Full SEM Analyzing — Structural Paths, Indirect Effects, Manuscript
Open-source skill.
Read reference/specs/output-variation-protocol.md before every generation.
Workflow
| Step |
Responsibility |
Executor |
Document |
Input |
Output |
| Additional tests |
Run Additional Tests |
Main Agent |
workflow/step04-run-additional-tests.md |
Prior step output |
Indirect/residual diagnostics |
| Subgroup |
Analyze Subgroups |
Main Agent |
workflow/step05-analyze-subgroups.md |
Prior step output |
Multigroup SEM |
| Modeling |
Fit Models |
Main Agent |
workflow/step06-fit-models.md |
Prior step output |
Alternative structural models |
| Comparison |
Compare Models |
Main Agent |
workflow/step07-compare-models.md |
Prior step output |
Cross-model synthesis |
| Manuscript |
Generate Manuscript |
Main Agent |
workflow/step08-generate-manuscript.md |
Prior step output |
methods.md + results.md |
Additional Inputs
Collect if not already provided during testing:
- Target discipline and journal (for reporting conventions — APA 7th, Structural Equation Modeling style, etc.)
- Research question / hypothesis (directional path predictions)
- Grouping variable (for multigroup invariance testing)
- Mediation structure (which paths are hypothesized as indirect)
- Estimator preference if deviating from testing-skill default (ML, MLR, WLSMV, DWLS)
Output Structure
output/
├── methods.md
├── results.md
├── tables/ ← lavaan/semopy parameter tables, fit-index tables (Markdown + CSV)
├── figures/ ← path diagram, residual plots, multigroup comparison plots (PNG, 300 DPI)
├── references.bib
├── code.R ← Style-varied lavaan script
└── code.py ← Style-varied semopy script (optional)
Key References (read before generation)
| File |
Purpose |
reference/specs/output-variation-protocol.md |
Output quality variation layers |
reference/specs/code-style-variation.md |
Seven-dimension code style diversity |
reference/patterns/sentence-bank.md |
4–6 phrasings per result type |
reference/rules/reporting-standards.md |
Hard rules for SEM reporting |
Reporting Standards
Same as vera-data-path-reviewing, plus:
- Indirect effects: always report with bias-corrected bootstrap 95% CI (≥ 5000 draws). Do not rely on Sobel z.
- Direct / indirect / total: report all three; when direct becomes non-significant after accounting for the indirect path, describe as "consistent with partial/full mediation" rather than proof of causality.
- Multigroup: report the Δχ², Δdf, Δp, ΔCFI for each invariance step (configural → metric → structural).
- Alternative models: compare with χ² difference test (nested) or AIC/BIC (non-nested); interpret ΔAIC > 10 as strong preference.
- Under MLR / Satorra–Bentler scaled estimators: Δχ² MUST be computed using the scaled difference statistic (Satorra & Bentler 2001), not by subtracting the two scaled χ² values. Simple subtraction of Satorra–Bentler-adjusted χ² gives a biased test. Use
lavaan::lavTestLRT(fit1, fit2, method="satorra.bentler.2001") (or 2010 variant for negative corrections). Report the scaled difference T_d, df, p. This applies to ALL nested-model comparisons, including measurement-invariance steps.
- Modification indices: only apply when theoretically justified; report which MIs were accepted and which rejected.
- Standardized path coefficients: β with SE or CI; asterisks for significance levels discouraged — report exact p.
Cross-Skill Interface
Method Unit Contract:
├── code_r → .R script (style-varied, lavaan)
├── code_python → .py script (style-varied, semopy, optional)
├── methods_md → methods.md (varied structure)
├── results_md → results.md (varied phrasing)
├── tables/ → Markdown + CSV
├── figures/ → PNGs 300 DPI (varied layout)
├── references_bib → .bib with cited references
└── comparison → cross-model narrative (in results.md)
Invoked directly after vera-data-path-reviewing or orchestrated by vera-data-application-pipelining.
1---2name: vera-data-path-generating3description: Full SEM analysis skill. Extends the initial structural model with indirect effects, alternative-path comparison, multigroup testing, residual review, and manuscript-ready methods/results. Trigger after vera-data-path-reviewing completes and its PART 0–2 artifacts are present (see ../../CROSS-SKILL-INTERFACE.md). If invoked directly without those artifacts, halts and prompts the user to run testing first or supply equivalent PART 0–2 code.4---56# Full SEM Analyzing — Structural Paths, Indirect Effects, Manuscript78Open-source skill.910Read `reference/specs/output-variation-protocol.md` before every generation.1112## Workflow1314| Step | Responsibility | Executor | Document | Input | Output |15|---|---|---|---|---|---|16| Additional tests | Run Additional Tests | Main Agent | `workflow/step04-run-additional-tests.md` | Prior step output | Indirect/residual diagnostics |17| Subgroup | Analyze Subgroups | Main Agent | `workflow/step05-analyze-subgroups.md` | Prior step output | Multigroup SEM |18| Modeling | Fit Models | Main Agent | `workflow/step06-fit-models.md` | Prior step output | Alternative structural models |19| Comparison | Compare Models | Main Agent | `workflow/step07-compare-models.md` | Prior step output | Cross-model synthesis |20| Manuscript | Generate Manuscript | Main Agent | `workflow/step08-generate-manuscript.md` | Prior step output | methods.md + results.md |2122## Additional Inputs2324Collect if not already provided during testing:25- Target discipline and journal (for reporting conventions — APA 7th, Structural Equation Modeling style, etc.)26- Research question / hypothesis (directional path predictions)27- Grouping variable (for multigroup invariance testing)28- Mediation structure (which paths are hypothesized as indirect)29- Estimator preference if deviating from testing-skill default (ML, MLR, WLSMV, DWLS)3031## Output Structure3233```34output/35├── methods.md36├── results.md37├── tables/ ← lavaan/semopy parameter tables, fit-index tables (Markdown + CSV)38├── figures/ ← path diagram, residual plots, multigroup comparison plots (PNG, 300 DPI)39├── references.bib40├── code.R ← Style-varied lavaan script41└── code.py ← Style-varied semopy script (optional)42```4344## Key References (read before generation)4546| File | Purpose |47|---|---|48| `reference/specs/output-variation-protocol.md` | Output quality variation layers |49| `reference/specs/code-style-variation.md` | Seven-dimension code style diversity |50| `reference/patterns/sentence-bank.md` | 4–6 phrasings per result type |51| `reference/rules/reporting-standards.md` | Hard rules for SEM reporting |5253## Reporting Standards5455Same as vera-data-path-reviewing, plus:56- **Indirect effects**: always report with bias-corrected bootstrap 95% CI (≥ 5000 draws). Do not rely on Sobel z.57- **Direct / indirect / total**: report all three; when direct becomes non-significant after accounting for the indirect path, describe as "consistent with partial/full mediation" rather than proof of causality.58- **Multigroup**: report the Δχ², Δdf, Δp, ΔCFI for each invariance step (configural → metric → structural).59- **Alternative models**: compare with χ² difference test (nested) or AIC/BIC (non-nested); interpret ΔAIC > 10 as strong preference.60- **Under MLR / Satorra–Bentler scaled estimators**: Δχ² MUST be computed using the **scaled difference statistic** (Satorra & Bentler 2001), not by subtracting the two scaled χ² values. Simple subtraction of Satorra–Bentler-adjusted χ² gives a biased test. Use `lavaan::lavTestLRT(fit1, fit2, method="satorra.bentler.2001")` (or 2010 variant for negative corrections). Report the scaled difference T_d, df, p. This applies to ALL nested-model comparisons, including measurement-invariance steps.61- **Modification indices**: only apply when theoretically justified; report which MIs were accepted and which rejected.62- **Standardized path coefficients**: β with SE or CI; asterisks for significance levels discouraged — report exact p.6364## Cross-Skill Interface6566```67Method Unit Contract:68├── code_r → .R script (style-varied, lavaan)69├── code_python → .py script (style-varied, semopy, optional)70├── methods_md → methods.md (varied structure)71├── results_md → results.md (varied phrasing)72├── tables/ → Markdown + CSV73├── figures/ → PNGs 300 DPI (varied layout)74├── references_bib → .bib with cited references75└── comparison → cross-model narrative (in results.md)76```7778Invoked directly after `vera-data-path-reviewing` or orchestrated by `vera-data-application-pipelining`.
VeraSuperHub