Efficiently computes trajectory-based GFC for each column of a matrix, reusing graph structure across all computations. Supports parallel execution via OpenMP.
Usage
compute.gfc.flow.matrix(
adj.list,
weight.list,
Y,
density = NULL,
modulation = c("CLOSEST", "NONE", "DENSITY", "EDGELEN", "DENSITY_EDGELEN"),
n.cores = 1L,
verbose = FALSE,
edge.length.quantile.thld = 0.9,
long.edge.fallback = c("allow_and_flag", "allow", "forbid"),
apply.relvalue.filter = TRUE,
min.rel.value.max = 1.1,
max.rel.value.min = 0.9,
apply.maxima.clustering = TRUE,
apply.minima.clustering = TRUE,
max.overlap.threshold = 0.15,
min.overlap.threshold = 0.15,
apply.geometric.filter = TRUE,
p.mean.nbrs.dist.threshold = 0.9,
p.mean.hopk.dist.threshold = 0.9,
p.deg.threshold = 0.9,
min.basin.size = 10L,
hop.k = 2L,
store.trajectories = TRUE,
max.trajectory.length = 10000L,
symmetric.seeding = TRUE
)Arguments
- adj.list
List of integer vectors (adjacency list, 1-based).
- weight.list
List of numeric vectors (edge weights).
- Y
Numeric matrix of function values (n.vertices x n.functions).
- density
Optional numeric vector of density values.
- modulation
Character string specifying gradient modulation.
- n.cores
Integer number of OpenMP threads. Default is 1 (sequential).
- verbose
Logical. Print progress messages.
- edge.length.quantile.thld
Numeric quantile threshold used by optional edge-length filtering.
- long.edge.fallback
Character CLOSEST fallback policy; see
compute.gfc.trajectory.- apply.relvalue.filter
Logical; apply relative-value-based basin filtering.
- min.rel.value.max
Numeric lower bound for local-maximum relative value during filtering.
- max.rel.value.min
Numeric upper bound for local-minimum relative value during filtering.
- apply.maxima.clustering
Logical; cluster nearby local maxima before downstream filtering.
- apply.minima.clustering
Logical; cluster nearby local minima before downstream filtering.
- max.overlap.threshold
Numeric overlap threshold used when clustering maxima.
- min.overlap.threshold
Numeric overlap threshold used when clustering minima.
- apply.geometric.filter
Logical; apply geometric filters to remove unstable basins.
- p.mean.nbrs.dist.threshold
Quantile threshold for mean neighbor distance filter.
- p.mean.hopk.dist.threshold
Quantile threshold for hop-k distance filter.
- p.deg.threshold
Quantile threshold for degree-based geometric filtering.
- min.basin.size
Minimum basin size retained after filtering.
- hop.k
Hop radius used for hop-based geometric diagnostics.
- store.trajectories
Logical; retain trajectory objects in each result.
- max.trajectory.length
Integer maximum allowed trajectory length.
- symmetric.seeding
Logical; if
TRUE, additionally seed trajectories from local maxima using descending flow.