Conversation
- Fixed spelling to "quasi-quotation" in R documentation - Added many new terms to inst/WORDLIST for spell checking - Sorted and deduplicated entries in inst/WORDLIST - Improved coverage of technical and domain-specific vocabulary - No functional code changes, documentation and wordlist only - Prepares for improved documentation and code quality tools
docs - Added efficacyStops and futilityStops to hasChanged methods - Updated .getDesignGroupSequentialOrWithInterimStops to use new params - Replaced -Inf with C_FUTILITY_BOUNDS_DEFAULT for futility bounds - Improved parameter comparison logic for design changes - Fixed typo: quasiquotation to quasi-quotation in documentation - Bumped package version to 4.4.0.9302 in DESCRIPTION
sequential design - Add .isBoundayStoppingActivated helper for boundary stop checks - Warn if delayedInformation is ignored due to interim stops - Use stricter argument validation for typeOfDesign and typeBetaSpending - Change exception type for invalid typeOfDesign when stops are specified
designPlan - Bump package version to 4.4.0.9303 in DESCRIPTION - Add simulationEnabled check to rejectPerStage assignment - Store lambda1 and lambda2 in designPlan object - Minor formatting adjustments for clarity - No changes to external interfaces or function signatures
and test coverage in rpact
- Refactor function signatures for better readability in f_core_assertions.R and f_design_group_sequential.R - Update documentation links in man files to use the new syntax for better compatibility - Adjust output format handling in f_logger.R and related tests - Update DESCRIPTION file to reflect the new roxygen2 version
- Update method calls to use 'self$' for accessing object properties - Refactor assignment operator for overallVarianceEvent to use '<-' instead of '<<-' - Ensure validation method for varianceEvents uses the correct property reference
- Change email from daniel.sabanes_bove@rconis.com to daniel.sabanes_bove@rpact.com
Contributor
There was a problem hiding this comment.
Pull request overview
This PR adds GitHub Copilot agent/instruction configuration for the rpact repository, bumps package development metadata, and includes a set of targeted bug fixes and maintenance improvements across design, simulation, output formatting, documentation, and tests.
Changes:
- Added
.github/copilot-instructions.mdplus four specialized agent configs under.github/agents/to guide Copilot behavior in different workflows. - Updated package metadata (
DESCRIPTION, wordlist, generated Rd cross-links, vignette tweak) and improved output-format handling/tests. - Fixed/adjusted several internal behaviors (e.g., dataset survival members, group sequential interim-stops handling, logging toggle support, minor C++ suppressions).
Reviewed changes
Copilot reviewed 28 out of 45 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| vignettes/rpact_getting_started.Rmd | Adds VS Code to the “auto code completion” editor list in the getting started vignette. |
| tests/testthat/test-pkgname.R | Adds regression/behavior tests for output format file I/O and rounding functions. |
| src/f_utilities.cpp | Adds suppress comments on template instantiations in getOrder() switch cases. |
| R/parameter_descriptions.R | Wraps/clarifies internal parameter description text for lambda1/lambda2. |
| R/f_simulation_multiarm_survival.R | Adds internal roxygen docs for .getSimulationSurvivalMultiArmStageEvents() and minor doc formatting. |
| R/f_logger.R | Adds logEnabled toggle to .logBase() to allow disabling logging. |
| R/f_design_plan_counts.R | Persists lambda1/lambda2 back into the returned design plan object. |
| R/f_design_group_sequential.R | Introduces interim-stop activation helper and improves handling/warnings for incompatible args when interim stops are used. |
| R/f_core_output_formats.R | Fixes roundFunction string matching, accepts roundFunction in file-based option values, and corrects pluralization when writing formats. |
| R/f_core_assertions.R | Formatting-only change to .assertAreValidFutilityBounds() signature layout. |
| R/class_summary.R | Avoids using probsH1$rejectPerStage in a simulation-enabled branch. |
| R/class_design.R | Makes hasChanged() signatures consistent and includes interim-stop parameters for inverse normal designs. |
| R/class_core_parameter_set.R | Documentation typo fix (“quasiquotation” → “quasi-quotation”). |
| R/class_analysis_dataset.R | Fixes member access (self$...) in survival dataset allocation ratio/variance validation and clarifies a commented placeholder. |
| man/setOutputFormat.Rd | Improves \seealso linking style for getOutputFormat(). |
| man/getTestActions.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getStageResults.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getSampleSizeSurvival.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getSampleSizeRates.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getSampleSizeMeans.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getSampleSizeCounts.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getRepeatedPValues.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getRepeatedConfidenceIntervals.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getPowerSurvival.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getPowerRates.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getPowerMeans.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getPowerCounts.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getPowerAndAverageSampleNumber.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getOutputFormat.Rd | Improves \seealso linking style for setOutputFormat(). |
| man/getGroupSequentialProbabilities.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getFinalPValue.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getFinalConfidenceInterval.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getDesignInverseNormal.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getDesignGroupSequential.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getDesignFisher.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getDesignConditionalDunnett.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getDesignCharacteristics.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getConditionalRejectionProbabilities.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getConditionalPower.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getClosedConditionalDunnettTestResults.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getClosedCombinationTestResults.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/getAnalysisResults.Rd | Updates \seealso links to the explicit \link[=...] form. |
| man/fetch.ParameterSet.Rd | Documentation typo fix (“quasiquotation” → “quasi-quotation”). |
| inst/WORDLIST | Expands/organizes spelling whitelist terms used by spell-check tooling. |
| DESCRIPTION | Bumps dev version/date, removes RoxygenNote, and adds Config/roxygen2/version. |
| .github/copilot-instructions.md | Adds repository-specific Copilot guidance for statistical risk, style, tests, and docs. |
| .github/agents/rpact_testcoverage.agent.md | Adds a Copilot agent profile for improving test coverage (testthat/covr). |
| .github/agents/rpact_github.agent.md | Adds a Copilot agent profile for GitHub issue/PR-driven workflow. |
| .github/agents/rpact_general.agent.md | Adds a Copilot agent profile for general package development. |
| .github/agents/rpact_bugfix_refactor.agent.md | Adds a Copilot agent profile for bugfixing and careful refactoring. |
Files not reviewed (17)
- man/fetch.ParameterSet.Rd: Language not supported
- man/getAnalysisResults.Rd: Language not supported
- man/getClosedCombinationTestResults.Rd: Language not supported
- man/getClosedConditionalDunnettTestResults.Rd: Language not supported
- man/getConditionalPower.Rd: Language not supported
- man/getConditionalRejectionProbabilities.Rd: Language not supported
- man/getDesignCharacteristics.Rd: Language not supported
- man/getDesignConditionalDunnett.Rd: Language not supported
- man/getDesignFisher.Rd: Language not supported
- man/getDesignGroupSequential.Rd: Language not supported
- man/getDesignInverseNormal.Rd: Language not supported
- man/getFinalConfidenceInterval.Rd: Language not supported
- man/getFinalPValue.Rd: Language not supported
- man/getGroupSequentialProbabilities.Rd: Language not supported
- man/getOutputFormat.Rd: Language not supported
- man/getPowerAndAverageSampleNumber.Rd: Language not supported
- man/getPowerCounts.Rd: Language not supported
Comment on lines
+1190
to
+1196
| .isBoundayStoppingActivated <- function(boundaryStops) { | ||
| if (anyNA(boundaryStops) || all(boundaryStops)) { | ||
| return(FALSE) | ||
| } | ||
|
|
||
| return(TRUE) | ||
| } |
| newDesign <- do.call(.getDesignGroupSequential, args) | ||
| newDesign$criticalValues[which(!efficacyStops)] <- Inf | ||
| newDesign$futilityBounds[which(!futilityStops)] <- -Inf | ||
| newDesign$futilityBounds[which(!futilityStops)] <- C_FUTILITY_BOUNDS_DEFAULT # TODO check -Inf |
Comment on lines
+96
to
+98
| [RStudio](https://posit.co/downloads/) / [Positron](https://positron.posit.co/) | ||
| / [Eclipse](https://www.eclipse.org): auto code completion makes it easy to use | ||
| / [VS Code](https://code.visualstudio.com) / | ||
| [Eclipse](https://www.eclipse.org): auto code completion makes it easy to use |
- Bump version to 4.4.0.9304 - Update date to 2026-06-03 - Correct function name from .isBoundayStoppingActivated to .isBoundaryStoppingActivated in f_design_group_sequential.R - Adjust conditional checks to use the corrected function name - Clean up formatting in rpact_getting_started.Rmd
- Add `TrialDesignFixed` class for fixed sample size trials. - Implement `getDesignFixed` function to create fixed design objects. - Update DESCRIPTION to require R version 4.1.0 or higher. - Export `getDesignFixed` in NAMESPACE. - Enhance internal validation functions for trial design checks.
- Modify `plot.TrialDesign` and `plot.TrialDesignSet` to allow NA as a valid plot type - Update validation to permit NA in `.assertIsValidPlotType` - Introduce new function `.assertIsTrialDesignGroupSequentialOrFixed` for design validation - Add documentation for `TrialDesignFixed` and `getDesignFixed` functions - Ensure compatibility with existing design functions and improve error handling
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This pull request introduces new GitHub Copilot agent configuration files and instructions for the
rpactpackage, updates package metadata, and applies several minor bugfixes and code quality improvements. The agent files clarify the roles and priorities for Copilot in different development contexts (general, bugfix, test coverage, GitHub-driven). The package metadata is updated for a new development version, and several small code and documentation corrections are made for clarity and correctness.Copilot agent and instructions infrastructure:
.github/agents/for specialized Copilot behavior: general development (rpact_general.agent.md), bugfix/refactor (rpact_bugfix_refactor.agent.md), test coverage (rpact_testcoverage.agent.md), and GitHub-driven work (rpact_github.agent.md). Each provides detailed priorities, workflow, and output expectations for Copilot in that context. [1] [2] [3] [4].github/copilot-instructions.mdwith package-specific guidance for Copilot, covering statistical risk, R style, API stability, test, and documentation discipline.Package metadata and documentation updates:
DESCRIPTIONfor development version4.4.0.9303(date updated), and addedConfig/roxygen2/version: 7.3.3.9000. [1] [2]Bugfixes and code quality improvements:
DatasetSurvivalandDatasetEnrichmentSurvivalclasses by ensuring correct usage of helper functions and member variables for allocation ratios and variance events. [1] [2]self$.datainstead of.datafor clarity and future maintainability.fetchfunction docs.API and code consistency:
hasChangedinTrialDesignFisherandTrialDesignInverseNormalclasses, and added missing parameters for completeness. [1] [2] [3]