ElPrincGraph: Core function to construct a principal elestic graph

Description Usage Arguments Value Examples

View source: R/BaseElPi.R

Description

The core function that takes the n m-dimensional points and construct a principal elastic graph using the grammars provided.

Usage

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ElPrincGraph(X, NumNodes = 100, NumEdges = Inf, Lambda, Mu, ElasticMatrix,
  NodesPositions, AdjustVect, verbose = FALSE, n.cores = 1,
  ClusType = "Sock", MinParOP = 20, CompileReport = FALSE,
  ShowTimer = FALSE, ComputeMSEP = TRUE, FinalEnergy = "Base",
  alpha = 0, beta = 0, gamma = 0, Mode = 1,
  MaxNumberOfIterations = 10, MaxFailedOperations = Inf, MaxSteps = Inf,
  GrammarOptimization = FALSE, eps = 0.01, TrimmingRadius = Inf,
  GrowGrammars = list(), ShrinkGrammars = list(), GrammarOrder = c("Grow",
  "Shrink"), FastSolve = FALSE, AvoidSolitary = FALSE, EmbPointProb = 1,
  AdjustElasticMatrix = NULL, AdjustElasticMatrix.Initial = NULL, ...)

Arguments

X

numerical 2D matrix, the n-by-m matrix with the position of n m-dimensional points

NumNodes

integer, the number of nodes of the principal graph

NumEdges

integer, the maximum nulber of edges

Lambda

real, the lambda parameter used the compute the elastic energy

Mu

real, the lambda parameter used the compute the elastic energy

ElasticMatrix

numerical 2D matrix, the k-by-k elastic matrix

NodesPositions

numerical 2D matrix, the k-by-m matrix with k m-dimensional positions of the nodes in the initial step

AdjustVect

boolean vector keeping track of the nodes for which the elasticity parameters have been adjusted. When true for a node its elasticity parameters will not be adjusted.

verbose
n.cores

either an integer (indicating the number of cores to used for the creation of a cluster) or cluster structure returned, e.g., by makeCluster. If a cluster structure is used, all the nodes must contains X (this is done using clusterExport)

ClusType

string, the type of cluster to use. It can gbe either "Sock" or "Fork". Currently fork clustering only works in Linux

MinParOP

integer, the minimum number of operations to use parallel computation

CompileReport

boolean, should a step-by-step report with various information on the contruction of the principal graph be compiled?

ShowTimer

boolean, should the time to construct the graph be computed and reported for each step?

ComputeMSEP

boolean, should MSEP be computed when building the report?

FinalEnergy

string indicating the final elastic emergy associated with the configuration. Currently it can be "Base" or "Penalized"

alpha

positive numeric, the value of the alpha parameter of the penalized elastic energy

beta

positive numeric, the value of the beta parameter of the penalized elastic energy

gamma
Mode

integer, the energy computation mode

MaxNumberOfIterations

integer, maximum number of steps to embed the nodes in the data

MaxFailedOperations

integer, the maximum allowed number of consecutive failed grammar operations, i.e. appplication of the single grammar operations, that did not produce any valid configuration

MaxSteps

integer, the maximum allowed number of steps of the algorithm. Each step is composed by the application of all the specified grammar operations

GrammarOptimization

boolean, should the grammar be used to optimize the graph? If true a number MaxSteps of operations will be applied.

eps

real, minimal relative change in the position of the nodes to stop embedment

TrimmingRadius

real, maximal distance of point from a node to affect its embedment

GrowGrammars

list of strings, the grammar to be used in the growth step

ShrinkGrammars

list of strings, the grammar to be used in the shrink step

GrammarOrder

vector of strings, the order of application of the grammars. Can be any combination of "Grow" and "Shrink"

FastSolve

boolean, should FastSolve be used when fitting the points to the data?

AvoidSolitary

boolean, should configurations with "solitary nodes", i.e., nodes without associted points be discarded?

EmbPointProb

numeric between 0 and 1. If less than 1 point will be sampled at each iteration. EmbPointProb indicates the probability of using each points. This is an *experimental* feature, which may helps speeding up the computation if a large number of points is present.

AdjustElasticMatrix

a penalization function to adjust the elastic matrices after a configuration has been chosen (e.g., AdjustByConstant). If NULL (the default), no penalization will be used.

AdjustElasticMatrix.Initial

a penalization function to adjust the elastic matrices of the initial configuration (e.g., AdjustByConstant). If NULL (the default), no penalization will be used.

Value

a named list with a number of elements:

NodePositions

A numeric matrix containing the positions of the nodes

ElasticMatrix

The elastic matrix of the graph

ReportTable

The report table for the graph construction

FinalReport

The report table associated with the final graph configuration

Lambda

The lambda parameter used during the graph construction

Mu

The mu parameter used during the graph construction

FastSolve

was FastSolve being used?

Examples

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This is a low level function. See  \code{\link{computeElasticPrincipalCircle}},
\code{\link{computeElasticPrincipalCurve}}, or \code{\link{computeElasticPrincipalTree}}
for examples

Albluca/ElPiGraph.R documentation built on June 10, 2018, 5:22 p.m.