For new basin analyses use create.basin.complex with explicit
adjacency, aligned edge lengths, and a scalar field. The function guide
vignette contains a complete task map and status-labeled export catalog.
Retired constructors
compute.gfc(), compute.basins.of.attraction(), compute.gfc.trajectory(),
compute.gfc.flow(), and create.basin.cx() raise migration errors.
Choose canonical geodesic_reachability, trajectory_flow, rtcb,
superlevel_merge_tree, or overlap_cell_complex as appropriate, and
translate refinement controls into simplify.params.
There is no merge_tree alias. Arguments are edge.length.list and field,
not weight.list and f.
as.basin.complex reconstructs compatible archived results
from their original graph and an available field; it is not a guarantee of
identical historical output.
Package ownership
Generic graph construction and algorithms belong to dgraphs; use its
current public help and object schemas. Examples include
dgraphs::create.path.graph() and dgraphs::detect.graph.endpoints().
Adaptive extrema use detect.adaptive.extrema in gflow;
dgraphs::detect.local.extrema() is a distinct fixed-radius method.
Both packages share the dgraphs::vertices() generic.
Layout packages such as grip own their layouts. Generic 3D rendering uses
ivue::plot3D.plain(), ivue::plot3D.cont(), ivue::plot3D.groups(),
ivue::layer3D.path(), and ivue::layer3D.edges().
Removed estimators
gflowx preserves archived response-smoothing and conditional-expectation
estimators. Current geosmooth is a separate package, not an automatic
replacement for all retired estimators. The one-dimensional magelo,
mabilo, fit.pwlm and related families were extracted to malo; no gflow
forwarders remain. Check the destination package's public help.
PHATE, diffusion/potential pseudotime, quadratic-form geodesics and
random-walk smoothing experiments are removed; no supported successor is
claimed here. Generic weighted-p-value helpers and fassoc* tests have no
public core adapter.
Association
Use lcor, lslope, and
lslope.neighborhood for graph-local estimates.
lcor.with.posterior summarizes supplied field draws and fits
no posterior model. gfcor and
gfassoc.membership accept successful canonical trajectory
complexes with both directions and an explicit support stage, as well as
archived basins_of_attraction inputs. Other canonical method families are
rejected; these descriptive summaries do not replace permutation tests.