Add additional stan model for joint likelihood #36
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…likelihood needed
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Pull request overview
Adds a second Stan model variant that uses a joint (rather than factorised) order-statistic likelihood for summary types 1/2, plus helper code to select/compile the desired model and analysis scripts to compare outputs.
Changes:
- Introduces a new Stan program
hierarchical_data_synthesis_summary_stats_joint.stanimplementing a joint density for three order statistics. - Adds an exported R helper
compile_stan_model()(with Rd + NAMESPACE update) to compile either the factorised or joint model. - Updates/introduces analysis scripts to toggle between Stan models and compare factorised vs joint results, plus basic tests for argument validation.
Reviewed changes
Copilot reviewed 8 out of 9 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/testthat/test-utils.R | Adds tests around compile_stan_model() argument validation. |
| R/utils.R | Adds exported compile_stan_model() helper to select model file and compile via rstan. |
| NAMESPACE | Exports compile_stan_model (roxygen-generated). |
| man/compile_stan_model.Rd | Roxygen-generated documentation for the new helper. |
| inst/stan/hierarchical_data_synthesis_summary_stats_joint.stan | New joint-likelihood Stan model for type-1/2 summaries. |
| analysis/new_simulation_study.R | Adds a STAN_MODEL switch to compile factorised vs joint model. |
| analysis/main_analysis.R | Adds a STAN_MODEL switch to compile factorised vs joint model. |
| analysis/compare_factorised_vs_joint.R | New analysis script to refit joint model and produce comparison outputs/tables. |
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Pull request overview
Copilot reviewed 8 out of 9 changed files in this pull request and generated 6 comments.
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This PR adds the additional stan model (using a joint rather than factorised likelihood).