112 update ses

.Rbuildignore

@@ -28,3 +28,4 @@ NUL
 ^codecov\.yml$
 ^CLAUDE\.md$
 ^references$
+^\.claude$

.github/workflows/R-CMD-check.yaml

@@ -27,6 +27,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      NOT_CRAN: true
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/test-coverage.yaml

@@ -14,6 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      NOT_CRAN: true
 
     steps:
       - uses: actions/checkout@v4

.gitignore

@@ -18,3 +18,4 @@ NUL
 cran-comments.md
 Rplots.pdf
 references/working/
+.claude/

CLAUDE.md

@@ -8,6 +8,12 @@ Implements the two one-sided tests (TOST) procedure to test equivalence for t-te
 
 Primary citation: Lakens (2017) <doi:10.1177/1948550617697177>
 
+## Workflow
+
+**Always work directly in the local repository** — edit files in place, run tests, and commit from the main checkout. Do NOT create git worktrees or separate working directories. This keeps the workflow simple and changes immediately visible in the user's IDE/editor.
+
+**Non-production files**: If separate R scripts, markdown files, or other working files are needed during development but are not intended for the package itself (e.g., scratch analyses, exploratory scripts, notes), place them in the `junk/` folder. This keeps the package source tree clean.
+
 ## Development Commands
 
 ```r
@@ -19,6 +25,20 @@ devtools::document()     # Generate documentation from roxygen2
 
 ## Code Style
 
+### R Script Section Headings
+Place the section title after a `#` (or `##` for sub-sections) followed by at least four trailing dashes (`-`), equal signs (`=`), or hashtags (`#`). Do NOT place lines of `#` signs before and after section headings.
+
+```r
+# Good
+# Load data --------
+## Clean variables ----
+
+# Bad
+######################
+# Load data
+######################
+```
+
 ### Naming Conventions
 - **Main functions**: `snake_case` (e.g., `t_TOST`, `boot_t_TOST`, `brunner_munzel`, `wilcox_TOST`)
 - **Legacy functions**: `camelCase` or mixed (e.g., `TOSTone`, `TOSTpaired`, `powerTOSTtwo`)

DESCRIPTION

@@ -40,5 +40,5 @@ LazyData: true
 Config/testthat/edition: 3
 Depends: 
     R (>= 3.5)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Language: en-US

NAMESPACE

@@ -4,6 +4,8 @@ S3method(boot_log_TOST,default)
 S3method(boot_log_TOST,formula)
 S3method(boot_ses_calc,default)
 S3method(boot_ses_calc,formula)
+S3method(boot_ses_test,default)
+S3method(boot_ses_test,formula)
 S3method(boot_smd_calc,default)
 S3method(boot_smd_calc,formula)
 S3method(boot_t_TOST,default)
@@ -48,6 +50,7 @@ export(boot_compare_smd)
 export(boot_cor_test)
 export(boot_log_TOST)
 export(boot_ses_calc)
+export(boot_ses_test)
 export(boot_smd_calc)
 export(boot_t_TOST)
 export(boot_t_test)
@@ -86,11 +89,13 @@ export(power_eq_f)
 export(power_t_TOST)
 export(power_twoprop)
 export(power_z_cor)
+export(rank_diff)
 export(rbs)
 export(ses_calc)
 export(simple_htest)
 export(smd_calc)
 export(t_TOST)
+export(trans_rank_prob)
 export(tsum_TOST)
 export(twoprop_test)
 export(wilcox_TOST)
@@ -110,6 +115,7 @@ importFrom(lifecycle,deprecated)
 importFrom(stats,complete.cases)
 importFrom(stats,cor)
 importFrom(stats,density)
+importFrom(stats,dlogis)
 importFrom(stats,dnorm)
 importFrom(stats,dt)
 importFrom(stats,integrate)

NEWS.md

@@ -7,6 +7,37 @@ NEWS
 
 ## New Features
 
+- New `trans_rank_prob()` function for transforming probability-scale effect sizes
+  between four scales: probability (concordance), difference (rank-biserial),
+  log-odds, and odds. Supports bidirectional transformation via `from` and `to`
+  arguments with delta-method standard errors and monotonic CI endpoint mapping.
+
+- `brunner_munzel()` gains a `scale` argument to report results on alternative
+  scales ("probability", "difference", "logodds", "odds") without changing the
+  underlying test. The default `scale = "probability"` preserves existing behavior.
+
+- `ses_calc()` estimate labels now use probability notation (e.g.,
+  `P(X>Y) - P(X<Y)` instead of `Rank-Biserial Correlation`). The `$method`
+  string and data frame row names retain human-readable names. Code that parses
+  `names(result$estimate)` may need updating.
+
+- `ses_calc()` paired sample labels use `P(Z>0)` notation (where Z = X - Y);
+  one-sample labels use `P(X>0)`.
+
+
+- Effect size calculators now support hypothesis testing and `htest` output:
+  - `ses_calc` and `boot_ses_calc` updated with `output`, `alternative`, and `null.value` arguments
+    - Default output is now `"htest"` class; use `output = "data.frame"` for legacy format
+    - Supports `"two.sided"`, `"less"`, `"greater"`, `"equivalence"`, and `"minimal.effect"` alternatives
+    - New Agresti/Lehmann placement-based SE method (`se_method = "agresti"`) with log-odds scale hypothesis testing
+    - Continuity correction for boundary cases (complete separation)
+  - `smd_calc` and `boot_smd_calc` updated with `output`, `alternative`, `null.value`, and `test_method` arguments
+    - Default output is now `"htest"` class; use `output = "data.frame"` for legacy format
+    - Supports the same alternative hypothesis options as `ses_calc`
+    - `test_method` argument (`"z"` or `"t"`) controls the reference distribution for `smd_calc`
+    - Degrees of freedom included in output when `test_method = "t"`
+    - Bootstrap p-values for `boot_smd_calc` computed from empirical distribution
+    - New `denom` argument for direct denominator selection (`"z"`, `"rm"`, `"pooled"`, `"avg"`, `"glass1"`, `"glass2"`), overriding `glass`, `rm_correction`, and `var.equal` as needed; informative messages on conflicts
 - Added `hodges_lehmann` function for robust location testing
   - Implements Hodges-Lehmann estimators (HL1 for one-sample/paired, HL2 for two-sample)
   - Supports exact permutation, randomization, and asymptotic (KDE-based) inference
@@ -19,8 +50,49 @@ NEWS
   - Handles null values (single or equivalence bounds) as reference lines
   - Automatically handles two-sample t-test estimates by computing mean difference
 
+- Added BCa (bias-corrected and accelerated) bootstrap confidence intervals as a new `boot_ci = "bca"` option for:
+  - `boot_t_test`, `boot_t_TOST`, `boot_log_TOST`, `boot_smd_calc`, `boot_ses_calc`, and `boot_cor_test`
+  - BCa intervals provide second-order accuracy by correcting for bias and skewness in the bootstrap distribution
+  - Acceleration factor computed via leave-one-out jackknife (pooled jackknife for two-sample designs)
+  - Informative errors for degenerate cases with suggestion to use `boot_ci = "perc"` as fallback
+
 ## Improvements
 
+- **Correlation SE improvements** for `z_cor_test()` and `corsum_test()`:
+  - Spearman's rho now uses the Bonett-Wright ρ-dependent SE formula
+    (`sqrt((1 + r^2/2) / (n - 3))`) instead of the fixed 1.06 constant,
+    providing better calibration across the full range of rho.
+  - `z_cor_test()` gains a `se_method` argument (`"analytic"` or `"jackknife"`)
+    for computing the standard error via leave-one-out resampling on the
+    Fisher z scale. The jackknife SE is used consistently for both the test
+    statistic and the confidence interval.
+  - Both functions now return `stderr` as a named vector with `z.se`
+    (Fisher z scale, used for inference) and `cor.se` (delta method SE on the
+    correlation scale, for descriptive purposes).
+  - The `method` string in the returned `htest` object now indicates the SE
+    type used (e.g., `"Pearson's product-moment correlation with approximate SE"`
+    or `"Spearman's rank correlation rho with jackknifed SE"`).
+
+- `simple_htest()`, `boot_t_test()`, `perm_t_test()`, and `hodges_lehmann()`
+  now produce more informative estimate labels that indicate the direction of
+  calculation (e.g., `"mean difference (treatment - control)"` when using the
+  formula interface).
+- For two-sample mean-based tests (`simple_htest` with t-test, `boot_t_test`,
+  `perm_t_test`), the mean difference is now appended as a third element of
+  `$estimate`, while preserving existing group means at positions 1-2
+  (backwards-compatible).
+- Paired test estimates are labeled to clarify the differencing operation,
+  e.g., `"mean of the differences (z = x - y)"`.
+- Wilcoxon/Mann-Whitney estimates in `simple_htest()` are labeled as
+  `"Hodges-Lehmann estimate"` with direction indicated.
+- `hodges_lehmann()` estimate labels updated for clarity: `"pseudomedian of x"`
+  for one-sample, `"Hodges-Lehmann estimate (x - y)"` for two-sample, and
+  `"Hodges-Lehmann estimate (z = x - y)"` for paired tests.
+- Trimmed mean labels in `boot_t_test()` and `perm_t_test()` now include the
+  trimming proportion, e.g., `"trimmed mean difference (x - y, tr = 0.1)"`.
+- A `$sample_size` element (named numeric vector) is now included in the
+  returned `htest` object for all four functions. For two-sample formula calls,
+  names reflect the actual factor levels.
 - **Permutation test terminology**: Clarified distinction between "Exact Permutation" (all permutations enumerated) and "Randomization" (permutations sampled with replacement) tests across `perm_t_test`, `hodges_lehmann`, and `brunner_munzel`
 - **p_method auto-selection**: Added intelligent default for `p_method` argument in permutation-based functions:
   - `NULL` (default): Automatically selects "exact" for exact permutation tests and "plusone" for randomization tests