Package: splitGraph 0.3.0

splitGraph: Dataset Dependency Graphs for Leakage-Aware Evaluation

Represent biomedical dataset structure as typed dependency graphs so that sample provenance, repeated-measure structure, study design, batch effects, and temporal relationships are explicit and inspectable. Validates dataset structure, detects sample-level overlap, derives deterministic split constraints, and produces a tool-agnostic split specification for leakage-aware evaluation workflows.

Authors:Selcuk Korkmaz [aut, cre]

splitGraph_0.3.0.tar.gz
splitGraph_0.3.0.zip(r-4.7-any)splitGraph_0.3.0.zip(r-4.6-any)splitGraph_0.3.0.zip(r-4.5-any)
splitGraph_0.3.0.tgz(r-4.6-any)splitGraph_0.3.0.tgz(r-4.5-any)
splitGraph_0.3.0.tar.gz(r-4.7-any)splitGraph_0.3.0.tar.gz(r-4.6-any)
splitGraph_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
splitGraph/json (API)

# Install 'splitGraph' in R:
install.packages('splitGraph', repos = c('https://selcukorkmaz.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/selcukorkmaz/splitgraph/issues

On CRAN:

Conda:

5.08 score 1 stars 7 scripts 193 downloads 44 exports 11 dependencies

Last updated from:bfa146978a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK143
source / vignettesOK184
linux-releaseOK156
macos-releaseOK160
macos-oldrelOK213
windows-develOK86
windows-releaseOK97
windows-oldrelOK100
wasm-releaseOK120

Exports:as_igraphas_split_specbuild_dependency_graphbuild_depgraphcreate_edgescreate_nodesdependency_constraintdependency_graphdepgraph_validation_reportderive_split_constraintsdetect_dependency_componentsdetect_shared_dependenciesgraph_edge_setgraph_from_metadatagraph_node_setgraph_query_resultgrouping_vectoringest_metadataleakage_risk_summarymigrate_dependency_graph_jsonmigrate_split_spec_jsonnew_depgraphnew_depgraph_edgesnew_depgraph_nodesquery_edge_typequery_neighborsquery_node_typequery_pathsquery_shortest_pathsread_dependency_graphread_split_specrelatedness_edges_from_kinshipspatial_edges_from_coordssplit_constraintsplit_specsplit_spec_validationsummarize_leakage_risksvalidate_depgraphvalidate_graphvalidate_graph_jsonvalidate_split_specvalidate_split_spec_jsonwrite_dependency_graphwrite_split_spec

Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrs

Adapter cookbook: from split_spec to native resamples
What this vignette is for | Build a split_spec to work with | Adapter 1 — base R: leave-one-group-out folds | Honoring block variables | Adapter 2 — rsample::group_vfold_cv() | Adapter 3 — rsample::rolling_origin() | Going across language boundaries via JSON | Letting the spec pick the adapter | When you need a custom adapter

Last update: 2026-07-07
Started: 2026-04-29

Cross-language handoff: R to JSON to Python to scikit-learn
Derive and serialize in R | Read in Python | Verify the round-trip | Drive scikit-learn | Why this matters

Last update: 2026-07-07
Started: 2026-07-02

Modeling site, platform, relatedness, and spatial structure
Cluster-style relations: site, region, platform, assay | Pairwise relation: genetic relatedness | Pairwise relation: spatial proximity | Deriving on a subset is leakage-safe | Thresholds are inputs, not modeling

Last update: 2026-07-07
Started: 2026-07-02

splitGraph: From Metadata to Leakage-Aware Split Design
Why splitGraph exists | A realistic toy dataset | Fast path: graph_from_metadata() | Ingest metadata and build typed nodes and edges | Assemble the dependency graph | Visualize the typed structure | Validate before you split | When you really do need to relax a check | Query the graph to inspect hidden structure | Derive split constraints from the graph | Batch constraints | Time constraints | Composite constraints | Cluster-style relations: site, region, platform, assay | Site | Region | Platform and assay | Pairwise relations: relatedness and spatial proximity | Time ordering can come from precedence edges alone | Translate the constraint into a split specification | Summarize the leakage picture in one object | Downstream handoff | Persisting the handoff | Case studies | Case study 1: repeated subjects in a longitudinal cohort | Case study 2: a subject reused across studies | Case study 3: partially observed technical metadata | Case study 4: choosing a defensible split strategy | When splitGraph is useful | What splitGraph is not for | Takeaway

Last update: 2026-07-07
Started: 2026-03-16

Readme and manuals

Help Manual

Help pageTopics
Translate splitGraph Constraints into Stable Split Specificationsas_split_spec summarize_leakage_risks validate_split_spec
Assemble and Validate Dependency Graphsas_igraph build_dependency_graph build_depgraph validate_depgraph validate_graph
Create Canonical Node and Edge Tablescreate_edges create_nodes
Validation Report Object for splitGraph Graphsdepgraph_validation_report leakage_risk_summary split_spec split_spec_validation
Derive Split Constraints from Dependency Graphsderive_split_constraints grouping_vector
Build a Dependency Graph Directly from a Metadata Tablegraph_from_metadata
Construct Core splitGraph S3 Objectsdependency_constraint dependency_graph graph_edge_set graph_node_set graph_query_result new_depgraph new_depgraph_edges new_depgraph_nodes split_constraint
Standardize Sample Metadataingest_metadata
Upgrade Serialized splitGraph JSON to the Current Schema Versionmigrate_dependency_graph_json migrate_json migrate_split_spec_json
Build Pairwise Leakage Edges from Continuous Similaritypairwise_edges relatedness_edges_from_kinship spatial_edges_from_coords
Query Dependency Graph Structuredetect_dependency_components detect_shared_dependencies query_edge_type query_neighbors query_node_type query_paths query_shortest_paths
Validate Serialized splitGraph JSON Against the Shipped Schemavalidate_graph_json validate_json validate_split_spec_json
Serialize a Dependency Graph to JSONread_dependency_graph write_dependency_graph
Serialize a Split Specification to JSONread_split_spec write_split_spec