https://docs.github.com/en/code-security/tutorials/secure-your-dependencies/dependabot-quickstart-guide
https://docs.github.com/en/code-security/how-tos/secure-your-supply-chain/secure-your-dependencies/configuring-dependabot-version-updates
https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file

* perf: replace object.size() with numhash() in prune_hash

object.size() walks the entire hash table structure on every
cache_fun() call, taking ~2ms per invocation. Since cache_fun is
called 15+ times per gs_design_ahr run (via expected_time/ahr and
gs_power_npe), this adds up to significant overhead.

Replace with numhash() which returns the entry count in O(1), and
use clrhash() for a simple eviction strategy when the limit is
exceeded.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* perf: replace dplyr full_join/select/arrange with base R in gs_design_npe

The output assembly in gs_design_npe used full_join (to merge H0 and
H1 probabilities), select, rename, and arrange from dplyr. Since
gs_design_npe is called once per gs_design_ahr and these operations
are on small data frames (6 rows), base R merge() and column
subsetting are much faster.

Combined with the gs_power_npe change, this yields ~50% overall
improvement for multi-analysis designs.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* perf: replace dplyr operations with base R in gs_design_ahr output

Replace mutate, full_join, select, arrange, and filter operations
in the output assembly section of gs_design_ahr with equivalent base
R operations (direct column assignment, merge, column subsetting,
order).

This eliminates the dplyr overhead for the final output formatting
which previously involved multiple tibble round-trips on small data
frames.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* perf: remove dplyr from hot-path functions (expected_time, gs_info_ahr)

Replace select(-n) with base R column removal, and replace
mutate/transmute in the info_frac loop of gs_design_ahr with
direct column assignment. These functions are called repeatedly
during uniroot iterations, so even small per-call savings add up.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* perf: preserve tibble output type and fix row ordering

Exported functions gs_power_npe and gs_design_npe must return tibbles
for backward compatibility. Add tibble::as_tibble() at the return
point to convert the base R data.frame used for fast internal
computation back to the expected output type.

Also fix row ordering in gs_design_npe to maintain upper-before-lower
within each analysis (matching the original arrange(analysis) with
upper-first convention).

Refine prune_hash to use a 100-entry limit per function, giving
predictable memory bounds (each entry is typically a few KB, so
~100KB per cached function).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* perf: redesign cache pruning based on empirical measurement

Profiling revealed that object.size() overcounts gs_power_npe cache
entries by ~600x (reports 1.8 MB per entry when true incremental cost
is ~3 KB). This is because object.size() walks into shared namespace
environments of function arguments, counting the same gsDesign2
namespace (833 KB) and gsDesign namespace (75 KB) for every entry.

Changes:
- Remove object.size() from the pruning path (both slow and inaccurate)
- Only check entry count before insertions, not on cache hits
- Set max_entries = 1024, justified by:
  - True cost: ~3 KB (gs_power_npe) to ~5 KB (ahr) per entry
  - 1024 entries ≈ 3-5 MB real memory
  - Supports ~200 cached designs in a session
  - A single design creates only 5-28 entries

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* return data frame instead

* update the change point in the calculation of expected accrual (#628)

* Migrate GitHub Actions to Node 24 (#626)

* Use dependabot to auto-update GitHub Actions versions (#632)

https://docs.github.com/en/code-security/tutorials/secure-your-dependencies/dependabot-quickstart-guide
https://docs.github.com/en/code-security/how-tos/secure-your-supply-chain/secure-your-dependencies/configuring-dependabot-version-updates
https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file

* Fix test-coverage workflow inputs for codecov/codecov-action@v6 (#634)

* Bump yihui/actions from 1.1.0 to 1.1.2 (#633)

Bumps [yihui/actions](https://github.com/yihui/actions) from 1.1.0 to 1.1.2.
- [Release notes](https://github.com/yihui/actions/releases)
- [Commits](yihui/actions@v1.1.0...v1.1.2)

---
updated-dependencies:
- dependency-name: yihui/actions
  dependency-version: 1.1.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Unify test names for consistency (#639)

* Increase tolerance for test of gsDesign::gsSurv() vs gs_power_ahr() (#637)

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Xie <xieyih@lctcvp7913.merck.com>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: Yujie Zhao <43153957+LittleBeannie@users.noreply.github.com>
Co-authored-by: John Blischak <jdblischak@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>