elpigraph.computeElasticPrincipalCircle¶
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elpigraph.
computeElasticPrincipalCircle
(X, NumNodes, NumEdges=inf, InitNodes=3, Lambda=0.01, Mu=0.1, GrammarOptimization=False, MaxSteps=inf, GrammarOrder=['Grow', 'Shrink'], MaxNumberOfIterations=10, TrimmingRadius=inf, eps=0.01, Do_PCA=True, InitNodePositions=None, AdjustVect=None, ElasticMatrix=None, InitEdges=None, CenterData=True, ComputeMSEP=True, verbose=False, ShowTimer=False, ReduceDimension=None, n_cores=1, MinParOp=20, nReps=1, Subsets=[], ProbPoint=1, Mode=1, FinalEnergy='Base', alpha=0, beta=0, Configuration='Line', ICOver=None, DensityRadius=None, AvoidSolitary=False, EmbPointProb=1, PointWeights=None, SampleIC=True, AvoidResampling=True, AdjustElasticMatrix=None, AdjustElasticMatrix_Initial=None, Lambda_Initial=None, Mu_Initial=None, DisplayWarnings=False, StoreGraphEvolution=False, GPU=False, FixNodesAtPoints=[], pseudotime=None, pseudotimeLambda=0.01, label=None, labelLambda=0.01, MaxNumberOfGraphCandidatesDict={'AddNode2Node': inf, 'BisectEdge': inf, 'RemoveNode': inf, 'ShrinkEdge': inf})[source]¶ Construct a principal elastic circle
This function is a wrapper to the computeElasticPrincipalGraph function that constructs the appropriate initial graph and grammars when constructing a circle
- 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
- Lambda: real,
- the lambda parameter used the compute the elastic energy
- Mu: real,
- the lambda parameter used the compute the elastic energy
- InitNodes: integer,
- number of points to include in the initial graph
- MaxNumberOfIterations: integer,
- maximum number of steps to embed the nodes in the data
- TrimmingRadius: real,
- maximal distance of point from a node to affect its embedment
- eps: real,
- minimal relative change in the position of the nodes to stop embedment
- Do_PCA: boolean,
- should data and initial node positions be PCA trnasformed?
- InitNodePositions: numerical 2D matrix,
- the k-by-m matrix with k m-dimensional positions of the nodes
in the initial step InitEdges: numerical 2D matrix,
the e-by-2 matrix with e end-points of the edges connecting the nodes- ElasticMatrix: numerical 2D matrix,
- the k-by-k elastic matrix
- CenterData: boolean,
- should data and initial node positions be centered?
- ComputeMSEP: boolean,
- should MSEP be computed when building the report?
- verbose: boolean,
- should debugging information be reported?
- ShowTimer: boolean,
- should the time to construct the graph be computed and reported for each step?
- ReduceDimension: integer vector,
- vector of principal components to retain when performing dimensionality reduction. If None all the components will be used
- drawAccuracyComplexity: boolean,
- should the accuracy VS complexity plot be reported?
- drawPCAView: boolean,
- should a 2D plot of the points and pricipal curve be dranw for the final configuration?
- drawEnergy: boolean,
- should changes of evergy VS the number of nodes be reported?
- 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) MinParOP: integer,
the minimum number of operations to use parallel computation- nReps: integer,
- number of replica of the construction
- ProbPoint: real
- between 0 and 1, probability of inclusing of a single point for each computation
- Subsets: list
- of column names (or column number). When specified a principal circle will be computed for each of the subsets specified.
- NumEdges: integer,
- the maximum nulber of edges
- Mode: integer,
- the energy computation mode
- FastSolve: boolean,
- should FastSolve be used when fitting the points to the data?
- ClusType: string,
- the type of cluster to use. It can gbe either “Sock” or “Fork”.
Currently fork clustering only works in Linux ICOver: string,
initial condition overlap mode. This can be used to alter the default behaviour for the initial configuration of theprincipal circle DensityRadius: numeric,
the radius used to estimate local density. This need to be set when ICOver is equal to “Density”- AvoidSolitary: boolean,
- should configurations with “solitary nodes”, i.e., nodes without associted points be discarded?
- 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
- 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: function
- a penalization function to adjust the elastic matrices after a configuration has been chosen (e.g., AdjustByConstant). If None (the default), no penalization will be used.
- 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.
- AdjustElasticMatrix_Initial: function
- a penalization function to adjust the elastic matrices of the initial configuration (e.g., AdjustByConstant). If None (the default), no penalization will be used.
- Lambda_Initial: real
- the lambda parameter used the construct the elastic matrix associted with ther initial configuration if needed. If None, the value of Lambda will be used.
- Mu_Initial: real,
- the mu parameter used the construct the elastic matrix associted with ther initial configuration if needed. If None, the value of Mu will be used.