Reference for the named parameter lists accepted by create.basin.complex().
Tables below are generated from the same defaults and resolvers as the
constructor. They show the default for a graph with 100 vertices. The RTCB
n.min default is max(20, ceiling(sqrt(n.vertices))); inspect
object$parameters for the exact settings used in your analysis.
Unknown names, invalid values, and method-inapplicable settings are errors.
Graph lengths and validation
edge.length.symmetry.tolerance is the nonnegative tolerance for matching
lengths on the two orientations of an undirected edge. Neighbor lists and
lengths are parallel; zero lengths are allowed. The inherited weight.list
name in lcor() and lslope() also supplies edge lengths, not vertex masses
or generic affinity weights. Derivative local correlation skips lengths at
or below 1e-10. Vertex mass weights support, whereas vertex density can change
the trajectory direction. Neither is inferred from the other.
Trajectory flow
modulation selects CLOSEST, NONE, DENSITY, EDGELEN or DENSITY_EDGELEN.
CLOSEST uses exact connected plateaus and the nearest improving boundary
edge; other modes require plateau.policy = "none". Density modes require
vertex.density. edge.length.quantile.thld in (0,1] controls the preferred
local edge-length threshold. long.edge.fallback is "allow_and_flag",
"allow", or "forbid" when only longer improving edges are available.
symmetric.seeding requests the backend's symmetric seed rule;
max.trajectory.length bounds stored path length and store.trajectories
controls path storage. tie.breaking = TRUE requires an explicit integer
tie.seed and perturbs construction values; FALSE requires a NULL seed.
primary.assignment.policy is "backend_primary",
"largest_membership_then_extremum", or "none". It chooses a single
convenience label without replacing overlapping membership.
Merge trees
plateau.tolerance = 0 is currently required: plateaus use exact equality.
The only elder rule is "birth_then_representative_vertex": higher birth
wins, with representative vertex breaking equal-birth ties. Assignment is
"elder_at_merge"; root death uses "component_opposite_extreme".
Persistence is in field units and is not a significance score.
Geodesic and relaxed trajectory basins
Geodesic reachability uses the edge-length quantile in (0,1], optional stored
trajectories, and "none" or "largest_membership_then_extremum" assignment.
RTCB exposes stopping and path-search controls: n.min limits the initial Dijkstra candidate region
(clamped to graph size); m.min is the minimum monotonicity in (-1,1); optional q.min
is the required favorable-change fraction in (0,1] and takes precedence over m.min;
run.max limits consecutive adverse steps.
tau0, kappa, k.max, h.max, d.path.max, and eta.step control the
path search: local tolerance is tau0*(1-progress)^kappa, k.max bounds
labels per vertex, h.max bounds hops, d.path.max bounds metric path length,
and eta.step is the field-change deadband for classifying steps. epsilon.d and eps.num are numerical
tolerances. sink.prune, sink.prune.max.iter, and max.paths.per.sink
control sink pruning and retained path counts. See
the details below for the path-budget interpretation.
With cumulative favorable field change G and adverse change L, the
path budget is lambda*G - L + tau >= -eps.num. Here lambda is
(1-m.min)/(1+m.min), or (1-q.min)/q.min when q.min is supplied.
These controls are method-specific, not interchangeable measures of scale.
Overlap cells
This family requires both directions. basin.merge.overlap.thld in [0,1]
controls basin merging. The three min.*.cell.size.thld integers control
minimum ascending/descending, ascending/ascending, and descending/descending
cell sizes. cell.graph.params is forwarded to the cell graph backend.
Primary assignment is "none"; overlapping cells are the authoritative result.
Refinement applicability and order
Every stage is disabled by default. Relative-value filtering, maxima and minima clustering, and geometric filtering apply to trajectory, geodesic and RTCB methods. Support filtering also applies to merge trees. Expansion applies only to geodesic and RTCB methods. No refinement stage applies to overlap cells. Nondefault settings in inapplicable stages are rejected even if disabled.
Stages run in the order above, followed by support filtering and expansion.
Relative thresholds compare extrema with the mean construction field;
clustering uses the overlap threshold in [0,1]. Geometric filters use the
listed percentiles and positive integer hop radius. Support filters require
minimum vertex count, trajectory count and normalized support mass; mass
thresholds need supplied mass. Expansion assigns uncovered vertices to the
nearest retained basin. Raw supports remain available independently of these
retained results. See the canonical workflow for worked refinement examples.
See also
create.basin.complex(), get.basin.table(), gfcor(),
gflow-package. Run vignette("function-guide", package = "gflow") for
the task map and vignette("basin_complex_workflow_vignette", package = "gflow")
for construction and refinement examples.
Resolved method defaults
trajectory_flow
modulation"CLOSEST"plateau.policy"connected_exact"edge.length.quantile.thld0.9long.edge.fallback"allow_and_flag"store.trajectoriesTRUEmax.trajectory.length10000Lsymmetric.seedingTRUEtie.breakingFALSEtie.seedNULLprimary.assignment.policy"backend_primary"
superlevel_merge_tree
plateau.tolerance0elder.rule"birth_then_representative_vertex"primary.assignment.policy"elder_at_merge"root.death.policy"component_opposite_extreme"
geodesic_reachability
edge.length.quantile.thld0.9store.trajectoriesFALSEprimary.assignment.policy"none"
rtcb
edge.length.quantile.thld0.9store.trajectoriesFALSEn.min20Lm.min0.7q.minNULLrun.max2Ltau00.1kappa1.5k.max24Lh.max1000Ld.path.maxInfeta.step0epsilon.d1e-12eps.num1e-12sink.pruneFALSEsink.prune.max.iter5Lmax.paths.per.sink64Lprimary.assignment.policy"backend_primary"