Description Usage Arguments Value Examples
The core function that takes the n mdimensional points and construct a principal elastic graph using the grammars provided.
1 2 3 4 5 6 7 8 9 10  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, ...)

X 
numerical 2D matrix, the nbym matrix with the position of n mdimensional 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 kbyk elastic matrix 
NodesPositions 
numerical 2D matrix, the kbym matrix with k mdimensional 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 stepbystep 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. 
a named list with a number of elements:
A numeric matrix containing the positions of the nodes
The elastic matrix of the graph
The report table for the graph construction
The report table associated with the final graph configuration
The lambda parameter used during the graph construction
The mu parameter used during the graph construction
was FastSolve being used?
1 2 3  This is a low level function. See \code{\link{computeElasticPrincipalCircle}},
\code{\link{computeElasticPrincipalCurve}}, or \code{\link{computeElasticPrincipalTree}}
for examples

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