Merge pull request #19 from kstawiski/v2

OmicSelector 2.0: Complete Phase 5 Implementation with TCGA Validation

Author: kstawiski

.github/workflows/pkgdown.yml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, v2]
+  pull_request:
+    branches: [main, master, v2]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -31,6 +31,7 @@ Imports:
     mlr3tuning (>= 0.20.0),
     mlr3fselect (>= 0.12.0),
     mlr3learners (>= 0.6.0),
+    mlr3filters (>= 0.7.0),
     mlr3measures,
     mlr3misc,
     paradox,
@@ -50,6 +51,7 @@ Suggests:
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
+    mlr3mbo,
     mlr3torch,
     torch,
     sva,
@@ -63,6 +65,7 @@ Suggests:
     jsonlite,
     plumber,
     ranger,
+    glmnet,
     xgboost,
     lightgbm,
     e1071,

NAMESPACE

@@ -9,8 +9,13 @@ S3method(print,NogueiraStability)
 S3method(print,OmicBenchmarkResult)
 S3method(print,OmicsInput)
 S3method(print,ReportData)
+S3method(print,SignatureSelectionResult)
 export(BenchmarkService)
+export(FilterGOF_KS)
+export(FilterHurdle)
+export(FilterZeroProp)
 export(FrozenComBat)
+export(OmicModalitySpec)
 export(OmicPipeline)
 export(OmicSelector_OmicSelector)
 export(OmicSelector_OmicSelector_wrapper)
@@ -51,21 +56,36 @@ export(OmicSelector_signature_overlap)
 export(OmicSelector_table)
 export(OmicSelector_vulcano_plot)
 export(OmicSelector_xgboost)
+export(OmicStackedEnsemble)
+export(OmicWeightedEnsemble)
+export(SequentialSelector)
+export(StabilityEnsemble)
+export(apply_frozen_combat_cv)
+export(balance_classes)
+export(build_correlation_adjacency)
 export(cache_stats)
 export(cached_filter)
 export(calibration_summary)
+export(check_batch_correction_leakage)
 export(check_dl_availability)
 export(check_feature_correlations)
 export(clear_cache)
+export(compare_gof_filters)
 export(compute_ece)
 export(compute_nogueira_stability)
+export(compute_shap_with_warnings)
 export(compute_stability_from_resample)
 export(create_explainer)
 export(create_frozen_combat_pipeop)
+export(create_hsfs_selector)
 export(create_mlp_learner)
 export(create_omic_cache)
 export(create_report_data)
+export(create_stability_ensemble)
 export(decompose_brier)
+export(export_bundle)
+export(export_onnx)
+export(export_vetiver)
 export(extract_features_from_resample)
 export(extract_selected_features)
 export(feature_importance)
@@ -75,22 +95,56 @@ export(fit_temperature_scaling)
 export(frozen_combat_correct)
 export(generate_cache_key)
 export(generate_tripod_report)
+export(get_consensus_features)
 export(get_modality_info)
+export(get_optimal_params)
 export(get_parallel_status)
+export(get_reliable_shap_features)
+export(get_selected_features_per_fold)
 export(list_deprecated_functions)
+export(load_bundle)
+export(make_autotuner_glmnet)
+export(make_autotuner_lightgbm)
+export(make_autotuner_ranger)
+export(make_autotuner_xgboost)
+export(make_gnn_learner)
+export(make_gof_filter)
+export(make_mlp_learner)
+export(make_tabtransformer_learner)
 export(memoize_with_split)
 export(merge_omics_data)
+export(noise_augment)
 export(omic_benchmark)
 export(omic_pipeline)
 export(partial_dependence)
+export(plot_signature_tradeoffs)
+export(plot_xai_importance)
+export(print_shap_warnings)
+export(print_xai_summary)
+export(register_gof_filters)
 export(reliability_diagram_data)
 export(reset_parallel)
+export(run_bayesian_benchmark)
+export(run_dl_benchmark)
+export(select_best_signature)
 export(setup_parallel)
 export(shap_values)
+export(smote_augment)
+export(stack_omics)
+export(tabddpm_generate)
 export(validate_no_leakage)
 export(validate_omics_input)
+export(validate_synthetic)
 export(with_parallel)
+export(xai_correlations)
+export(xai_explainer_mlr3)
+export(xai_importance)
+export(xai_pdp)
+export(xai_pipeline)
+export(xai_shap)
 import(R6)
+importFrom(R6,R6Class)
+importFrom(mlr3pipelines,"%>>%")
 importFrom(mlr3pipelines,`%>>%`)
 importFrom(stats,aov)
 importFrom(stats,cor)