Package index

Basin construction and conversion

create.basin.complex(): Create a Canonical Basin Complex
as.basin.complex(): Convert an Object to a Canonical Basin Complex
compute.basins.of.attraction(): Compute Basins of Attraction for Local Extrema
compute.gfc(): Compute Gradient Flow Complex
compute.gfc.trajectory() compute.gfc.flow(): Compute Gradient Flow Complex Using Trajectory-First Approach
create.basin.cx(): Create a Gradient Flow Basin Complex on a Weighted Graph
compute.gfc.basins(): Compute Gradient Flow Basins with Optional Modulation
find.gflow.basins(): Find Gradient-Flow Basins on a Weighted Graph
create.gflow.cx(): Create Graph Flow Complex with Harmonic Extension
create.morse.smale.complex(): Create Morse-Smale Complex Object

Stable accessors and summaries

get.basin.table(): Extract the Canonical Basin Table
get.basin.membership(): Extract Canonical Basin Membership
get.basin.assignment(): Extract Canonical Primary Basin Assignments
get.basin.merge.tree(): Extract a Canonical Basin Merge Tree
get.basin.trajectory.forest(): Extract a Canonical Basin Trajectory Forest
get.basin.cells(): Extract Canonical Basin Cells
basin(): Extract Basin of Attraction
basins(): Extract All Basins of Attraction
get.basin(): Get Basin by Label
get.gflow.build.identity(): Report the Loaded gflow Build Identity

Extrema and merge trees

detect.adaptive.extrema(): Detect Adaptive Local Extrema in a Graph
find.critical.points(): Find Critical Points in Function Grid
find.local.extrema(): Detect Local Extrema on a Graph with Labeled Basins
compute.extrema.hop.nbhds(): Computes Local Extrema Hop Neighborhoods in a Graph Function
get.nbrs(): Extract Neighborhood Component by Label ID
relabel.extrema(): Relabel extrema with sequential labels after filtering
compute.persistence(): Compute Persistent Homology for Graphs
plot(<basin.merge.tree>): Plot a Crossing-Free Basin Merge Tree and Persistence Barcode
cut(<basin.merge.tree>): Cut a Basin Merge Tree at a Scalar-Field Height
as.dendrogram(<basin.merge.tree>): Convert a Basin Merge Tree to a Dendrogram
get.basin.merge.tree.layout(): Extract a Validated Basin Merge-Tree Layout
extremality.summary(): Summarize Extrema from Riemannian Extremality Analysis
compute.pextrema.nbhds(): Detect probabilistic extrema in an rdgraph fitted surface
maxp(): Compute Local Maximum Probability for a Vertex
minp(): Compute Local Minimum Probability for a Vertex
analyze.extrema.distribution(): Analyze Extrema Distribution and Suggest Spurious Classification Parameters
classify.spurious.extrema(): Classify Spurious Extrema Using Multiple Criteria
compare(<retained.extrema>): Compare Function Values of Retained Extrema at Different Thresholds
create.hop.nbhd.extrema.df2(): Enhanced Version of create.hop.nbhd.extrema.df with Improved Spurious Classification
suggest.threshold(): Interactive Threshold Selection Based on Expected Number of Extrema

cluster.local.extrema(): Cluster Local Extrema Based on Basin Overlap
filter.basins(): Filter Basins by Retaining Only Specified Extrema
filter.basins.by.relvalue(): Filter Basins by Relative Value Threshold
expand.basins.to.cover(): Expand Basins to Cover All Graph Vertices
generate.refinement.report(): Generate Text Report of Basin Refinement Process
replace.basin.label(): Replace a Basin Label in Gradient Flow Object
uncovered.vertices.gfc.flow(): Get Uncovered Vertices from GFC Flow Result
count.feature.carriers(): Count Feature Carriers Within a Vertex/Sample Subset
set.boundary(): Compute Boundary Vertices of a Subset in a Graph

Trajectories, cells, and flow graphs

construct.madag(): Construct Monotonic Ascent DAG (MADAG) from a Source Vertex
madag.bottlenecks(): Identify Bottleneck Vertices in a Cell
construct.gflow.graph(): Construct Gradient Flow Graph from Merged Basins
construct.graph.gradient.flow(): Graph Gradient Flow Analysis
compute.graph.gradient.flow(): Compute Gradient Flow Information for Vertices in a Graph
compute.gfc.modulation(): Compute Gradient Flow Modulation Weights
build.se.tree(): Build Spurious Extrema Tree for a Single Spurious Extremum
extract.gradient.trajectory(): Extract Gradient Trajectory from Basin
extract.cell.trajectory(): Extract Complete Gradient Trajectory Through Cell
vertex.cell.trajectory.gfc.flow(): Get Trajectory for a Vertex Within a Specific Cell
filter.cells.by.criteria(): Filter Gradient Flow Cells by Multiple Criteria
filter.cells.by.vertex.count(): Filter Gradient Flow Cells by Vertex Count
cell.y.values(): Extract Response Values by Super-Cell
compute.tube.lens.corridor(): Compute a tube-lens corridor between two vertices in a weighted graph
construct.path.through.waypoints(): Construct a Connected Graph Path Through Waypoint Vertices
trajectory.distances.to.vertex(): Compute Trajectory Distances to a Target Vertex
vertex.distances.to.trajectory(): Compute Vertex Distances to a Trajectory
fit.trajectory.smooth.splines(): Fit Smooth-Spline Curves to the Mean/Median 3D Trajectory
graph.constrained.gradient.flow.trajectories(): Compute Constrained Gradient Flow Trajectories
compute.gradient.trajectory(): Compute Gradient Trajectory
compute.morse.smale.cells(): Compute Morse-Smale Cells

Harmonic extension

compute.harmonic.extension(): Compute Harmonic Extension of Trajectory Coordinates
select.max.density.trajectory(): Select Trajectory with Maximal Mean Density
apply.harmonic.extension(): Apply Harmonic Extension to Local Subgraph
analyze.harmonic.extensions(): Analyze Harmonic Extensions for Local Extrema
compare(<harmonic.methods>): Compare Multiple Harmonic Extension Methods
visualize.smoothing.steps(): Visualize Smoothing Steps from Gradient Flow Complex

Local association

lcor(): Local Correlation Coefficients on Graphs
lslope() lslope.vector.vector(): Gradient-Restricted Local Slope
lslope.neighborhood(): Neighborhood Local Regression Coefficient
permutation.test.lcor(): Permutation Test for Local Correlation Screening
lcor.with.posterior(): Compute Local Correlation with Posterior Uncertainty Propagation

Flow-aware association

gfcor(): Gradient Flow Correlation Analysis
gfassoc.membership(): Compute Basin and Cell Membership from Gradient Basins
gfassoc.polarity(): Compute Polarity Coordinates for a Fitted Surface
gfassoc.overlap(): Compute Soft Overlap Matrices Between Basin Structures
gfassoc.deviation(): Compute Deviation from Independence for Overlap Matrix

Domain-specific visualization and supporting grid tools

label.extrema.3d(): Label Local Extrema in 3D Plot
label.extrema.leaders.3d(): Label Local Extrema With Leader Segments in 3D Plot
label.extremality.3d(): Label Extremality-Based Local Extrema in 3D Plot
draw.basin(): Draw Basin Vertices in 3D Space
critical.points.plot(): Plot Critical Points
grid.critical.points.plot(): Plot Critical Points on Grid
function.contours.plot(): Plot Function Contours
gradient.trajectory.plot(): Plot Gradient Trajectory
gradient.trajectories.plot(): Plot Gradient Trajectories
morse.analysis.plot(): Plot Morse Analysis
morse.smale.cells.plot(): Plot Morse-Smale Cells
morse.smale.complex.plot(): Plot Morse-Smale Complex from Function
morse.smale.complex.plot.from.critical(): Plot Morse-Smale Complex from Critical Points
separatrices.with.cells.plot(): Plot Separatrices with Cells
create.grid(): Create Uniform 2D Grid
evaluate.function.on.grid(): Evaluate Function on Grid
evaluate.function.on.grid.as.vector(): Evaluate Function on Grid as Vector
create.lmin.lmax.labels(): Create Labels for Local Maxima and Minima in Morse-Smale Complex
create.lmin.lmax.label.indicators(): Create Label Tables and Indicator Vectors for Morse-Smale Complex Critical Points
create.lmin.lmax.contingency.table(): Create Contingency Table of Local Maxima and Minima Relationships
morse.smale.complex.lmin.lmax.summary(): Process Complete Morse-Smale Complex Analysis Pipeline
prof.fn(): Extract Most Abundant ASVs with Taxonomy Information
find.longest.true.stretch(): Finds the Longest Stretch of Consecutive TRUE Values in a Logical Vector
elapsed.time(): Format and Print Elapsed Time

Dependency re-export

reexports vertices: Objects exported from other packages

Package help and basin displays

gflow gflow-package: gflow: Basin-Complex Exploration and Flow-Aware Association
gflow-migration: Migrating to the Basin and Flow API
summary(<basin_complex>) print(<summary.basin_complex>): Summarize a Canonical Basin Complex
plot(<basin_complex>): Plot a Canonical Basin Complex

Additional object methods and historical helpers

Existing method and helper documentation is retained here. For supported public entry points, use the task sections above.

as.data.frame(<harmonic_extension>): Create Data Frame of Extended Coordinates
basin-parameters: Basin Construction Parameters
basin(<basins_of_attraction>): Extract Basin of Attraction for a Specific Extremum
basin(<cx.merge>): Merge Two Basins in a Basin Complex
basin(<feature.carriers>): Count Feature Carriers Within a Basin in a gfc.flow Object
basin(<prev.eval>): Evaluates a range of prevalence thresholds for DA analysis
basin(<trajectories>): Extract Basin Trajectories from GFC Objects
basin(<trajectories.gfc.flow>): Extract Trajectories for a Basin (gfc.flow)
basin(<vertices>): Extract Vertices Belonging to a Single Basin in a gfc.flow Object
basins(<basins_of_attraction>): Extract All Basins of Attraction
basins(<merge>): Merge Two Basins in a Gradient Flow Complex
basins(<union>): Union of Gradient Flow Basins
break.ties(): Break Ties with Adaptive Noise
cell.trajectories(<gfc.flow>): Extract Trajectories for a Given Gradient Flow Cell (gfc.flow)
cell.trajectories(<max.edge.length>): Compute Maximum Edge Length for Each Cell Trajectory
cell.trajectories(<monotonicity>): Compute Monotonicity Statistics for Cell Trajectories
cell.vertices(): Get Cell Vertices for a (min, max) Pair
cell.vertices.gfc.flow(): Find Vertices in the Same Cell
compute.carriers.per.trajectory.mat(): Compute carriers-per-trajectory matrix \(k_{jT}\) for many phylotypes
compute.cell.vertices(): Compute Cell Vertices (Intersection of Ascending and Descending Basins)
compute.gfc.flow.matrix(): Compute GFC Flow for Multiple Functions
compute.overlap.distance.matrix(): Compute Pairwise Overlap Distance Matrix
compute.partition.cell.stats(): Compute Partition Cell Response Variable Statistics
compute_asc_desc_cell_intersection_matrix(): Compute Ascending-Descending Cell Intersection Matrix
construct.basin.cx.graph(): Construct Basin Complex Graph
count.cell.memberships(): Count Cell Membership Statistics
count.multi.memberships.gfc.flow(): Count Multi-Membership Statistics
create.hop.nbhd.extrema.df(): Create Data Frame of Extrema Information from Hop Neighborhoods
create.lmin.lmax.frequency.tables(): Create Frequency Tables and LaTeX Captions for Morse-Smale Complex Critical Points
create.taxonomic.labels(): Create Taxonomic Labels for Vertices
destination.minimum.identify(): Identify Destination Minimum
extract.da.tables.by.prevalence(): Extract per-prevalence differential abundance tables from a basin.prev.eval result
extract.gradient.flow.cells(): Extract Gradient Flow Cells for a Local Maximum Basin
extract.vertices.terminating.at(): Extract All Trajectories Terminating at Specific Extremum
extrema.summary(): Create a summary data frame of extrema information
find.ascending.trajectory.from.point(): Find Ascending Trajectory from Point
find.critical.points.continuous(): Find Critical Points with Continuous Coordinates
find.descending.trajectory.from.point(): Find Descending Trajectory from Point
find.line.intersection(): Find Line Intersection
find.separatrices(): Find Separatrices from Saddle Points
get.absorbed.extrema.info(): Get All Absorbed Extrema for a Merged Basin
get.basin.of.gfc.basins(): Extract Basin by Extremum Vertex or Name
get.basin.vertices(): Extract vertices belonging to a specific basin from a basin complex
get.extrema.type.from.label(): Determine Extrema Type from Label
get.harmonic.repair.vertices(): Get Vertices for Harmonic Repair
get.summary(): Get Summary Row by Label
get.trajectories.by.status(): Get Trajectories by Endpoint Status
graph.MS.cx(): Constructs the Morse-Smale complex of a function defined on graph vertices
identify(<gradient.flow.cells>): Identify All Gradient Flow Cells
is.valid.cell(): Validate Gradient Flow Cell
list.basins(): List Basins
list.basins(<gfc.flow>): List Basins for gfc.flow
list.cells(): List Cells
list.cells(<gfc.flow>): List All Cells in Gradient Flow Result
list.retained(): List Retained Extrema
list.spurious(): List Spurious Extrema
lmax(): Extract Local Maxima
lmax(<basin_summary>): Extract Local Maxima from Basin Summary
lmax(<basins>): Identify Basins of Attraction of Local Maxima on a Weighted Graph
lmin(): Extract Local Minima
lmin(<basin_summary>): Extract Local Minima from Basin Summary
lmin(<basins>): Identify Basins of Attraction of Local Minima on a Weighted Graph
merge(<clustered.basins>): Merge Clustered Basins of Attraction with Trajectory Preservation
merge(<gfc.basins>): Merge Basins for compute.gfc() Results
merge(<gfc.flow.basins>): Merge Basins in a Trajectory-First Gradient Flow Complex (gfc.flow)
merge(<two.extrema>) merge(<two.basins>): Merge Two Specified Local Extrema with Trajectory Preservation
morse.smale.graph.persistence(): Morse-Smale Graph Persistence Analysis
plot(<basin_cx>): Plot method for basin_cx objects
plot(<feature.prevalence>): Plot Feature Prevalence from Carrier Summaries
plot(<gfc_modulation>): Plot Diagnostics for Gradient Flow Modulation
plot(<gflow_graph>): Plot Method for Gradient Flow Graph Objects
plot(<gflow_local_extrema>): Plot Local Extrema Detection Results
plot(<graphMScx>): Plot Method for graphMScx Objects
plot(<morse.smale.trajectories.from.point>): Plot Morse-Smale Trajectories from Point
plot_extrema_stability(): Visualize Extrema on hop_idx vs value plot
print(<basin_cx>): Print Method for Basin Complex Objects
print(<basins_of_attraction>): Print Method for Refined Basins
print(<gfc.flow>): Print Method for gfc.flow Objects
print(<gfc_basins>): Print Method for gfc_basins Objects
print(<gfc_cell_trajectories>): Print Method for gfc_cell_trajectories Objects
print(<gfc_modulation>): Print Method for gfc_modulation Objects
print(<gfcor>): Print Method for Gradient Flow Correlation
print(<gflow_cx>): Print Method for gflow_cx Objects
print(<gflow_graph>): Print Method for Gradient Flow Graph Objects
print(<gradient_flow_cells>): Print Method for Gradient Flow Cells
print(<harmonic_extension>): Print Method for harmonic_extension Objects
print(<lcor.posterior>): Print a Local-Correlation Posterior Result
print(<lcor_matrix_matrix_result>): Print Method for lcor_matrix_matrix_result
print(<lcor_permutation_test>): Print a Local-Correlation Permutation Test
print(<lcor_vector_matrix_result>): Print Method for lcor_vector_matrix_result
print(<lslope_gradient_result>): Print Method for Gradient-Restricted Local Slope Results
print(<lslope_matrix_matrix_result>): Print Method for Matrix-Matrix Local Slope Results
print(<lslope_neighborhood_result>): Print Method for Neighborhood Local Slope Results
print(<lslope_vector_matrix_result>): Print Method for Vector-Matrix Local Slope Results
print(<madag>): Print Method for madag Objects
print(<se_tree>): Print Method for se_tree Objects
print(<summary.basin_cx>): Print Method for Basin Complex Summary Objects
print(<summary.gfc_basin_trajectories>): Print Method for summary.gfc_basin_trajectories Objects
print(<summary.gfc_cell_trajectories>): Print Method for summary.gfc_cell_trajectories Objects
print(<summary.gfcor>): Print Method for Gradient Flow Correlation Summary
print(<summary.gflow_basins>): Print Summary of Gradient-Flow Basin Results
print(<summary.gflow_graph>): Print Summary for Gradient Flow Graph Objects
print(<summary.gflow_local_extrema>): Print Summary of Local Extrema Detection Results
print(<summary.ggflow>): Print Gradient Flow Structure Summary
print(<summary.lcor.posterior>): Print a Local-Correlation Posterior Summary
relabel.basins.gfc.flow(): Relabel Basins in a Trajectory-First Gradient Flow Complex (gfc.flow)
replace.basin.label.basin_cx(): Replace a Basin Label in a Basin Complex Object
select.closest.longest.trajectory(): Select Best Trajectory by Distance and Length
separatrices.plot(): Plot Separatrices
show.basin(): Show Basin Details from a Basin Complex
show.basin(<basin_cx>): Show Basin Details from a Basin Complex
summarize.prev.eval(): Summarize systematic prevalence evaluation results and recommend a threshold
summary(<basin_cx>): Summary Method for Basin Complex Objects
summary(<basins_of_attraction>): Summarize Basins of Attraction
summary(<gfc.flow>): Summary Method for gfc.flow Objects
summary(<gfc_basin_trajectories>): Summary Method for gfc_basin_trajectories Objects
summary(<gfc_cell_trajectories>): Summary Method for gfc_cell_trajectories Objects
summary(<gfcor>): Summary Method for Gradient Flow Correlation
summary(<gflow_basins>): Summarize Gradient-Flow Basin Results
summary(<gflow_graph>): Summary Method for Gradient Flow Graph Objects
summary(<gflow_local_extrema>): Summarize Local Extrema Detection Results
summary(<ggflow>): Summarize Gradient Flow Structure
summary(<gradient_flow_cells>): Summary Method for Gradient Flow Cells
summary(<lcor.posterior>): Summarize a Local-Correlation Posterior Result
summary(<lcor_matrix_matrix_result>): Summary Method for lcor_matrix_matrix_result
summary(<lcor_vector_matrix_result>): Summary Method for lcor_vector_matrix_result
summary(<lslope_matrix_matrix_result>): Summary Method for Matrix-Matrix Local Slope Results
summary(<lslope_vector_matrix_result>): Summary Method for Vector-Matrix Local Slope Results
summary(<madag>): Summary Method for madag Objects
taxon.sig.frequency(): Taxon-level significance frequency across prevalence thresholds
trajectory.edges.gfc.flow(): Convert Trajectory to Edge List
trajectory.vertices.gfc.flow(): Get All Trajectory Vertices as a Single Vector
two.stage.basin.fdr(): Two-stage FDR control for basin-specific differential abundance scans
vertex.all.trajectories.gfc.flow(): Get All Trajectories Passing Through a Vertex
vertex.cell.all(): Get All Cells for a Vertex (alias for vertex.cell.gfc.flow)
vertex.cell.gfc.flow(): Identify Cell Membership for a Single Vertex
vertex.cells.gfc.flow(): Identify Cell Membership for Multiple Vertices
vertex.primary.cell.gfc.flow(): Get Primary Cell Membership (Single-Valued)
vertices(<feature.carriers>): Count Feature Carriers Over an Explicit Vertex Set
vertices(<gflow_local_extrema>): Extract Vertices of a Specific Local Extremum

Basin construction and conversion

Stable accessors and summaries

Extrema and merge trees

Refinement and membership

Trajectories, cells, and flow graphs

Harmonic extension

Local association

Flow-aware association

Domain-specific visualization and supporting grid tools

Dependency re-export

Package help and basin displays

Additional object methods and historical helpers