Add multiple imputation functions for response output#408
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| insightsengineering/tern@main, | ||
| insightsengineering/rtables@main, | ||
| insightsengineering/rtables.officer@main | ||
| Config/roxygen2/version: 8.0.0 |
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This is why you have a lot of diffs in your document() you have update to roxygen 8.0.0 FYI.
I will update it in a separate PR
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Pull request overview
This PR adds support utilities to generate multiple-imputation outputs for binary response analyses, including pooling helpers and p-value categorization, and wires them into package exports/documentation.
Changes:
- Added
resp_multiple_imputation()/h_impute_analyze_resp()for scenario-based binary response imputation + CMH risk-difference/p-value aggregation. - Added
pool_rubin_scalar(),pool_z_stat(), andcategorize_pval()(plus tests and docs) to support pooling and p-value labeling. - Updated exports, pkgdown reference, NEWS, and a snapshot to reflect the new outputs.
Reviewed changes
Copilot reviewed 11 out of 18 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/testthat/test-resp_imputation.R | Adds tests for imputation-per-scenario and pooled outputs. |
| tests/testthat/test-pval_cat.R | Adds tests for p-value category normalization and assignment. |
| tests/testthat/test-pool_funs.R | Adds tests for Rubin and z-stat pooling helpers. |
| tests/testthat/_snaps/estimate_proportion_diff.md | Updates snapshot to include se_diff output. |
| R/resp_imputation.R | Implements impute+analyze helper and scenario-level multiple imputation wrapper. |
| R/pval_cat.R | Implements p-value category validation and categorization. |
| R/pool_funs.R | Implements pooling helpers for scalar estimates and z statistics. |
| NEWS.md | Documents newly added functions. |
| NAMESPACE | Exports new public functions. |
| man/resp_multiple_imputation.Rd | Adds generated documentation for resp_multiple_imputation(). |
| man/pool_z_stat.Rd | Adds generated documentation for pool_z_stat(). |
| man/pool_rubin_scalar.Rd | Adds generated documentation for pool_rubin_scalar(). |
| man/h_normalize_pvalcat.Rd | Adds generated documentation for h_normalize_pvalcat(). |
| man/h_impute_analyze_resp.Rd | Adds generated documentation for h_impute_analyze_resp(). |
| man/categorize_pval.Rd | Adds generated documentation for categorize_pval(). |
| DESCRIPTION | Updates roxygen metadata field(s). |
| .gitignore | Ignores .Renviron. |
| _pkgdown.yml | Adds new functions to pkgdown reference index. |
Files not reviewed (6)
- man/categorize_pval.Rd: Generated file
- man/h_impute_analyze_resp.Rd: Generated file
- man/h_normalize_pvalcat.Rd: Generated file
- man/pool_rubin_scalar.Rd: Generated file
- man/pool_z_stat.Rd: Generated file
- man/resp_multiple_imputation.Rd: Generated file
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@danielinteractive rebase on the new roxygen2 8.0.0 dev branch so you have a clean PR. otherwise lgtm!
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* add draft imputation functions * add pval category functions * add pooling functions * add imputation/analysis functions * add to NEWS, refresh docs * fix assertion * ignore .Renviron * update snapshot * Update WORDLIST Hilferty * rewrite namespace with roxygen 8.0.0 --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> Co-authored-by: munoztd0 <dtord@its.jnj.com>
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Please see NEWS.md for the updates.
This is needed for binary response multiple imputation outputs.
Notes:
This depends on 1490: additional stats insightsengineering/tern#1491
I did not run a full
devtools::document()because there are many unrelated updates. Maybe worth to run this on thedevbranch to clean it up?