ApplyOptimalGraphGrammarOpeation: Application of the grammar operation. This in an internal...
In Albluca/ElPiGraph.R: Elastic principal graph construction

Application of the grammar operation. This in an internal function that should not be used in by the end-user

ApplyOptimalGraphGrammarOpeation(X, NodePositions, ElasticMatrix,
  AdjustVect = NULL, operationtypes, SquaredX = NULL, verbose = FALSE,
  n.cores = 1, EnvCl = NULL, MinParOP = 20, MaxNumberOfIterations = 100,
  eps = 0.01, TrimmingRadius = Inf, Mode = 1, FinalEnergy = "Base",
  alpha = 1, beta = 1, gamma = 1, FastSolve = FALSE, EmbPointProb = 1,
  AvoidSolitary = FALSE, AdjustElasticMatrix = NULL, ...)

`X`	numerical 2D matrix, the n-by-m matrix with the position of n m-dimensional points
`NodePositions`	numerical 2D matrix, the k-by-m matrix with the position of k m-dimensional points
`ElasticMatrix`	numerical 2D matrix, the k-by-k elastic matrix
`AdjustVect`
`operationtypes`	string vector containing the operation to use
`SquaredX`	rowSums(X^2), if NULL it will be computed
`verbose`	boolean. Should addition information be displayed
`n.cores`	integer. How many cores to use. If EnvCl is not NULL, that cliuster setup will be used, otherwise a SOCK cluster willbe used
`EnvCl`	a cluster structure returned, e.g., by makeCluster. If a cluster structure is used, all the nodes must be able to access all the variable needed by PrimitiveElasticGraphEmbedment
`MinParOP`	integer, the minimum number of operations to use parallel computation
`MaxNumberOfIterations`	is an integer number indicating the maximum number of iterations for the EM algorithm
`eps`	a real number indicating the minimal relative change in the nodenpositions to be considered the graph embedded (convergence criteria)
`TrimmingRadius`	is a real value indicating the trimming radius, a parameter required for robust principal graphs (see https://github.com/auranic/Elastic-principal-graphs/wiki/Robust-principal-graphs)
`Mode`	integer, the energy mode. It can be 1 (difference is computed using the position of the nodes) and 2 (difference is computed using the changes in elestic energy of the configuraztions)
`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`
`FastSolve`	boolean, should FastSolve be used when fitting the points to the data?
`EmbPointProb`	numeric between 0 and 1. If less than 1 point will be sampled at each iteration. Prob indicate 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.
`AvoidSolitary`	boolean, should configurations with "solitary nodes", i.e., nodes without associted points be discarded?
`AdjustElasticMatrix`
`...`