Package index • landscapeR

All functions

AnalysisSpecification-class: Versioned analysis specification for one target-axis run
ArchetypeClassifier-class: Virtual class for Stage 0.5b archetype classifiers
AssociationAbstention-class: Typed abstention before metadata association
AssociationStrategy-class CrossSectionalBinaryAssociationStrategy-class CrossSectionalContinuousAssociationStrategy-class CrossSectionalOrderedAssociationStrategy-class IndependentTimeCourseLinearAssociationStrategy-class RepeatedTimeCourseLmerAssociationStrategy-class: Virtual class for component-association strategies
ComponentAbstention-class: Explicit abstention from component nomination
ComponentProposal-class: Effect-first exploratory component proposal
Decomposer-class: Virtual class for Stage 1 comparative decomposition strategies
DecompositionResult-class: Typed result of a Stage 1 decomposition
DecompositionResult() dr_V_star() dr_sigma() dr_coords() dr_warnings() dr_V_k() dr_sigma_k() dr_coords_k() dr_k(): Construct a validated DecompositionResult
DynamicsEstimator-class: Virtual class for Stage 2 dynamics estimation strategies
FitAssessor-class: Virtual class for Stage 0.75 distributional fit assessors
Generator-class: Virtual class for Stage 0 synthetic data generators
HeterogeneousSubspaceGroundTruth-class: Ground truth for heterogeneous Stage 1 sample-subspace recovery
InterpretationMap-class: Virtual class for Stage 0.5c per-domain interpretation maps
K1DoubleWellGroundTruth-class: Ground truth for the generic K=1 end-to-end double-well calibration control
MetadataAssociationAtlas-class: Component-by-metadata association evidence
PermutationEvidence-class: Search-aware permutation evidence
PipelineConfig-class: Pipeline configuration
PotentialGroundTruth-class: Ground truth for Stage 2 quasi-potential recovery tests
ProvenanceStep-class: Provenance step recorded by each stage
SamplingDesign-class: Versioned sampling-design declaration
SignatureExtractor-class: Virtual class for Stage 0.5a signature extractors
StagePlotEvidence-class: Stored evidence for Stage 1 and Stage 2 scientific plots
StageResult-class: Typed result returned by every stage function
StateTransitionData-class: Inter-stage container
StateTransitionData(): Construct a StateTransitionData object
SubspaceGroundTruth-class: Ground truth for Stage 0/1 decomposition recovery tests
TopologyGroundTruth-class: Ground truth for Stage 0.5 archetype topology tests
VisualEvidenceView-class: Validated evidence prepared for a scientific figure
abstention_digest(): Extract the canonical digest of a component abstention
abstention_permutation_evidence(): Extract permutation evidence from a component abstention
abstention_provenance(): Extract complete abstention provenance
abstention_ranking(): Extract the ranked evidence from a component abstention
analysis_specification(): Construct a validated analysis specification
assess_component_identifiability(): Assess component-axis identifiability under design-preserving resampling
assess_fit(): Assess where real data sits in each archetype's null distribution
assess_stage1_holdout(): Assess frozen Stage 1 holdout evidence
associate_component(): Compute one component association
associate_metadata(): Associate Stage 1 components with eligible metadata
association_abstention_diagnostic(): Extract the diagnostic from an association abstention
association_applicable(): Test whether an association strategy applies
association_strategy_id(): Return an association strategy provenance identifier
atlas_associations(): Extract association rows from an atlas
atlas_digest(): Extract the canonical digest of a metadata-association atlas
atlas_evidence_contract(): Extract the interpretation evidence contract
atlas_exclusions(): Extract metadata exclusions from an atlas
atlas_observations(): Extract raw eligible component distributions from an atlas
atlas_provenance(): Extract deterministic atlas provenance
canonical_digest(): Compute a canonical deterministic digest for an AnalysisSpecification
classify_archetype(): Classify data into a trajectory archetype
component_loading_geometry(): Declare the loading geometry used to align decomposition components
confirm_component(): Confirm a proposed component by an explicit analyst decision
control_ladder(): Run the Stage 1 control ladder
cross_sectional(): Declare a cross-sectional sampling design
declare_sampling_design(): Attach a sampling design to a StateTransitionData container
decompose() .decompose_impl(<HogsvdAveraged>,<StateTransitionData>) .decompose_impl(<HogsvdPrereduced>,<StateTransitionData>) .decompose_impl(<SvdDecomposer>,<StateTransitionData>): Decompose one or more omic layers into state-space axes
estimate_dynamics() .estimate_dynamics_impl(<KdeLogDensityEstimator>,<StateTransitionData>) supported_sampling_designs(<KdeLogDensityEstimator>): Estimate quasi-potential dynamics on decomposition coordinates
execute_stage1_benchmark_development(): Run the fast non-evidentiary Stage 1 development tier
execute_stage1_benchmark_full(): Execute the complete frozen Stage 1 evidence protocol
extract_signature(): Extract a descriptor vector from a StateTransitionData object
generate(): Generate synthetic StateTransitionData with embedded ground truth
get_strategy(): Retrieve an implementation constructor from the registry
independent_time_course(): Declare an independent destructive-sampling time course
interpret(): Map an archetype to named component roles for a specific domain
k1_double_well_calibration(): Run the generic K=1 double-well calibration path
landscapeR landscapeR-package: landscapeR: Comparative Decomposition and State-Transition Dynamics
landscapeR_palette(): Canonical landscapeR colour palettes
list_strategies(): List registered implementations, optionally filtered by contract
longitudinal(): Declare a longitudinal sampling design
migrate(): Migrate a StateTransitionData object to a target schema version
migrate_analysis_specification(): Migrate an AnalysisSpecification v1 object to v2
plot(<AssociationAbstention>): Plot an association abstention
plot(<ComponentAbstention>): Plot a component-nomination abstention
plot(<ComponentProposal>): Plot an effect-first component proposal
plot(<MetadataAssociationAtlas>): Plot a metadata-association atlas
plot(<PermutationEvidence>): Plot search-aware permutation evidence
plot_component_identifiability(): Plot component-axis identifiability evidence
plot_components(): Component gallery coloured by canonically aligned sample metadata
plot_decomposition(): Plot sample coordinates on the recovered state-transition axis (Stage 1 output)
plot_potential(): Plot the quasi-potential landscape (Stage 2 output)
plot_spectrum(): Plot singular value spectra with a BBP model reference
potential_recovery_benchmark(): Measure Stage 2 quasi-potential recovery on a synthetic potential control
prepare_plot_evidence(): Prepare provenance-bound evidence for Stage 1 or Stage 2 plots
project_into(): Project a secondary cohort into the state-space of a primary cohort
proposal_digest(): Extract the canonical digest of a component proposal
proposal_identifiability(): Extract component-axis identifiability evidence
proposal_observations(): Extract raw target distributions from a component proposal
proposal_permutation_evidence(): Extract search-aware permutation evidence from a proposal
proposal_provenance(): Extract complete proposal provenance
proposal_ranking(): Extract the ranked table from a component proposal
propose_component(): Nominate a component from a metadata-association atlas
read_stage1_evidence_artifact(): Read a verified full Stage 1 evidence artifact
record_provenance(): Append a provenance step to a StateTransitionData object
recovery_benchmark(): Measure Stage 1 subspace recovery on a synthetic control
register_migration(): Register a schema migration function
register_strategy(): Register an algorithm implementation under a stage contract
run_pipeline(): Run the pipeline sequentially (development / testing helper)
run_stage1_benchmark_replicate(): Run one deterministic benchmark replicate
save_landscapeR_plot(): Save a landscapeR figure at publication scale
scale_colour_landscapeR(): Canonical landscapeR colour scale
scale_fill_landscapeR(): Canonical landscapeR fill scale
scientific_caption(): Retrieve a landscapeR scientific figure caption
select_stage1_candidate(): Select the Stage 1 baseline from calibration evidence
setup_rng(): Set up reproducible parallel-safe RNG
shared_axis(): Extract the primary shared gene axis from a Stage 1 result
stage1_benchmark_manifest(): Construct the frozen Stage 1 heterogeneous benchmark manifest
stage1_benchmark_progress(): Inspect local Stage 1 execution progress
stage1_candidate_smoke(): Run the frozen Stage 1 heterogeneous-feature smoke harness
stage1_development_manifest(): Construct the deterministic non-evidentiary Stage 1 development manifest
stage_failure(): Construct a failed StageResult
stage_success(): Construct a successful StageResult
strategy_registration_history(): Inspect deterministic strategy-registration provenance
supported_sampling_designs(): Query the sampling designs supported by a DynamicsEstimator strategy
synthetic_branching_control(): Generate a destructive-sampling developmental branching control
synthetic_control(): Generate one synthetic control dataset
synthetic_k1_double_well_control(): Generate a K=1 expression control with a planted double-well coordinate
synthetic_potential_control(): Generate a synthetic potential control via Langevin simulation
theme_landscapeR(): Publication theme for landscapeR figures
validate_stage1_benchmark_manifest(): Validate a Stage 1 benchmark manifest
verify_stage1_benchmark_artifact(): Verify a Stage 1 benchmark artifact hash manifest
verify_stage1_evidence_artifact(): Verify a full Stage 1 evidence artifact
visual_evidence(): Extract the typed visual evidence for a scientific result
visual_evidence_caption(): Build the publication caption for visual evidence
visual_evidence_diagnostics(): Extract visual-evidence diagnostics
visual_evidence_display(): Extract one named display-ready visual-evidence item
visual_evidence_display_names(): List recorded display-ready visual-evidence items
visual_evidence_observations(): Extract visual-evidence observations
visual_evidence_state(): Extract structured visual-evidence state
visual_evidence_summaries(): Extract visual-evidence summaries
visual_evidence_surface(): Identify a visual-evidence decision surface
write_stage1_benchmark_artifact(): Write an immutable Stage 1 benchmark artifact