PyMetaAnalysis 0.3.0__tar.gz → 0.4.0__tar.gz

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/CHANGELOG.md

@@ -6,6 +6,26 @@ Changes planned for the next release accumulate under `Unreleased`.
 
 ## Unreleased
 
+## 0.4.0 - 2026-07-23
+
+### Added
+
+- leave-one-out Meta-regression refits with model-level diagnostics,
+  coefficient changes, explicit unidentifiable-deletion records, and preserved
+  provenance.
+- exact Meta-regression externally standardized residuals, Cook's distances,
+  DFBETAS, transparent screening thresholds, and fixed-version R `metafor`
+  cross-software fixtures.
+- Meta-regression term VIF, moderator-level GVIF/GSIF, and weighted,
+  column-scaled condition diagnostics with variance-decomposition proportions,
+  heuristic-only flags, and R `metafor` cross-software fixtures.
+- explicit named Meta-regression linear contrasts with nonzero null values,
+  individual z/t inference, joint chi-squared/F tests, labeled coefficient
+  matrices, and R `metafor` cross-software fixtures.
+- opt-in Riley Meta-regression true-effect prediction intervals using
+  `t_(k-p-1)`, with explicit residual-df validation, preserved refit
+  configuration, and fixed-version R `metafor` boundary references.
+
 ## 0.3.0 - 2026-07-22
 
 ### Added

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/CITATION.cff

@@ -8,8 +8,8 @@ authors:
   - family-names: Ding
     given-names: Zhaobo
     email: ding.zb@yahoo.com
-version: 0.3.0
-date-released: 2026-07-22
+version: 0.4.0
+date-released: 2026-07-23
 repository-code: https://github.com/ZhaoboDing/PyMetaAnalysis
 url: https://zhaoboding.github.io/PyMetaAnalysis/
 license: MIT

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyMetaAnalysis
-Version: 0.3.0
+Version: 0.4.0
 Summary: A pandas-first, auditable meta-analysis library for Python
 Project-URL: Documentation, https://zhaoboding.github.io/PyMetaAnalysis/
 Project-URL: Source, https://github.com/ZhaoboDing/PyMetaAnalysis
@@ -28,7 +28,7 @@ Requires-Dist: actionlint-py>=1.7.12.24; extra == 'dev'
 Requires-Dist: build>=1.2; extra == 'dev'
 Requires-Dist: mypy>=1.10; extra == 'dev'
 Requires-Dist: pandas-stubs>=2.0; extra == 'dev'
-Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: ruff<0.17,>=0.16; extra == 'dev'
 Requires-Dist: scipy-stubs>=1.10; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: mkdocs>=1.6; extra == 'docs'
@@ -177,11 +177,23 @@ Rows excluded by missing-value or sparse-data policies remain in
 `study_results` with a stable `row_id`, `included=False`, and an
 `exclusion_reason`.
 
-## Sensitivity and plots
+## Diagnostics, contrasts, and plots
 
 ```python
 leave_one_out = result.leave_one_out().to_dataframe()
 cumulative = result.cumulative(order="publication_year").to_dataframe()
+regression_deleted = regression.leave_one_out()
+regression_coefficient_changes = regression_deleted.coefficients
+regression_influence = regression.influence()
+flagged_diagnostics = regression_influence.flagged
+collinearity = regression.collinearity()
+term_vif = collinearity.term_vif
+moderator_gvif = collinearity.moderator_gvif
+condition_indices = collinearity.condition_indices
+south_vs_east = regression.contrast(
+    {"region[South]": 1.0, "region[East]": -1.0},
+    name="South - East",
+)
 
 ax = result.forest(show_prediction_interval=True)
 ax = result.funnel()
@@ -189,9 +201,20 @@ ax = result.funnel()
 
 Plotting methods return Matplotlib axes and never call `show()`. Funnel plots
 are descriptive small-study-effect diagnostics, not proof of publication bias.
-An eligible single-numeric-moderator Meta-regression result additionally
-provides `regression.bubble()` with fitted confidence and optional prediction
-bands.
+Meta-regression leave-one-out results also expose a long-form coefficient
+change table. Exact influence diagnostics add externally standardized
+residuals, Cook's distance, DFBETAS, and explicit heuristic screening
+thresholds without automatically excluding studies. Meta-regression
+collinearity diagnostics add `metafor`-compatible VIF/GVIF plus weighted,
+column-scaled condition indices and variance-decomposition proportions.
+Their documented references are review aids, not automatic variable-selection
+rules. Explicit named linear contrasts provide individual z/t inference and
+full-rank joint chi-squared/F tests without silently adjusting for multiple
+testing. An eligible
+single-numeric-moderator Meta-regression result additionally provides
+`regression.bubble()` with fitted confidence and optional prediction bands.
+Mixed-effects Meta-regression supports its documented default prediction rule
+and an explicit Riley `t_(k-p-1)` alternative.
 
 ## Documentation
 

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/README.md

@@ -128,11 +128,23 @@ Rows excluded by missing-value or sparse-data policies remain in
 `study_results` with a stable `row_id`, `included=False`, and an
 `exclusion_reason`.
 
-## Sensitivity and plots
+## Diagnostics, contrasts, and plots
 
 ```python
 leave_one_out = result.leave_one_out().to_dataframe()
 cumulative = result.cumulative(order="publication_year").to_dataframe()
+regression_deleted = regression.leave_one_out()
+regression_coefficient_changes = regression_deleted.coefficients
+regression_influence = regression.influence()
+flagged_diagnostics = regression_influence.flagged
+collinearity = regression.collinearity()
+term_vif = collinearity.term_vif
+moderator_gvif = collinearity.moderator_gvif
+condition_indices = collinearity.condition_indices
+south_vs_east = regression.contrast(
+    {"region[South]": 1.0, "region[East]": -1.0},
+    name="South - East",
+)
 
 ax = result.forest(show_prediction_interval=True)
 ax = result.funnel()
@@ -140,9 +152,20 @@ ax = result.funnel()
 
 Plotting methods return Matplotlib axes and never call `show()`. Funnel plots
 are descriptive small-study-effect diagnostics, not proof of publication bias.
-An eligible single-numeric-moderator Meta-regression result additionally
-provides `regression.bubble()` with fitted confidence and optional prediction
-bands.
+Meta-regression leave-one-out results also expose a long-form coefficient
+change table. Exact influence diagnostics add externally standardized
+residuals, Cook's distance, DFBETAS, and explicit heuristic screening
+thresholds without automatically excluding studies. Meta-regression
+collinearity diagnostics add `metafor`-compatible VIF/GVIF plus weighted,
+column-scaled condition indices and variance-decomposition proportions.
+Their documented references are review aids, not automatic variable-selection
+rules. Explicit named linear contrasts provide individual z/t inference and
+full-rank joint chi-squared/F tests without silently adjusting for multiple
+testing. An eligible
+single-numeric-moderator Meta-regression result additionally provides
+`regression.bubble()` with fitted confidence and optional prediction bands.
+Mixed-effects Meta-regression supports its documented default prediction rule
+and an explicit Riley `t_(k-p-1)` alternative.
 
 ## Documentation
 

pymetaanalysis-0.4.0/docs/adr/0003-meta-regression-prediction-intervals.md

@@ -0,0 +1,70 @@
+# ADR 0003: Meta-regression prediction-interval choices
+
+- Status: Accepted
+- Date: 2026-07-23
+
+## Context
+
+For a mixed-effects Meta-regression prediction at design vector `x`, the
+estimated true-effect variance combines residual heterogeneity with
+uncertainty in the fitted mean:
+
+```text
+Var_prediction = tau^2 + x' Cov(beta_hat) x
+```
+
+The critical-value distribution remains a methodological choice. Common
+software offers a default normal-or-t rule and a Riley alternative with one
+fewer residual degree of freedom. Neither approximation removes uncertainty
+from estimating tau-squared, and changing the package default would alter
+existing results.
+
+## Decision
+
+`meta_regression()` accepts
+`prediction_interval_method="default" | "riley"` for mixed-effects models.
+The canonical resolved method is stored in
+`result.method.prediction_interval_method`.
+
+The default remains `normal_or_t_k_minus_p`:
+
+- normal coefficient inference uses a standard normal prediction critical
+  value;
+- either Hartung-Knapp mode uses a t critical value with `k-p` degrees of
+  freedom.
+
+The opt-in Riley method uses a t critical value with `k-p-1` degrees of
+freedom regardless of the coefficient-inference distribution:
+
+```text
+prediction = x' beta_hat
+PI_Riley = prediction +/- t_(k-p-1) *
+           sqrt(tau^2 + x' Cov(beta_hat) x)
+```
+
+Riley intervals require `k-p >= 2`. Requesting Riley for a common-effect model
+or a mixed model without enough residual degrees of freedom raises a domain
+error. The selection is preserved by deleted-study refits and reused by
+`predict()` and `bubble()`.
+
+Both rules predict the distribution of true effects in a new study at the
+specified moderator values. They do not add an unknown sampling variance for
+a future observed effect.
+
+## Validation
+
+The committed fixed-version R `metafor` fixture records default and
+`predtype="Riley"` predictions for normal and Hartung-Knapp inference,
+multivariable moderator values, and a zero-tau-squared boundary. Unit tests
+also check the critical-value formula and invalid degrees of freedom.
+Property-based tests verify symmetry, unchanged mean-effect inference, and
+the Riley interval's greater width relative to the default rule.
+
+## Consequences
+
+- existing fits retain their numerical default;
+- the alternative is explicit, auditable, and reproducible;
+- Riley is documented as an alternative approximation rather than an
+  automatic small-sample correction;
+- future prediction-interval rules require a separate statistical decision
+  and independent reference coverage.

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/docs/getting-started.md

@@ -71,7 +71,7 @@ result.ci
 result.standard_error
 result.tau2
 result.q
-result.i2       # a proportion from 0 to 1
+result.i2  # a proportion from 0 to 1
 result.h2
 result.i2_method
 ```

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/docs/guides/meta-regression.md

@@ -136,6 +136,23 @@ precision weights, normalized precision weights, and leverage. A regression
 precision weight is not a universal percentage contribution to every
 coefficient.
 
+## Leave-one-out sensitivity
+
+Use exact deleted-model refits to inspect dependence on individual studies:
+
+```python
+diagnostics = result.leave_one_out()
+
+print(diagnostics.table)
+print(diagnostics.coefficients)
+```
+
+Every successful deletion re-estimates residual tau-squared, coefficients, and
+inference with the same resolved model configuration. Deletions that make the
+design unidentifiable are retained explicitly instead of aborting the other
+refits. See [sensitivity analysis](sensitivity-analysis.md) for the result
+contract and interpretation limits.
+
 ## Predict at moderator values
 
 Prediction replays the fitted numeric and categorical encoding:
@@ -157,6 +174,16 @@ in a new study with those moderators. The interval does not include an
 additional, unknown sampling variance for a future observed estimate. Unknown
 categories and missing prediction inputs are rejected.
 
+The default prediction rule follows coefficient inference: it uses a normal
+critical value with `inference_method="normal"` and `t_(k-p)` with either
+Hartung-Knapp method. Set `prediction_interval_method="riley"` while fitting to
+use a `t_(k-p-1)` prediction critical value instead. Riley therefore needs at
+least two residual degrees of freedom and is usually wider, especially in
+small samples. It is an explicit alternative approximation, not an automatic
+claim of superior coverage. The selected canonical method is retained in
+`result.method.prediction_interval_method` and reused by `predict()` and
+`bubble()`.
+
 ## Plot a single numeric moderator
 
 After installing the `plot` extra, an intercept-containing model with exactly
@@ -172,9 +199,9 @@ ax = result.bubble(
 ```
 
 Bubble area is proportional to normalized fitted precision weight. The fitted
-line and interval bands reuse `result.predict()`, including the selected normal
-or Hartung-Knapp covariance and critical value. A prediction band is available
-only for mixed-effects models.
+line and interval bands reuse `result.predict()`, including the selected
+coefficient covariance and prediction-interval rule. A prediction band is
+available only for mixed-effects models.
 
 PyMetaAnalysis rejects bubble plots for categorical, multiple-moderator, or
 no-intercept fits. Drawing a marginal or partial-effect line for those models
@@ -197,6 +224,125 @@ the public value is truncated to zero and the negative raw value is retained
 with a warning. Pseudo-R² is not the proportion of outcome variance explained
 in ordinary individual-level regression.
 
+## Inspect deleted-study influence
+
+Use exact deletion diagnostics when a study appears unusual or the fitted
+association may depend strongly on one row:
+
+```python
+influence = result.influence()
+
+influence.table
+influence.dfbetas
+influence.flagged
+```
+
+Every included study is omitted once, with tau-squared and coefficient
+inference re-estimated under the original settings. The result reports the
+externally standardized deleted residual, Cook's distance, and term-specific
+DFBETAS values. Failed reduced models remain visible rather than being silently
+dropped.
+
+The result also exposes its numerical screening thresholds. These thresholds
+identify rows for review; they do not prove that a study is erroneous,
+authorize automatic exclusion, or correct for trying multiple model
+specifications. See [sensitivity analysis](sensitivity-analysis.md) for the
+full output and interpretation contract.
+
+## Inspect moderator collinearity
+
+Use `collinearity()` to inspect coefficient inflation and the geometry of the
+fitted weighted design:
+
+```python
+collinearity = result.collinearity()
+
+collinearity.term_vif
+collinearity.moderator_gvif
+collinearity.condition_indices
+collinearity.variance_proportions
+collinearity.concerning_dimensions
+```
+
+`term_vif` contains one VIF and its square-root standard-error inflation factor
+(`sif`) for every encoded non-intercept term. `moderator_gvif` keeps all dummy
+terms for one categorical moderator together and reports its GVIF plus the
+dimension-adjusted `gsif = gvif ** (1 / (2 * term_count))`. This grouping makes
+a multi-level moderator comparable without pretending that each treatment-
+coded term is a separate scientific variable.
+
+The condition table uses the fitted inverse-variance weights and normalizes
+each weighted design column before singular-value decomposition. It is
+therefore invariant to positive changes of moderator units. The result retains
+the original unweighted, scale-dependent design condition number separately as
+`raw_condition_number`.
+
+The fixed references of condition index greater than 30 and variance
+proportion greater than 0.5 are conventional screening heuristics. A
+`concerning` dimension must meet the condition-index reference and concentrate
+more than half of the coefficient variance for at least two terms. The library
+does not attach automatic cutoffs to VIF/GVIF, remove variables, refit models,
+or turn these diagnostics into evidence for a preferred specification.
+
+## Test explicit linear contrasts
+
+Inspect `result.design_info.term_names`, then define a scientific comparison by
+term name rather than coefficient position:
+
+```python
+south_vs_east = result.contrast(
+    {
+        "region[South]": 1.0,
+        "region[East]": -1.0,
+    },
+    name="South - East",
+)
+
+south_vs_east.table
+south_vs_east.contrast_matrix
+south_vs_east.joint_test
+```
+
+The default null hypothesis is `C beta = 0`. Use `rhs=` for a nonzero null:
+
+```python
+age_threshold = result.contrast(
+    {"mean_age": 1.0},
+    name="Age slope equals 0.02",
+    rhs=0.02,
+)
+```
+
+For several prespecified hypotheses, pass a named mapping of mappings:
+
+```python
+contrasts = result.contrast(
+    {
+        "South - East": {
+            "region[South]": 1.0,
+            "region[East]": -1.0,
+        },
+        "Age slope": {"mean_age": 1.0},
+    },
+    rhs={
+        "South - East": 0.0,
+        "Age slope": 0.02,
+    },
+)
+```
+
+A DataFrame is also accepted: rows are named contrasts and columns are fitted
+term names. Unspecified fitted terms receive weight zero. Unknown terms,
+nonfinite weights, zero rows, duplicate names, and rank-deficient multi-row
+contrast matrices are errors rather than implicit repairs.
+
+Each row reports the contrast estimate, standard error, null value,
+estimate-minus-null, z or t statistic, unadjusted p-value, and confidence
+interval for `C beta`. A full-row-rank set also receives a joint chi-squared or
+F test in `joint_test`. Individual p-values are deliberately not adjusted for
+multiple testing; prespecify the contrast family and apply an external
+multiplicity procedure when the scientific protocol requires one.
+
 ## Missing values, provenance, and reports
 
 `missing="raise"` identifies every missing effect, uncertainty, study label,

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/docs/guides/r-interoperability.md

@@ -19,6 +19,9 @@ fixtures used by this project.
 | Continuous group summaries | `meta_continuous()` | `escalc()` then `rma.uni()` | `metacont()` |
 | Subgroups | `subgroup=` on a high-level call | separate fits or a moderator model | `subgroup=` |
 | Leave-one-out | `result.leave_one_out()` | `leave1out()` for supported fits | `metainf()` |
+| Meta-regression influence | `regression.influence()` | `influence()`, `rstudent()`, `cooks.distance()`, `dfbetas()` | — |
+| Meta-regression collinearity | `regression.collinearity()` | `vif()` plus weighted design diagnostics | — |
+| Meta-regression linear contrasts | `regression.contrast(...)` | `anova(..., X=..., rhs=...)` | — |
 | Cumulative analysis | `result.cumulative()` | `cumul()` | `metacum()` |
 
 PyMetaAnalysis intentionally has no `metabin`, `metacont`, or `rma` aliases.
@@ -88,6 +91,14 @@ Eligible random-effects fits include the documented HTS prediction interval.
 R packages offer additional prediction-interval choices, so matching the mean
 interval does not by itself guarantee a matching prediction interval.
 
+Meta-regression uses a separate prediction rule. Its default corresponds to
+`predict(fit)` in `metafor`: normal inference uses a normal critical value and
+Hartung-Knapp inference uses `t_(k-p)`. PyMetaAnalysis
+`prediction_interval_method="riley"` corresponds to
+`predict(fit, predtype="Riley")`, using `t_(k-p-1)` for the true-effect
+prediction interval while leaving the mean-effect confidence interval
+unchanged.
+
 ## Sparse binary studies
 
 The closest names are:
@@ -171,6 +182,7 @@ as numerically equivalent.
 ## Primary R references
 
 - [`metafor::rma.uni`](https://wviechtb.github.io/metafor/reference/rma.uni.html)
+- [`metafor::predict.rma`](https://wviechtb.github.io/metafor/reference/predict.rma.html)
 - [`metafor::rma.mh`](https://wviechtb.github.io/metafor/reference/rma.mh.html)
 - [`metafor::escalc`](https://wviechtb.github.io/metafor/reference/escalc.html)
 - [`meta::metagen`](https://search.r-project.org/CRAN/refmans/meta/html/metagen.html)

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/docs/guides/sensitivity-analysis.md

@@ -31,6 +31,81 @@ requires at least two included studies so each refit retains one. Random-effects
 analysis requires at least three so every refit retains the two studies needed
 to estimate tau-squared.
 
+### Meta-regression leave-one-out analysis
+
+`MetaRegressionResult.leave_one_out()` repeats the fitted regression while
+omitting each included study:
+
+```python
+diagnostics = regression.leave_one_out()
+
+print(diagnostics.table)
+print(diagnostics.coefficients)
+```
+
+The returned `MetaRegressionLeaveOneOutResult` retains `original` and a
+`results` tuple aligned with the omitted-study rows. Its model table reports
+the refitted residual heterogeneity, global moderator test, condition number,
+and warnings. Its long-form coefficient table reports every refitted term and
+`estimate_change`, defined as the deleted estimate minus the full-model
+estimate.
+
+Deleting a study can make a categorical level disappear or otherwise make the
+design matrix unidentifiable. That deletion is retained with
+`refit_success=False`, an exception type and message, unavailable numeric
+fields, and `None` in the matching `results` position. Other deletions continue
+to be fitted. Use `diagnostics.failed` to inspect these rows. A failed deletion
+does not by itself label that study as influential; it shows that the fitted
+design depends on the study for identifiability.
+
+The original model must have at least `k >= p + 2`, so deleting one study can
+still leave more studies than coefficients. Each successful refit re-estimates
+tau-squared and coefficient inference with the original model settings.
+
+### Meta-regression influence diagnostics
+
+`MetaRegressionResult.influence()` builds on the same exact deleted-model
+refits:
+
+```python
+influence = regression.influence()
+
+print(influence.table)
+print(influence.dfbetas)
+print(influence.flagged)
+```
+
+`MetaRegressionInfluenceResult` contains the underlying `leave_one_out`
+workflow and its omission-aligned `results`. The case-level `table` adds:
+
+- the deleted residual, its standard error, and the externally standardized
+  residual;
+- Cook's distance based on the full-model coefficient covariance;
+- the largest absolute DFBETAS value across fitted terms;
+- the original leverage and normalized precision weight;
+- separate outlier and influence screening flags.
+
+The long-form `dfbetas` table records the unstandardized `dfbeta` as
+full-model minus deleted-model coefficient, its deletion-based standard-error
+reference, the resulting DFBETAS value, and its threshold flag for each term.
+Failed deletion fits retain their exception type and message in `table`, use
+`NaN` diagnostics, and retain one unavailable row per term in `dfbetas`.
+
+The screening references are explicit in both the result attributes and table:
+
+- `abs(externally_standardized_residual) > z(0.975)` is a pointwise,
+  asymptotic potential-outlier reference;
+- Cook's distance is flagged above the median of a chi-squared distribution
+  with `p` degrees of freedom;
+- `abs(DFBETAS) > 1` flags a coefficient-specific change.
+
+`potentially_influential` combines only the Cook's-distance and DFBETAS rules;
+`flagged` also includes the residual outlier screen. These cutoffs are
+heuristic diagnostics, not hypothesis-test conclusions, multiplicity-adjusted
+decision rules, or instructions to exclude a study. Inspect subject-matter
+differences, data quality, protocol decisions, and model specification before
+acting on them.
+
 ## Cumulative analysis
 
 By default, cumulative analysis follows input order:
@@ -80,6 +155,9 @@ Every refit reuses the original result's:
 - binary continuity corrections and RD zero-variance policy, or the continuous
   effect-size convention.
 
+Meta-regression refits additionally reuse the intercept choice, inference
+method, moderator order, and complete explicit categorical level definitions.
+
 Derived results retain provenance that maps their local calculations back to
 the original `row_id` values.
 
@@ -106,3 +184,7 @@ design, outcome definition, risk of bias, and numerical leverage. They are not
 by themselves a reason to exclude the study. Likewise, a cumulative trend can
 describe the historical evidence path but does not remove time-related changes
 in methods, populations, or publication processes.
+
+The current Meta-regression workflow reports exact deleted-model fits and
+coefficient changes. It does not yet calculate Cook's distance, DFBETAS, or an
+automatic influential-study flag.

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/docs/guides/zero-events.md

@@ -9,8 +9,8 @@ corrections from the pooled Mantel-Haenszel correction.
 For study-level OR/RR effects, the default settings are:
 
 ```python
-continuity_correction=0.5
-correction_scope="only_zero_studies"
+continuity_correction = 0.5
+correction_scope = "only_zero_studies"
 ```
 
 The correction is added to every cell of an included study containing at least
@@ -43,7 +43,7 @@ variance. This includes double-zero, double-all, and opposite-boundary tables.
 The default policy retains these studies:
 
 ```python
-rd_zero_variance="correct"
+rd_zero_variance = "correct"
 ```
 
 The RD itself remains the raw treatment risk minus control risk. Corrected
@@ -51,7 +51,7 @@ counts are used only to form a positive sampling variance. To exclude all such
 studies before pooling, Q, tau-squared, and weight calculations, use:
 
 ```python
-rd_zero_variance="exclude"
+rd_zero_variance = "exclude"
 ```
 
 Excluded rows remain in `result.study_results` with
@@ -63,8 +63,8 @@ RD-specific; setting `exclude` for OR or RR is rejected.
 Exact common-effect Mantel-Haenszel OR/RR pooling uses raw tables by default:
 
 ```python
-mh_continuity_correction=None
-mh_correction_scope="only_zero_studies"
+mh_continuity_correction = None
+mh_correction_scope = "only_zero_studies"
 ```
 
 `continuity_correction` still controls the study-level effects used for display

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/docs/index.md

@@ -84,11 +84,12 @@ lists unsupported methods explicitly.
 
 ## Project status
 
-PyMetaAnalysis 0.2.1 fixes documentation and repository links in the PyPI
-project description. Version 0.2.0 added direct generic standard-error input
-to the initial public analysis scope. The project has not undergone a formal
-external statistical audit. Pin the package version for consequential work
-and independently check important analyses. See the repository
+PyMetaAnalysis 0.4.0 extends Meta-regression with exact leave-one-out and
+influence diagnostics, VIF/GVIF and weighted condition diagnostics, explicit
+linear contrasts, and opt-in Riley prediction intervals. The project has not
+undergone a formal external statistical audit. Pin the package version for
+consequential work and independently check important analyses. See the
+repository
 [changelog](https://github.com/ZhaoboDing/PyMetaAnalysis/blob/main/CHANGELOG.md)
 and [contribution guide](development.md). For manuscripts and archived
 analyses, see [citing PyMetaAnalysis](citation.md).

{pymetaanalysis-0.3.0 → pymetaanalysis-0.4.0}/docs/limitations.md

@@ -19,22 +19,29 @@ deferred functionality explicit.
 - forest and descriptive funnel plots;
 - structured provenance and reports;
 - study-level Meta-regression with numeric and explicitly encoded categorical
-  moderators, generalized DL/PM/REML, and normal/Hartung-Knapp inference.
+  moderators, generalized DL/PM/REML, normal/Hartung-Knapp inference, and
+  exact leave-one-out refits plus externally standardized residual, Cook's
+  distance, DFBETAS, VIF/GVIF, weighted condition diagnostics, and explicit
+  linear contrasts;
+- default normal/`t_(k-p)` and opt-in Riley `t_(k-p-1)` true-effect
+  prediction intervals for mixed-effects Meta-regression.
 
 ## Not currently implemented
 
 - Peto odds ratios;
 - Mantel-Haenszel risk differences or random-effects MH pooling;
 - formula parsing, automatic interactions/splines, stepwise moderator
-  selection, multiplicity correction, or arbitrary linear contrasts;
+  selection, automatic pairwise contrasts, or multiplicity correction;
 - multilevel, multivariate, network, dose-response, diagnostic-accuracy, or
   individual-participant-data meta-analysis;
 - robust variance estimation or dependent-effect clustering;
 - single proportions, incidence rates, correlations, or survival outcomes;
 - Knapp-Hartung variants beyond the two documented choices;
-- alternative prediction-interval methods;
+- prediction-interval methods beyond the documented default and Riley rules;
 - formal funnel-asymmetry, trim-and-fill, selection-model, or publication-bias
   procedures;
+- Meta-regression DFFITS, covariance ratios, influence plots, or simulated and
+  re-estimated VIF variants;
 - automatic conversion from confidence intervals, p-values, or raw papers to
   study effects;
 - risk-of-bias assessment, certainty grading, protocol management, or study
@@ -78,7 +85,7 @@ workflow must version those artifacts separately.
 
 ## Stability and review status
 
-The package version is currently `0.2.1`. Public APIs and serialized schemas
+The package version is currently `0.4.0`. Public APIs and serialized schemas
 may change during the 0.x series. Pin versions in analysis environments and
 inspect changelog/schema updates before upgrading.