kCFC: Functional clustering and identifying substructures of...

Description Usage Arguments Value References Examples

Description

Functional clustering and identifying substructures of longitudinal data using kCFC.

Usage

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kCFC(y, t, k = 3, kSeed = 123, maxIter = 125,
  optnsSW = list(methodMuCovEst = "smooth", FVEthreshold = 0.9,
  methodBwCov = "GCV", methodBwMu = "GCV"), optnsCS = list(methodMuCovEst
  = "smooth", FVEthreshold = 0.7, methodBwCov = "GCV", methodBwMu = "GCV"))

Arguments

y

A list of n vectors containing the observed values for each individual. Missing values specified by NAs are supported for dense case (dataType='dense').

t

A list of n vectors containing the observation time points for each individual corresponding to y.

k

A scalar defining the number of clusters to define; default 3. Values that define very small clusters (eg.cluster size <=3) will potentiall err.

kSeed

A scalar valid seed number to ensure replication; default: 123

maxIter

A scalar defining the maximum number of iterations allowed; default 20, common for both the simple kmeans initially and the subsequent k-centres

optnsSW

A list of options control parameters specified by list(name=value) to be used for sample-wide FPCA; by default: "list( methodMuCovEst ='smooth', FVEthreshold= 0.90, methodBwCov = 'GCV', methodBwMu = 'GCV' )". See ‘Details in ?FPCA’.

optnsCS

A list of options control parameters specified by list(name=value) to be used for cluster-specific FPCA; by default: "list( methodMuCovEst ='smooth', FVEthreshold= 0.70, methodBwCov = 'GCV', methodBwMu = 'GCV' )". See ‘Details in ?FPCA’.

Value

A list containing the following fields:

cluster

A vector of levels 1:k, indicating the cluster to which each curve is allocated.

fpcaList

A list with the fpcaObj for each separate cluster.

iterToConv

A number indicating how many iterations where required until convergence.

References

Jeng-Min Chiou, Pai-Ling Li, "Functional clustering and identifying substructures of longitudinal data." Journal of the Royal Statistical Society 69 (2007): 679-699

Examples

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data(medfly25) 
Flies <- MakeFPCAInputs(medfly25$ID, medfly25$Days, medfly25$nEggs)
kcfcObj <- kCFC(Flies$Ly[1:250], Flies$Lt[1:250], # using only 250 for speed consideration 
                 optnsSW = list(methodMuCovEst = 'smooth', userBwCov = 2, FVEthreshold = 0.90),
                 optnsCS = list(methodMuCovEst = 'smooth', userBwCov = 2, FVEthreshold = 0.70))

functionaldata/tPACE documentation built on May 16, 2019, 3:38 p.m.