Microsoft.VisualBasic.DataMining.Bonsai 5.0.9762.11310.

Namespaces 3 Types 11 Members 134

01 Namespaces

Microsoft.VisualBasic.DataMining.Bonsai

The Bonsai tree based model toolkit: node and tree structures, likelihood scoring, an optimizer, point sets, layout and the Bonsai API.

Type	Summary	Members
Bonsai	Public entry point for the Bonsai high-dimensional data visualisation.	19
BonsaiNode	A node in the Bonsai tree.	39
BonsaiTree	The Bonsai tree-reconstruction engine.	30
Likelihood	Pure numeric core of the Bonsai likelihood model.	14
Optimizer	Lightweight numerical optimisers used by the Bonsai core.	2
PointSet	A point set of high-dimensional observations, stripped of all single-cell biology semantics.	22
TreeLayout	Tree layout routines that turn the reconstructed Bonsai topology (parent/child + branch times) into a two-dimensional embedding, mirroring the distortion-free 2D visualisation tha…	2

Microsoft.VisualBasic.DataMining.Bonsai.BonsaiTree

Type	Summary	Members
NNIState	Saved topology state for an NNI move so it can be reverted exactly when the move does not improve the likelihood.	0
SPRState	Saved topology state for an SPR move (prune subtree X, regraft it onto a new parent Epar).	0

Microsoft.VisualBasic.DataMining.Bonsai.Optimizer

Type	Summary	Members
ObjWithGrad	Delegate for a scalar objective that also returns its gradient.	3
ScalarFunc	Delegate for a 1-D scalar function f(t) whose root we want.	3