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Changelog

Source: NEWS.md

gflow 0.2.0 (unreleased)

Bug fixes

  • lcor.with.posterior() now validates every feature before computation and rejects inconsistent draw counts instead of silently truncating later features. Inputs must be finite numeric fields with a common positive draw count, and the credible level must be strictly between zero and one. Supplied feature and vertex names are validated and preserved in results. A single draw remains supported, with an undefined (NA) standard deviation.

Further craftsmanship improvements

  • Canonical trajectory complexes with both directions can now be passed to gfcor() and gfassoc.membership() with an explicit raw/retained support choice. Graph, vertex identity, field and refinement compatibility are checked before calling the existing association kernel. Archived input behavior is preserved.

  • Local-correlation help now defines its finite-graph edge cosine, anisotropy conditions and logratio limitations. The legacy sign mode is documented as unit weighting. pairs computes requested matrix-column pairs in their supplied order, allowing bounded blocks without a full association array.

  • Seeded permutation tests restore RNG state, support explicit within-group permutations, forward statistic settings and print the null/statistic contract.

  • R >= 4.1.0 and dgraphs >= 0.2.0 are required. Graph boundary adapters support published list and development object APIs; optional viewer diagnostics name the required ivue version and installation route. Push/PR checks cover operating systems, the minimum R series, and serial/OpenMP builds.

  • The guide links its complete catalog to help and opens with four task routes. Installed basin-parameters help derives defaults from constructor definitions. A developer map records implementation ownership, memory costs and interrupt limits without reorganizing stable numerical kernels.

  • Removed the installed metric-graph low-pass Shiny demo: it called a retired estimator that is no longer exported by gflow. Its historical source remains in Git history; smoothing belongs to the separate smoothing projects.

User experience

  • Added a complete-help source installation route, a package-help quick start, runnable local-correlation examples, and a visual introduction shared by the README and installed task guide. Guides now adapt to narrow screens.
  • Basin summaries print bounded rankings, diagnostics, and distinct raw, retained, and assigned vertex coverage. Explicit plot views show merge trees, primary assignments, or overlap counts. Failed results are labeled in field views and rejected by analytical views; numerical construction is unchanged.
  • Added a task-organized documentation website built from the maintained help and vignettes, with the package marked as unreleased.

User guides

  • Added installed task-oriented function and example-graph vignettes, with complete export/S3 coverage checks and public migration help.
  • Corrected the README constructor call, documented archived-object limits in flow-aware association, and made overlap assignment and permutation assumptions explicit in the existing workflows.
  • Corrected RTCB terminology to relaxed trajectory-constrained basins, matching the implemented constrained-path search.
  • Earlier extraction milestones below are history, not evidence that removed forwarders or experimental APIs remain available.

Earlier development changes

Retire duplicate generic 3D renderers

  • Removed the internal plot3D.plain(), plot3D.cont(), plot3D.cltrs(), plot3D.tree(), and plot3D.path() implementations. Use ivue’s plot3D.plain(), plot3D.cont(), plot3D.groups(), layer3D.edges(), and layer3D.path(), respectively.
  • Cluster highlights, selected-sample displays, and disk-embedding displays now return ivue browser widgets. Their additional scene controls use the ivue API; native additions belong in callback layers before widget capture. No compatibility aliases were added. The function-height plot3D.graph() was also removed in the graph extraction; use documented dgraphs or application plotting code. Domain-specific 2D functions remain available as listed in the function guide.

Separate adaptive extrema from dgraphs

  • Renamed detect.local.extrema() to detect.adaptive.extrema(), returning class gflow_local_extrema with separate summary, print, plot, and vertex methods. The old function name is no longer exported by gflow.
  • Re-exported dgraphs::vertices() as the shared generic so vertex extraction works for both packages’ objects regardless of attachment order.
  • Fixed center inclusion in vertices(..., include.center = TRUE) and retained the requested maxima/minima setting for summaries of empty results.

Migrate graph work to dgraphs

  • Removed the remaining generic graph construction, conversion, clustering, endpoint, path, diagnostic, and plotting exports. Use dgraphs where the migration guide identifies a verified successor.

Move retired estimators out of the core package

  • Removed PHATE, sparse diffusion/potential pseudotime, random-walk smoothing, distance-quantile analysis, quadratic-form geodesics, and their native support from gflow.
  • The archived graph-regression and conditional-expectation estimators remain available from gflowx; gflowx is no longer a gflow dependency.

Use the consolidated analysis surface

  • Centered the public package story on canonical basin/flow objects, post-construction exploration, local association, and flow-aware association.

  • De-exported generic weighted-p-value helpers, clustering summaries, interactive selection/widgets, and remaining support utilities.

  • Added breaking-release migration guidance, now accessible in installed gflow-migration help and the function guide.

  • Moved fitted-model local-slope testing and subject-neighborhood diagnostics to gflowx; restricted posterior local correlation to supplied field draws; and made the package spline wrapper internal.

  • Consolidated association entry points around lcor(), newly exported lslope(), gfcor(), and their explicit inference layers. Shape-specific lcor helpers and generic conditional-mean fassoc* support are now private.

  • De-exported generic statistics, preprocessing, grid, sampling, histogram, divergence, Wasserstein, synthetic-data, and miscellaneous plotting helpers. Subsequent renderer cleanup removed the generic widget exports; native domain-specific extrema-labeling functions remain public. Duplicate matrix preprocessing helpers were removed.

  • Retired compute.gfc(), compute.basins.of.attraction(), compute.gfc.trajectory(), compute.gfc.flow(), and create.basin.cx() with classed migration errors. Added archived gfc.flow, basins_of_attraction, and basin_cx conversion methods.

  • Migrated canonical basin construction to private geodesic, trajectory, and overlap-cell backends so active package and downstream code no longer depends on legacy exported constructors.

  • Added canonical post-construction basin refinement for relative-value filtering, extrema clustering, geometric filtering, support filtering, and basin expansion, with explicit per-stage provenance and preserved raw membership.

  • Removed the temporary generic graph compatibility exports. Use the corresponding dgraphs:: functions directly for graph construction, conversion, connected components, paths, distances, endpoint diagnostics, graph selection, and stability summaries.

  • Added canonical RTCB and overlap-cell-complex adapters, including complete RTCB parameter provenance and preservation of merged/unmerged basin, cell, overlap, cluster-mapping, graph, and simplified-field structures.

  • Added deterministic exact-plateau superlevel and sublevel merge trees to create.basin.complex(), including component-wise roots, elder ties, hierarchical support, branch assignment, merge events, and nonnegative persistence.

  • Added canonical trajectory_flow and geodesic_reachability adapters to create.basin.complex(). The adapters preserve raw overlap separately from primary assignment, retain legacy backend objects for provenance, normalize set memberships, and isolate seeded tie breaking from the global RNG state.

  • Added the Phase B canonical basin-complex API:

    • create.basin.complex() now validates graph geometry, fields, mass, density, method parameters, and refinement parameters into a stable basin_complex schema.
    • Added non-colliding get.basin.*() table, membership, assignment, merge-tree, trajectory, and cell accessors plus print, summary, plot, conversion, and data-frame methods.
    • All five method adapters, canonical refinement, downstream migration, archived-object conversion, and strict legacy-constructor retirement are now implemented. See the canonical basin-complex workflow vignette for runnable examples and lifecycle guidance.

  • Phase 1 legacy-1D decoupling pass completed:

    • Internal consumers that previously depended on legacy magelo/mabilo-style 1D smoothers now use spline-based replacements.
    • magelo.with.external.BB() now uses a spline backend while preserving its legacy output structure for compatibility.
    • Added consistent deprecation warnings across legacy exported 1D regression entry points (magelo, amagelo, mabilo, mabilo.plus, mabilog, magelog, fit.pwlm*, and get.magelo.MAB).

  • At that intermediate stage, legacy 1D model-averaging APIs were marked experimental; their extraction and hard removal were subsequently completed.

  • Phase 3 extraction started with new malo package:

    • fit.pwlm* and the 1D get.*MAB* benchmarking/model-comparison families now have native implementations in malo.
    • gflow legacy entry points for these families now delegate to malo when available (with in-package fallback retained for compatibility).

  • Hard removal of legacy 1D get.*MAB* and related helpers from gflow:

    • bias_utils compatibility wrappers were removed from gflow.
    • These APIs are now available only from malo.

  • Hard migration of remaining legacy 1D exported APIs from gflow to malo:

    • magelo, amagelo, mabilo, mabilo.plus, mabilog, magelog, magelo.with.external.BB, generate.dirichlet.weights, and fit.pwlm* are now thin forwarders to malo with no in-package fallback.

  • Native/header cleanup after 1D migration:

    • Removed legacy 1D src implementations and symbol registrations from gflow.
    • Removed obsolete legacy 1D headers from inst/include/gflow and pruned stale 1D declarations from msr2.h.

  • Migration operational cleanup:

    • Updated collaborator installation docs to require installing malo before using legacy 1D forwarders in gflow.
    • CI workflow now installs malo explicitly in rdgraph test jobs.
    • Forwarder-focused tests now skip cleanly when malo is unavailable.
    • Removed unused legacy 1D header artifacts from inst/include/gflow (lm.h, ray_agemalo.hpp, uggmalog.hpp).
    • Removed legacy maelog implementation and native symbols from gflow (R API, native sources, headers, and Rd docs).
    • Hard-cut removal of all remaining 1D forwarders from gflow: magelo, amagelo, mabilo, mabilo.plus, mabilog, magelog, magelo.with.external.BB, generate.dirichlet.weights, fit.pwlm, and fit.pwlm.optimal are no longer exported by gflow.

gflow 0.1.0 — 2025-09-21

  • Historical initial-release milestone; a CRAN publication for this version was not found in the current or archived CRAN listings checked on 2026-09-15.
  • Implements geometric tools for intrinsic-structure modeling, Morse–Smale regression, and related utilities.