
  8. package/dist/src/analysis/hooks.js +20 -1
  9. package/dist/src/analysis/hooks.js.map +1 -1
  10. package/dist/src/ars/bridge.d.ts +20 -0
  11. package/dist/src/ars/bridge.js +132 -0
  12. package/dist/src/ars/bridge.js.map +1 -0
  13. package/dist/src/ars/contracts.d.ts +55 -0
  14. package/dist/src/ars/contracts.js +2 -0
  15. package/dist/src/ars/contracts.js.map +1 -0
  16. package/dist/src/ars/panel-plan.d.ts +4 -0
  17. package/dist/src/ars/panel-plan.js +11 -0
  18. package/dist/src/ars/panel-plan.js.map +1 -0
  19. package/dist/src/ars/pi-panel-executor.d.ts +30 -0
  20. package/dist/src/ars/pi-panel-executor.js +140 -0
  21. package/dist/src/ars/pi-panel-executor.js.map +1 -0
  22. package/dist/src/ars/profile.d.ts +36 -0
  23. package/dist/src/ars/profile.js +119 -0
  24. package/dist/src/ars/profile.js.map +1 -0
  25. package/dist/src/ars/re-review.d.ts +22 -0
  26. package/dist/src/ars/re-review.js +172 -0
  27. package/dist/src/ars/re-review.js.map +1 -0
  28. package/dist/src/branding.d.ts +2 -4
  29. package/dist/src/branding.js +3 -5
  30. package/dist/src/branding.js.map +1 -1
  31. package/dist/src/bundled-tools.d.ts +3 -0
  32. package/dist/src/bundled-tools.js +21 -0
  33. package/dist/src/bundled-tools.js.map +1 -0
  34. package/dist/src/chat.js +6 -5
  35. package/dist/src/chat.js.map +1 -1
  36. package/dist/src/creation/contracts.d.ts +38 -0
  37. package/dist/src/creation/contracts.js +2 -0
  38. package/dist/src/creation/contracts.js.map +1 -0
  39. package/dist/src/creation/service.d.ts +7 -0
  40. package/dist/src/creation/service.js +196 -0
  41. package/dist/src/creation/service.js.map +1 -0
  42. package/dist/src/index.d.ts +10 -0
  43. package/dist/src/index.js +10 -0
  44. package/dist/src/index.js.map +1 -1
  45. package/dist/src/install/installer.js +32 -10
  46. package/dist/src/install/installer.js.map +1 -1
  47. package/dist/src/orchestration/personas.d.ts +15 -0
  48. package/dist/src/orchestration/personas.js +51 -0
  49. package/dist/src/orchestration/personas.js.map +1 -0
  50. package/dist/src/orchestration/pi-executor.d.ts +1 -0
  51. package/dist/src/orchestration/pi-executor.js +1 -1
  52. package/dist/src/orchestration/pi-executor.js.map +1 -1
  53. package/dist/src/panel/extension.js +29 -8
  54. package/dist/src/panel/extension.js.map +1 -1
  55. package/dist/src/panel/server.js +14 -5
  56. package/dist/src/panel/server.js.map +1 -1
  57. package/dist/src/project/paths.d.ts +3 -0
  58. package/dist/src/project/paths.js +7 -0
  59. package/dist/src/project/paths.js.map +1 -1
  60. package/dist/src/rules/user-rules.d.ts +8 -0
  61. package/dist/src/rules/user-rules.js +36 -0
  62. package/dist/src/rules/user-rules.js.map +1 -0
  63. package/dist/src/skills/contracts.d.ts +4 -4
  64. package/dist/src/skills/recommended.js +1 -1
  65. package/dist/src/skills/registry.js +49 -28
  66. package/dist/src/skills/registry.js.map +1 -1
  67. package/dist/src/style/cli-ui.js +0 -1
  68. package/dist/src/style/cli-ui.js.map +1 -1
  69. package/package.json +14 -3
  70. package/scripts/rebrand-pi.mjs +6 -0
  71. package/skills/recommended/catalog.json +2 -11
  72. package/vendor/ars/.claude/CLAUDE.md +371 -0
  73. package/vendor/ars/.command-invariants.toml +24 -0
  74. package/vendor/ars/CITATION.cff +35 -0
  75. package/vendor/ars/LICENSE +417 -0
  76. package/vendor/ars/MODE_REGISTRY.md +76 -0
  77. package/vendor/ars/NOTICE.md +26 -0
  78. package/vendor/ars/POSITIONING.md +99 -0
  79. package/vendor/ars/PSYCLAW_SOURCE.json +10 -0
  80. package/vendor/ars/README.md +751 -0
  81. package/vendor/ars/SECURITY.md +52 -0
  82. package/vendor/ars/THIRD_PARTY.md +70 -0
  83. package/vendor/ars/academic-paper/SKILL.md +542 -0
  84. package/vendor/ars/academic-paper/agents/abstract_bilingual_agent.md +171 -0
  85. package/vendor/ars/academic-paper/agents/argument_builder_agent.md +276 -0
  86. package/vendor/ars/academic-paper/agents/citation_compliance_agent.md +422 -0
  87. package/vendor/ars/academic-paper/agents/draft_writer_agent.md +656 -0
  88. package/vendor/ars/academic-paper/agents/formatter_agent.md +999 -0
  89. package/vendor/ars/academic-paper/agents/intake_agent.md +393 -0
  90. package/vendor/ars/academic-paper/agents/literature_strategist_agent.md +626 -0
  91. package/vendor/ars/academic-paper/agents/peer_reviewer_agent.md +516 -0
  92. package/vendor/ars/academic-paper/agents/revision_coach_agent.md +334 -0
  93. package/vendor/ars/academic-paper/agents/socratic_mentor_agent.md +527 -0
  94. package/vendor/ars/academic-paper/agents/structure_architect_agent.md +401 -0
  95. package/vendor/ars/academic-paper/agents/visualization_agent.md +441 -0
  96. package/vendor/ars/academic-paper/examples/chinese_paper_example.md +278 -0
  97. package/vendor/ars/academic-paper/examples/clinical_citation_verification_checklist.md +95 -0
  98. package/vendor/ars/academic-paper/examples/clinical_epistemic_status_example.md +100 -0
  99. package/vendor/ars/academic-paper/examples/commitment_ledger_example.md +147 -0
  100. package/vendor/ars/academic-paper/examples/imrad_hei_example.md +234 -0
  101. package/vendor/ars/academic-paper/examples/literature_review_example.md +260 -0
  102. package/vendor/ars/academic-paper/examples/plan_mode_guided_writing.md +600 -0
  103. package/vendor/ars/academic-paper/examples/revision_mode_example.md +344 -0
  104. package/vendor/ars/academic-paper/examples/revision_recovery_example.md +506 -0
  105. package/vendor/ars/academic-paper/examples/version_family_reconciliation_example.md +89 -0
  106. package/vendor/ars/academic-paper/references/abstract_writing_guide.md +169 -0
  107. package/vendor/ars/academic-paper/references/academic_writing_style.md +188 -0
  108. package/vendor/ars/academic-paper/references/anti_leakage_protocol.md +83 -0
  109. package/vendor/ars/academic-paper/references/apa7_chinese_citation_guide.md +364 -0
  110. package/vendor/ars/academic-paper/references/apa7_extended_guide.md +198 -0
  111. package/vendor/ars/academic-paper/references/changelog.md +11 -0
  112. package/vendor/ars/academic-paper/references/citation_format_switcher.md +228 -0
  113. package/vendor/ars/academic-paper/references/committee_correspondence_protocol.md +158 -0
  114. package/vendor/ars/academic-paper/references/credit_authorship_guide.md +308 -0
  115. package/vendor/ars/academic-paper/references/disclosure_mode_protocol.md +478 -0
  116. package/vendor/ars/academic-paper/references/domain_evidence_profiles.md +38 -0
  117. package/vendor/ars/academic-paper/references/failure_paths.md +349 -0
  118. package/vendor/ars/academic-paper/references/funding_statement_guide.md +319 -0
  119. package/vendor/ars/academic-paper/references/hei_domain_glossary.md +169 -0
  120. package/vendor/ars/academic-paper/references/intro_title_rhetoric_guide.md +114 -0
  121. package/vendor/ars/academic-paper/references/journal_submission_guide.md +249 -0
  122. package/vendor/ars/academic-paper/references/latex_template_reference.md +378 -0
  123. package/vendor/ars/academic-paper/references/mode_selection_guide.md +378 -0
  124. package/vendor/ars/academic-paper/references/paper_structure_patterns.md +330 -0
  125. package/vendor/ars/academic-paper/references/plan_mode_protocol.md +112 -0
  126. package/vendor/ars/academic-paper/references/policy_anchor_disclosure_protocol.md +200 -0
  127. package/vendor/ars/academic-paper/references/policy_anchor_table.md +157 -0
  128. package/vendor/ars/academic-paper/references/revision_patch_protocol.md +173 -0
  129. package/vendor/ars/academic-paper/references/statistical_visualization_standards.md +750 -0
  130. package/vendor/ars/academic-paper/references/venue_disclosure_policies.md +259 -0
  131. package/vendor/ars/academic-paper/references/vlm_figure_verification.md +126 -0
  132. package/vendor/ars/academic-paper/references/workflow_phase_details.md +135 -0
  133. package/vendor/ars/academic-paper/references/writing_judgment_framework.md +59 -0
  134. package/vendor/ars/academic-paper/references/writing_quality_check.md +173 -0
  135. package/vendor/ars/academic-paper/templates/bilingual_abstract_template.md +78 -0
  136. package/vendor/ars/academic-paper/templates/case_study_template.md +129 -0
  137. package/vendor/ars/academic-paper/templates/conference_paper_template.md +108 -0
  138. package/vendor/ars/academic-paper/templates/credit_statement_template.md +132 -0
  139. package/vendor/ars/academic-paper/templates/funding_statement_template.md +290 -0
  140. package/vendor/ars/academic-paper/templates/imrad_template.md +183 -0
  141. package/vendor/ars/academic-paper/templates/latex_article_template.tex +199 -0
  142. package/vendor/ars/academic-paper/templates/literature_review_template.md +135 -0
  143. package/vendor/ars/academic-paper/templates/policy_brief_template.md +139 -0
  144. package/vendor/ars/academic-paper/templates/revision_tracking_template.md +199 -0
  145. package/vendor/ars/academic-paper/templates/theoretical_paper_template.md +119 -0
  146. package/vendor/ars/academic-paper-reviewer/SKILL.md +491 -0
  147. package/vendor/ars/academic-paper-reviewer/agents/devils_advocate_reviewer_agent.md +443 -0
  148. package/vendor/ars/academic-paper-reviewer/agents/domain_reviewer_agent.md +412 -0
  149. package/vendor/ars/academic-paper-reviewer/agents/editorial_synthesizer_agent.md +478 -0
  150. package/vendor/ars/academic-paper-reviewer/agents/eic_agent.md +339 -0
  151. package/vendor/ars/academic-paper-reviewer/agents/field_analyst_agent.md +221 -0
  152. package/vendor/ars/academic-paper-reviewer/agents/methodology_reviewer_agent.md +449 -0
  153. package/vendor/ars/academic-paper-reviewer/agents/perspective_reviewer_agent.md +427 -0
  154. package/vendor/ars/academic-paper-reviewer/examples/hei_paper_review_example.md +391 -0
  155. package/vendor/ars/academic-paper-reviewer/examples/interdisciplinary_review_example.md +299 -0
  156. package/vendor/ars/academic-paper-reviewer/examples/subclaim_decomposition_example.md +80 -0
  157. package/vendor/ars/academic-paper-reviewer/references/calibration_mode_protocol.md +256 -0
  158. package/vendor/ars/academic-paper-reviewer/references/changelog.md +10 -0
  159. package/vendor/ars/academic-paper-reviewer/references/editorial_decision_standards.md +236 -0
  160. package/vendor/ars/academic-paper-reviewer/references/guided_mode_protocol.md +34 -0
  161. package/vendor/ars/academic-paper-reviewer/references/integration_guide.md +15 -0
  162. package/vendor/ars/academic-paper-reviewer/references/quality_rubrics.md +84 -0
  163. package/vendor/ars/academic-paper-reviewer/references/re_review_mode_protocol.md +340 -0
  164. package/vendor/ars/academic-paper-reviewer/references/review_criteria_framework.md +98 -0
  165. package/vendor/ars/academic-paper-reviewer/references/review_panel_provenance_protocol.md +197 -0
  166. package/vendor/ars/academic-paper-reviewer/references/review_quality_thinking.md +58 -0
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  169. package/vendor/ars/academic-paper-reviewer/references/statistical_reporting_standards.md +505 -0
  170. package/vendor/ars/academic-paper-reviewer/references/top_journals_by_field.md +206 -0
  171. package/vendor/ars/academic-paper-reviewer/templates/editorial_decision_template.md +235 -0
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  175. package/vendor/ars/academic-pipeline/agents/claim_ref_alignment_audit_agent.md +382 -0
  176. package/vendor/ars/academic-pipeline/agents/collaboration_depth_agent.md +164 -0
  177. package/vendor/ars/academic-pipeline/agents/integrity_verification_agent.md +870 -0
  178. package/vendor/ars/academic-pipeline/agents/pipeline_orchestrator_agent.md +1379 -0
  179. package/vendor/ars/academic-pipeline/agents/state_tracker_agent.md +622 -0
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  181. package/vendor/ars/academic-pipeline/examples/integrity_failure_recovery.md +389 -0
  182. package/vendor/ars/academic-pipeline/examples/mid_entry_example.md +414 -0
  183. package/vendor/ars/academic-pipeline/references/adapters/.gitkeep +0 -0
  184. package/vendor/ars/academic-pipeline/references/adapters/overview.md +153 -0
  185. package/vendor/ars/academic-pipeline/references/ai_research_failure_modes.md +185 -0
  186. package/vendor/ars/academic-pipeline/references/changelog.md +14 -0
  187. package/vendor/ars/academic-pipeline/references/claim_audit_calibration_protocol.md +175 -0
  188. package/vendor/ars/academic-pipeline/references/claim_verification_protocol.md +282 -0
  189. package/vendor/ars/academic-pipeline/references/external_review_protocol.md +131 -0
  190. package/vendor/ars/academic-pipeline/references/integrity_review_protocol.md +110 -0
  191. package/vendor/ars/academic-pipeline/references/literature_corpus_consumers.md +193 -0
  192. package/vendor/ars/academic-pipeline/references/mode_advisor.md +135 -0
  193. package/vendor/ars/academic-pipeline/references/passport_as_reset_boundary.md +132 -0
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  204. package/vendor/ars/agents/report_compiler_agent.md +341 -0
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  207. package/vendor/ars/commands/ars-3w.md +10 -0
  208. package/vendor/ars/commands/ars-abstract.md +10 -0
  209. package/vendor/ars/commands/ars-cache-invalidate.md +20 -0
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  213. package/vendor/ars/commands/ars-full.md +9 -0
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+ # Statistical Reporting Standards — Statistical Reporting Standards & APA 7.0 Format Quick Reference
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+
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+ This document defines the complete review standards for statistical reporting in quantitative research. `methodology_reviewer_agent` uses this document as the primary reference in Step 4a (Statistical Reporting Adequacy).
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+
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+ ---
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+
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+ ## 1. Universal Statistical Reporting Checklist
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+
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+ All quantitative research papers **must** report the following items. Check each item during review:
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+
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+ ### 1.1 Descriptive Statistics
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+
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+ | Item | Standard | Common Omission |
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+ |------|----------|----------------|
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+ | Mean (*M*) | Must be reported for all continuous variables | Only overall reported, not by group |
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+ | Standard deviation (*SD*) | Must appear paired with the mean | Standard error (*SE*) used incorrectly in place of SD |
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+ | Sample size (*N* / *n*) | Both total and group sample sizes must be reported | Sample attrition during analysis unexplained |
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+ | Range | Report Min-Max or interquartile range | Completely absent, unable to judge distribution characteristics |
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+ | Categorical variable distribution | Report frequency (*f*) and percentage (%) | Only percentage reported, missing raw frequency |
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+
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+ ### 1.2 Effect Size
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+
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+ | Item | Standard | Common Omission |
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+ |------|----------|----------------|
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+ | Reporting obligation | **All statistical tests must be accompanied by effect sizes** — APA 7.0 mandatory requirement | Only *p*-value reported, no effect size |
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+ | Select appropriate metric | Choose effect size metric corresponding to the analysis method (see Section 2) | Inappropriate effect size metric used |
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+ | Interpretation | Must provide Cohen's conventional benchmarks or field-specific benchmarks | Numbers reported but magnitude not interpreted |
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+
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+ **Common Effect Size Metrics Quick Reference:**
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+
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+ | Analysis Method | Effect Size Metric | Small/Medium/Large (Cohen's Convention) |
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+ |----------------|-------------------|----------------------------------------|
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+ | *t*-test | Cohen's *d* | 0.2 / 0.5 / 0.8 |
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+ | ANOVA | *eta*-squared | .01 / .06 / .14 |
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+ | ANOVA (partial) | partial *eta*-squared | .01 / .06 / .14 |
36
+ | Correlation | *r* | .10 / .30 / .50 |
37
+ | Regression | *R*-squared, *f*-squared | *f*-squared: .02 / .15 / .35 |
38
+ | Chi-square | Cramer's *V*, *phi* | *V*: .10 / .30 / .50 (*df*=1) |
39
+ | Odds Ratio | OR | 1.5 / 2.5 / 4.3 (Rosenthal) |
40
+
41
+ ### 1.3 Confidence Intervals
42
+
43
+ | Item | Standard | Common Omission |
44
+ |------|----------|----------------|
45
+ | CI reporting | All effect sizes and key estimates **should** report 95% CI | CI completely absent |
46
+ | Format | 95% CI [lower bound, upper bound] | Inconsistent format or using parentheses instead of brackets |
47
+ | Interpretation | Describe the substantive meaning of the CI, not just statistical meaning | Only checking whether CI includes zero, not interpreting width |
48
+
49
+ ### 1.4 Statistical Significance
50
+
51
+ | Item | Standard | Common Omission |
52
+ |------|----------|----------------|
53
+ | *p*-value format | Report exact *p* value (e.g., *p* = .032) | Only reporting *p* < .05 or *p* > .05 |
54
+ | *p* < .001 | Can report *p* < .001 when *p* is very small | Reporting *p* = .000 (raw statistical software output) |
55
+ | Alpha level | Declare alpha level a priori | Failure to state whether alpha = .05 or another value |
56
+ | Multiple comparisons | Use Bonferroni, Holm, FDR correction | Multiple comparisons without any correction |
57
+ | Non-significant results | Must be fully reported; cannot be hidden | Selectively reporting only significant results |
58
+
59
+ ### 1.5 Statistical Power
60
+
61
+ | Item | Standard | Common Omission |
62
+ |------|----------|----------------|
63
+ | A priori power analysis | State target power (typically >= .80), assumed effect size, alpha, required sample size | Power analysis completely absent |
64
+ | Effect size source | Based on prior research, pilot study, or theoretical expectation | Using Cohen's convention without explanation |
65
+ | Tool | Use G*Power, pwr package, etc. | Tool not specified |
66
+ | Post-hoc power | Report observed power for non-significant results | Type II error risk not discussed for non-significant results |
67
+ | Sensitivity analysis | Report the minimum detectable effect size given *N* | Sensitivity analysis not conducted |
68
+
69
+ ### 1.6 Missing Data Handling
70
+
71
+ | Item | Standard | Common Omission |
72
+ |------|----------|----------------|
73
+ | Missing data reporting | Report missing data amount and proportion for each variable | Missing data situation not reported |
74
+ | Missing mechanism | Discuss MCAR / MAR / MNAR | MCAR assumed without testing |
75
+ | Handling method | State the method used: listwise deletion / pairwise deletion / MI / FIML | Not stated or only using listwise deletion |
76
+ | Sensitivity analysis | Compare result robustness across different missing data handling methods | Only one method used, sensitivity not tested |
77
+
78
+ ### 1.7 Assumption Testing
79
+
80
+ | Assumption | Applicable Analysis | Testing Method | Common Omission |
81
+ |-----------|-------------------|---------------|----------------|
82
+ | Normality | *t*-test, ANOVA, regression | Shapiro-Wilk / K-S / Q-Q plot / skewness & kurtosis | Completely untested or only invoking CLT |
83
+ | Homogeneity of variance | Independent *t*-test, ANOVA | Levene's test | Not reported or alternative method not used when violated |
84
+ | Linearity | Regression, correlation | Residual plot / scatter plot | Linearity assumed without testing |
85
+ | Independence | Most parametric tests | Durbin-Watson / research design explanation | Nested data not handled |
86
+ | Multicollinearity | Multiple regression | VIF, tolerance, correlation matrix | VIF not reported or reported but not addressed |
87
+ | Residual normality / homoscedasticity | Regression | Residual plot, Breusch-Pagan | Residuals not checked after model fitting |
88
+
89
+ ---
90
+
91
+ ## 2. Method-Specific Checklists
92
+
93
+ ### 2.1 *t*-test (Independent / Paired Samples)
94
+
95
+ | Check Item | Description |
96
+ |-----------|-------------|
97
+ | Report *t* statistic | *t*(df) = X.XX, *p* = .XXX |
98
+ | Independent vs paired | Correct selection? Paired designs need to report pairing logic |
99
+ | Effect size | Cohen's *d* (independent) or *d*_z (paired) |
100
+ | Assumption testing | Normality (important for small samples), homogeneity of variance (independent *t*-test) |
101
+ | Welch's *t*-test | Is Welch correction used when variances are unequal? |
102
+ | Directionality | Is one-tailed vs two-tailed supported by a priori theoretical basis? |
103
+
104
+ ### 2.2 ANOVA (One-Way / Factorial / Repeated Measures)
105
+
106
+ | Check Item | Description |
107
+ |-----------|-------------|
108
+ | Report *F* statistic | *F*(df1, df2) = X.XX, *p* = .XXX |
109
+ | Effect size | *eta*-squared, partial *eta*-squared, or *omega*-squared |
110
+ | Post-hoc comparisons | When main effect is significant, are post-hoc tests done (Tukey / Bonferroni / Games-Howell)? |
111
+ | Interaction effects | In factorial designs, are interactions interpreted? Are simple effects tested? |
112
+ | Sphericity assumption | For repeated measures, is Mauchly's test reported + Greenhouse-Geisser / Huynh-Feldt correction? |
113
+ | Assumption testing | Normality, homogeneity of variance (Levene's), independence of between-group observations |
114
+ | Unequal group sizes | When group sizes differ substantially, is Type III SS used? |
115
+
116
+ ### 2.3 Regression Analysis (Linear / Logistic)
117
+
118
+ #### Linear Regression
119
+
120
+ | Check Item | Description |
121
+ |-----------|-------------|
122
+ | Model summary | *R*-squared, adjusted *R*-squared, *F* test for model |
123
+ | Coefficient table | *B*, *SE*, *beta*, *t*, *p*, 95% CI for *B* |
124
+ | Multicollinearity | VIF (< 5 or < 10 depending on field convention), tolerance |
125
+ | Residual diagnostics | Normality, homoscedasticity, linearity, outliers (Cook's *D*) |
126
+ | Variable selection | Rationale for enter vs stepwise method |
127
+ | Effect size | *R*-squared, *f*-squared, Cohen's *f*-squared |
128
+
129
+ #### Logistic Regression
130
+
131
+ | Check Item | Description |
132
+ |-----------|-------------|
133
+ | Model fit | Hosmer-Lemeshow / chi-squared / -2LL / Nagelkerke *R*-squared |
134
+ | Coefficient reporting | *B*, *SE*, Wald, OR, 95% CI for OR |
135
+ | Classification accuracy | Classification table, sensitivity, specificity, AUC/ROC |
136
+ | Assumptions | Independence of observations, linearity in the logit (linear relationship between continuous predictors and logit) |
137
+ | Sample size | At least 10-20 events per predictor variable (EPV rule) |
138
+
139
+ ### 2.4 Structural Equation Modeling (SEM)
140
+
141
+ | Check Item | Standard |
142
+ |-----------|----------|
143
+ | Sample size | Typically >= 200; or 5-10 times the number of estimated parameters |
144
+ | Model fit indices | **Must report multiple indices simultaneously** (at least 4) |
145
+ | CFI / TLI | >= .95 (good); >= .90 (acceptable) |
146
+ | RMSEA | <= .06 (good); <= .08 (acceptable); must report 90% CI |
147
+ | SRMR | <= .08 |
148
+ | chi-squared/df | <= 3 (some scholars suggest <= 2) |
149
+ | Factor loadings | Standardized >= .50 (ideal >= .70) |
150
+ | Measurement model | CFA before SEM (two-step approach) — Anderson & Gerbing (1988) |
151
+ | Reliability and validity | CR >= .70, AVE >= .50, discriminant validity (Fornell-Larcker / HTMT) |
152
+ | Modification indices | When using modification indices, must have theoretical support |
153
+ | Normality | Multivariate normality (Mardia's coefficient); when violated, use robust ML or bootstrapping |
154
+
155
+ ### 2.5 Hierarchical Linear Modeling (HLM / MLM)
156
+
157
+ | Check Item | Standard |
158
+ |-----------|----------|
159
+ | Nested structure | Clearly explain each level (e.g., students -> classes -> schools) |
160
+ | ICC | Report Intraclass Correlation Coefficient; ICC > .05 supports using MLM |
161
+ | Random effects | Report random intercept and (if applicable) random slope variances |
162
+ | Fixed effects | Report coefficients, *SE*, *t* / *z*, *p*, CI |
163
+ | Between-group sample size | Level-2 unit count (typically recommended >= 30) |
164
+ | Centering | Explain whether grand-mean centering or group-mean centering is used and why |
165
+ | Model comparison | Use deviance (-2LL), AIC, BIC to compare nested models |
166
+ | Effect size | Pseudo *R*-squared (e.g., Snijders & Bosker's *R*-squared) |
167
+
168
+ ### 2.6 Chi-Square Test
169
+
170
+ | Check Item | Description |
171
+ |-----------|-------------|
172
+ | Reporting format | chi-squared(df, *N* = XX) = X.XX, *p* = .XXX |
173
+ | Effect size | Cramer's *V* (larger than 2x2) or *phi* (2x2) |
174
+ | Expected frequencies | All cells expected frequency >= 5; if any cell < 5, use Fisher's exact test |
175
+ | Independence | Are observations truly independent? (Repeated measures are not suitable for ordinary chi-square) |
176
+ | Residual analysis | When significant, check standardized residuals to determine which cells contribute to significance |
177
+
178
+ ### 2.7 Non-Parametric Tests
179
+
180
+ | Check Item | Description |
181
+ |-----------|-------------|
182
+ | Justification for use | Clearly explain why parametric tests are not used (e.g., normality violation, ordinal scale) |
183
+ | Method selection | Mann-Whitney *U* / Wilcoxon / Kruskal-Wallis / Friedman — is the correct test matched |
184
+ | Effect size | *r* = *Z* / sqrt(*N*) (Mann-Whitney); *W* (Kendall's) |
185
+ | Reporting format | Report test statistic, *p*-value, effect size |
186
+ | Post-hoc comparisons | After significant Kruskal-Wallis, pairwise comparisons + correction needed |
187
+
188
+ ---
189
+
190
+ ## 3. APA 7th Edition Statistical Format Quick Reference
191
+
192
+ ### 3.1 Number Formatting
193
+
194
+ | Rule | Correct | Incorrect |
195
+ |------|---------|-----------|
196
+ | *p*-value no leading zero | *p* = .032 | *p* = 0.032 |
197
+ | Statistics that can exceed 1.0 have leading zero | *M* = 0.75 | *M* = .75 |
198
+ | Statistics that cannot exceed 1.0 have no leading zero | *r* = .45 | *r* = 0.45 |
199
+ | Generally 2 decimal places | *M* = 3.45 | *M* = 3.4 |
200
+ | *p*-value 2-3 decimal places | *p* = .03 or *p* = .032 | *p* = .0321 |
201
+ | Percentages 0-1 decimal places | 45.2% | 45.2381% |
202
+
203
+ **Statistics that cannot exceed 1.0** (no leading zero): correlation coefficients (*r*, *R*), proportions (*p*-value), Cramer's *V*, *phi*, *eta*-squared, *R*-squared, *beta* (standardized regression coefficient)
204
+
205
+ **Statistics that can exceed 1.0** (leading zero): *M*, *SD*, *B* (unstandardized regression coefficient), Cohen's *d*, *t*, *F*, chi-squared
206
+
207
+ ### 3.2 Statistical Symbol Italicization Rules
208
+
209
+ | Italic | Non-italic |
210
+ |--------|-----------|
211
+ | *M*, *SD*, *SE* | df |
212
+ | *N* (total sample), *n* (subsample) | SS, MS |
213
+ | *t*, *F*, *p*, *r*, *R*, *z* | OR, CI, VIF |
214
+ | *d*, *f*-squared, *eta*-squared, *omega*-squared | AIC, BIC, CFI, TLI |
215
+ | *B*, *beta* | RMSEA, SRMR |
216
+ | *chi*-squared | ICC |
217
+ | *U*, *W* (non-parametric statistics) | ANOVA, SEM, HLM |
218
+
219
+ ### 3.3 Statistical Results Reporting Format Examples
220
+
221
+ | Analysis Method | APA Format Example |
222
+ |----------------|-------------------|
223
+ | Independent samples *t*-test | *t*(58) = 2.45, *p* = .017, *d* = 0.63, 95% CI [0.12, 1.14] |
224
+ | Paired samples *t*-test | *t*(29) = -3.12, *p* = .004, *d*_z = 0.57 |
225
+ | One-way ANOVA | *F*(2, 87) = 4.56, *p* = .013, partial *eta*-squared = .09 |
226
+ | Linear regression | *B* = 0.34, *SE* = 0.12, *beta* = .28, *t*(95) = 2.83, *p* = .006, 95% CI [0.10, 0.58] |
227
+ | Logistic regression | *B* = 1.24, *SE* = 0.45, Wald = 7.59, *p* = .006, OR = 3.46, 95% CI [1.43, 8.37] |
228
+ | Chi-square | chi-squared(2, *N* = 150) = 8.34, *p* = .015, *V* = .24 |
229
+ | Mann-Whitney | *U* = 245.00, *z* = -2.31, *p* = .021, *r* = .29 |
230
+ | SEM fit | chi-squared(52) = 78.34, *p* = .011, CFI = .97, TLI = .96, RMSEA = .045 [.018, .068], SRMR = .038 |
231
+ | HLM fixed effects | *gamma*_10 = 0.45, *SE* = 0.15, *t*(28) = 3.00, *p* = .006 |
232
+
233
+ ### 3.4 Table Format Standards
234
+
235
+ | Rule | Description |
236
+ |------|-------------|
237
+ | Three-line table | APA tables have only three horizontal lines (above header, below header, bottom of table), no vertical lines |
238
+ | Table numbering | Table 1, Table 2... (bold), title on the line below the number (italic) |
239
+ | Note levels | General note (Note.) -> Specific note (superscript a, b) -> Significance (*p* < .05, **p* < .01) |
240
+ | Asterisks | \**p* < .05. \*\**p* < .01. \*\*\**p* < .001. |
241
+ | Alignment | Numbers right-aligned, decimal points aligned |
242
+
243
+ ---
244
+
245
+ ## 4. Statistical Red Flags
246
+
247
+ The following patterns during review should raise red flags, requiring further investigation or author clarification:
248
+
249
+ > **Triage levels, not finding severities (#574 A3).** The HIGH/MEDIUM/LOW labels in the tables below rank how urgently a red flag deserves scrutiny — they are detection triage, never a severity vocabulary. When a red flag becomes a reported weakness, its severity is the Schema 6 enum (Critical / Major / Minor), assigned by decision impact per the Finding Contract — never copied from the triage label.
250
+
251
+ ### 4.1 P-hacking Indicators
252
+
253
+ | Red Flag | Description | Severity |
254
+ |----------|-------------|----------|
255
+ | Many *p* near .05 | Multiple results with *p* concentrated in the .04-.05 range | HIGH |
256
+ | Selective reporting | Only significant results reported, non-significant ones disappeared | HIGH |
257
+ | Vague analysis strategy | Analysis strategy not stated a priori, appears exploratory in hindsight | MEDIUM |
258
+ | Unexpected subgroups | Post-hoc subgroup decomposition to find significant results | MEDIUM |
259
+ | Flexible sample size | No pre-defined stopping rule (sequential testing without correction) | HIGH |
260
+ | "Excluding outliers" | Large number of outliers excluded with unclear criteria | MEDIUM |
261
+
262
+ ### 4.2 HARKing (Hypothesizing After Results are Known)
263
+
264
+ | Red Flag | Description | Severity |
265
+ |----------|-------------|----------|
266
+ | Perfect hypothesis-result match | All hypotheses supported without exception | MEDIUM |
267
+ | Exploratory analysis packaged as confirmatory | Literature review clearly constructed post-hoc | HIGH |
268
+ | Hypothesis directionality change | Originally predicted positive but result was negative, yet claimed "as expected" | HIGH |
269
+ | No pre-registration | No OSF / AsPredicted pre-registration link provided (not mandatory but recommended) | LOW |
270
+
271
+ ### 4.3 Missing Effect Sizes and Confidence Intervals
272
+
273
+ | Red Flag | Description | Severity |
274
+ |----------|-------------|----------|
275
+ | No effect sizes reported at all | Conclusions based solely on *p*-values | HIGH |
276
+ | CI completely absent | Cannot judge estimation precision | MEDIUM |
277
+ | Extremely wide CI | CI spans from small to large effect sizes, imprecise estimation | MEDIUM |
278
+ | Inconsistent effect sizes | Reported effect sizes inconsistent with calculations from raw data | HIGH |
279
+
280
+ ### 4.4 Sample Size Issues
281
+
282
+ | Red Flag | Description | Severity |
283
+ |----------|-------------|----------|
284
+ | No power analysis | Sample size lacks a priori calculation basis | MEDIUM |
285
+ | Sample too small | In regression analysis, *N* < 10 x number of predictors | HIGH |
286
+ | Unexplained sample attrition | Large gap between starting *N* and final *N* without explanation | MEDIUM |
287
+ | SEM small sample | *N* < 200 without small sample correction | MEDIUM |
288
+ | HLM Level-2 insufficient | Level-2 units < 30 | MEDIUM |
289
+
290
+ ### 4.5 Uncorrected Multiple Comparisons
291
+
292
+ | Red Flag | Description | Severity |
293
+ |----------|-------------|----------|
294
+ | Multiple *t*-tests instead of ANOVA | 3+ group comparisons using multiple *t*-tests | HIGH |
295
+ | No post-hoc after ANOVA | Main effect significant but claiming group differences without post-hoc tests | MEDIUM |
296
+ | Multiple DVs uncorrected | Multiple dependent variables tested separately on the same dataset without Bonferroni or FDR | MEDIUM |
297
+ | Multiple model comparisons | Trying multiple models but only reporting "the best one" | HIGH |
298
+
299
+ ### 4.6 Assumption Violation
300
+
301
+ | Red Flag | Description | Severity |
302
+ |----------|-------------|----------|
303
+ | Assumption testing completely absent | Skipping normality/homogeneity/linearity tests | MEDIUM |
304
+ | Violations not addressed | Violations reported but original analysis still used | HIGH |
305
+ | CLT as excuse | "Because *N* > 30, normality can be ignored" without actual testing | LOW |
306
+ | Excessive VIF | VIF > 10 but no action taken | HIGH |
307
+
308
+ ### 4.7 Other Red Flags
309
+
310
+ | Red Flag | Description | Severity |
311
+ |----------|-------------|----------|
312
+ | *p* = .000 | Raw statistical software output, should be *p* < .001 | LOW |
313
+ | df inconsistent with *N* | *N* derived from degrees of freedom doesn't match reported *N* | HIGH |
314
+ | Inconsistent table numbers | Text narrative contradicts table values | HIGH |
315
+ | Statistical software not stated | Not reporting SPSS / R / Stata / Mplus and version | LOW |
316
+ | Causal language | Non-experimental designs (correlational/survey) using causal inference language | MEDIUM |
317
+ | Unreachable mean (GRIM) | A reported mean of discrete-scale data cannot be produced by any integer sum at the reported *N* and precision | HIGH |
318
+ | Unreachable SD (GRIMMER) | A reported SD of discrete-scale data is not attainable by any response distribution consistent with the reported mean and *N* | HIGH |
319
+ | *p* incompatible with statistic and df | The reported *p* matches neither tail reading of the reported test statistic at the reported df | HIGH |
320
+
321
+ ---
322
+
323
+ ## 5. Common Statistical Methods in Higher Education Research
324
+
325
+ Higher education research papers frequently involve the following topics and corresponding analysis methods. This table can be referenced during review to judge whether method selection is appropriate.
326
+
327
+ ### 5.1 Recommended Methods by Research Question Type
328
+
329
+ | Research Question Type | Recommended Method | Description |
330
+ |-----------------------|-------------------|-------------|
331
+ | Two-group comparison (e.g., experimental vs control) | Independent samples *t*-test / Mann-Whitney | Depending on data normality |
332
+ | Multi-group comparison (e.g., different institution types) | ANOVA / Kruskal-Wallis | Mean comparison for 3+ groups |
333
+ | Pre-post comparison | Paired *t*-test / Wilcoxon | Change within the same group |
334
+ | Predictive analysis (continuous DV) | Multiple regression | Multiple predictors' effects on continuous outcome |
335
+ | Predictive analysis (binary DV) | Logistic regression | E.g., graduation/dropout, pass/fail |
336
+ | Nested data (students -> schools) | HLM / MLM | Higher education data naturally has nested structure |
337
+ | Latent constructs and path analysis | SEM / CFA | Measuring unobservable constructs (e.g., teaching quality) |
338
+ | Scale reliability and validity | EFA -> CFA | Scale development or validation |
339
+ | Categorical variable association | Chi-square / Fisher's exact | Cross-tabulation analysis |
340
+ | Longitudinal data | Growth curve models / Latent growth models | Tracking student trajectories over multiple years |
341
+ | Large-scale datasets | Weighted analysis / sampling design correction | Accounting for sampling design when using national survey data |
342
+
343
+ ### 5.2 Special Considerations for Higher Education Research
344
+
345
+ | Consideration | Description |
346
+ |--------------|-------------|
347
+ | **Nested structure** | Higher education data almost always has nesting (students -> departments -> institutions); ignoring it underestimates standard errors and inflates Type I error |
348
+ | **Sampling design** | When using national databases (e.g., MOE statistics, public higher education data), must account for sampling weights and clustering |
349
+ | **Selection bias** | Students self-select into departments/institutions, not randomly assigned; consider propensity score matching or Heckman correction |
350
+ | **Ceiling effects** | Satisfaction surveys often show extreme skewness; need to check and consider Tobit model or non-parametric methods |
351
+ | **Small population** | Taiwan has a limited number of universities (~150); census surveys are not appropriate for inferential statistics (census, not sample) |
352
+ | **Time series** | Analyzing multi-year enrollment trends requires considering autocorrelation |
353
+ | **Multiple roles** | Same faculty completing multiple surveys (e.g., teaching evaluations) -> observations not independent |
354
+
355
+ ---
356
+
357
+ ## 6. Statistical Reporting Completeness Judgement
358
+
359
+ `methodology_reviewer_agent` assesses each applicable item against the study design, analysis, reporting standard, and target venue. There is no weighted completeness score: a missing decision-bearing item cannot be offset by complete presentation items.
360
+
361
+ | Item | Criterion-bound judgement |
362
+ |---|---|
363
+ | Descriptive statistics | `COMPLETE` / `PARTLY_COMPLETE` / `MISSING` / `NOT_APPLICABLE`, with the applicable reporting requirement |
364
+ | Effect sizes | same states, with the analyses to which the requirement applies |
365
+ | Confidence intervals or other uncertainty | same states, with the estimates to which the requirement applies |
366
+ | Assumption checks | same states, naming only assumptions required by the methods used |
367
+ | Power or precision justification | same states, when required by design or inference |
368
+ | Missing-data handling | same states, with the observed omission or method anchored |
369
+ | Format and table requirements | same states, separated from substantive statistical validity |
370
+ | Red-flag follow-up | each triggered item investigated and resolved, left unresolved, or marked not applicable |
371
+
372
+ For every `PARTLY_COMPLETE` or `MISSING` item, identify the manuscript location, the criterion source, why the omission matters, and whether it affects a substantive conclusion or only reporting clarity. Synthesize the result narratively; do not convert item states or counts into points, percentages, or a decision category.
373
+
374
+ ---
375
+
376
+ ## 7. Quick Reference: Recommended Review Sequence
377
+
378
+ Methodology reviewer should follow this sequence when reviewing statistical reporting:
379
+
380
+ ```
381
+ Step 1: Confirm research question -> analysis method correspondence is reasonable (Section 5)
382
+ Step 2: Check whether assumption testing is reported (Section 1.7)
383
+ Step 3: Check universal checklist item by item (Sections 1.1-1.6)
384
+ Step 4: Consult method-specific checklist (Section 2)
385
+ Step 5: Scan red flag list (Section 4)
386
+ Step 6: Verify APA formatting (Section 3)
387
+ Step 7: Produce the criterion-bound completeness judgement and narrative synthesis (Section 6)
388
+ ```
389
+
390
+ ---
391
+
392
+ ## 8. Bounded Arithmetic Recompute Procedures (#610)
393
+
394
+ > **Epistemic status — read this before anything below.** This layer does
395
+ > not replace the human reviewer, and it does not make the reviewer's
396
+ > arithmetic trustworthy. What the engineering can force is narrow and
397
+ > should be named honestly: the receipt grammar (methodology seat, sprint
398
+ > Phase 2) forces every recomputation attempt to be *declared, structured,
399
+ > and auditable* — required fields present, closed enums respected, each
400
+ > mismatch linked to exactly one weakness. Triggering likewise rests on a
401
+ > mandatory declaration with adjudicated honesty, never machine-checked
402
+ > triggering: when nothing is recomputable the seat must say so
403
+ > (`no_recomputable_statistics:`), and the checker verifies only that the
404
+ > declaration exists — never that it is true; a false attestation over
405
+ > recomputable statistics surfaces at adjudication as `MISSED` verdicts.
406
+ > It cannot force the arithmetic
407
+ > inside a receipt to be correct; model arithmetic is not deterministic, and
408
+ > a fully conforming receipt built on wrong arithmetic is still wrong.
409
+ > Correctness is decided by human adjudication against the four-verdict
410
+ > scale (`VERIFIED` / `CLAIM_ONLY` / `MISCOMPUTED` / `MISSED`) defined in
411
+ > `docs/design/2026-08-02-610-statistical-recompute-baseline-spec.md` §7.1.
412
+ > Everything in this section is a bounded aid to that human judgment, never
413
+ > a substitute for it.
414
+
415
+ Four bounded procedures cover the recomputable slice of the red flags in
416
+ Section 4. Normative worked cases and undecidable boundaries live in the
417
+ #610 spec §5; this section is the reviewer-facing operating summary. Outside
418
+ a procedure's boundary the honest status is `not_computable` with its closed
419
+ reason — never an extended or improvised calculation.
420
+
421
+ ### 8.1 `p_from_test_statistic`
422
+
423
+ Recompute a reported *p* from a named test family, statistic, and df.
424
+ Prerequisites: test family, statistic value, required df, reported *p*, and
425
+ the tail rule where it matters. *F* and chi-square are upper-tail by family;
426
+ *t*/*z* results must never silently become two-tailed. **When the paper
427
+ states no tail, the receipt must show BOTH labeled values (two-tailed and
428
+ one-tailed)** — a single-tail comparison alone supports no verdict. If the
429
+ tail choice flips the verdict, the status is `not_computable`
430
+ (`tail_ambiguous`). Adjusted, bootstrap, permutation, or exact *p* values
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+ without their procedure are `not_computable` (`nonstandard_p_procedure`).
432
+
433
+ ### 8.2 `grim`
434
+
435
+ Test whether a reported mean of discrete-scale data is reachable. Apply only
436
+ to an unweighted mean with known discrete granularity, known item-specific
437
+ analytic *N*, and a stated precision/rounding rule. **The completed
438
+ procedure requires the rounding interval implied by the reported precision
439
+ AND the nearest attainable values straddling the reported mean** — an
440
+ integer-product observation without the rounding-interval reachability check
441
+ is not a completed GRIM procedure. Continuous, weighted, imputed,
442
+ transformed, composite, or item-averaged values with unknown granularity are
443
+ `not_computable`.
444
+
445
+ ### 8.3 `grimmer`
446
+
447
+ Inherits every GRIM prerequisite and additionally requires the SD convention
448
+ (sample vs population), reported precision, and finite discrete support. A
449
+ mismatch needs a completed reachability proof over the bounded response
450
+ space; intuition that an SD "looks too small" is not a procedure. If the
451
+ mean itself is GRIM-inconsistent, the status is `not_computable`
452
+ (`mean_grim_inconsistent`).
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+
454
+ ### 8.4 `n_from_df`
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+
456
+ Invert a reported df to a required sample size under a NAMED test-specific
457
+ identity (`df=N-1` one-sample/paired *t*; `df=N1+N2-2` equal-variance
458
+ independent *t*; the identity is not universal and the receipt must name
459
+ it). Welch–Satterthwaite, Kenward–Roger, corrected repeated-measures,
460
+ multiple-imputation, and mixed/clustered/robust/survey-weighted analyses are
461
+ `not_computable` unless their required inputs are present. Chi-square df
462
+ usually encode table dimensions and cannot be inverted to *N*.
463
+
464
+ ### 8.5 Red-flag classification (arithmetic rows)
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+
466
+ Every arithmetic-flavored red-flag row in Section 4 is classified below so
467
+ that no row is silently claimed "solved" by the four procedures (#610 spec
468
+ §8). Inclusion criterion: a Section 4 row appears here exactly when its red
469
+ flag concerns reported numeric values or quantities derivable from them —
470
+ whether by recomputation or by direct comparison against a stated numeric
471
+ threshold; rows about narrative, design, or process conduct (causal
472
+ language, HARKing, selective reporting, software not stated) stay outside
473
+ this classification. Classes: **covered** (a bounded procedure recomputes it — emit a
474
+ receipt when attempted), **reporting-only** (noticing and citing suffices;
475
+ there is nothing to recompute), **direct-threshold** (a read-off comparison
476
+ against a stated numeric threshold; report as a finding, no receipt), and
477
+ **not_computable** (arithmetic in nature, but no bounded procedure exists
478
+ yet — must NOT be presented as verified).
479
+
480
+ | Red-flag row (Section 4) | Classification | Handling |
481
+ |---|---|---|
482
+ | df inconsistent with *N* (4.7) | covered | `n_from_df` receipt |
483
+ | Unreachable mean — GRIM (4.7) | covered | `grim` receipt |
484
+ | Unreachable SD — GRIMMER (4.7) | covered | `grimmer` receipt |
485
+ | *p* incompatible with statistic and df (4.7) | covered | `p_from_test_statistic` receipt |
486
+ | Inconsistent effect sizes (4.3) | not_computable | No bounded effect-size consistency procedure exists yet (a future separate addition per the #610 spec); flag the inconsistency as a finding, never as a verified recomputation |
487
+ | Many *p* near .05 (4.1) | reporting-only | Distributional suspicion; cite the values, no recompute |
488
+ | Sample too small, *N* < 10 × predictors (4.4) | direct-threshold | Read-off comparison; finding only |
489
+ | SEM small sample, *N* < 200 (4.4) | direct-threshold | Read-off comparison; finding only |
490
+ | HLM Level-2 units < 30 (4.4) | direct-threshold | Read-off comparison; finding only |
491
+ | Excessive VIF > 10 (4.6) | direct-threshold | Read-off comparison; finding only |
492
+ | *p* = .000 (4.7) | reporting-only | Format defect; no recompute |
493
+ | Inconsistent table numbers (4.7) | reporting-only | Internal-consistency contradiction; cite both surfaces, no bounded recompute |
494
+
495
+ ### 8.6 Receipt grammar pointer
496
+
497
+ Under a sprint contract, every attempted recomputation is recorded as an
498
+ `AR<n>` Arithmetic Receipt in the methodology Phase 2 card — grammar,
499
+ conditional fields, and mismatch-to-weakness linkage are normative in the
500
+ agent's Phase 2 section (canonical source:
501
+ `references/reviewer_sprint_prompt_source.md`, `methodology-receipt`
502
+ fragment) and machine-checked by `scripts/check_phase_conformance.py`.
503
+ Method references: Brown & Heathers (2017) GRIM,
504
+ <https://doi.org/10.1177/1948550616673876>; Anaya (2016) GRIMMER,
505
+ <https://doi.org/10.7287/peerj.preprints.2400v1>.