R: K-Means Clustering and Alignment

kmeans_align {fdasrvf}

R Documentation

K-Means Clustering and Alignment

Description

This function clusters functions and aligns using the elastic square-root slope (srsf) framework.

Usage

kmeans_align(
  f,
  time,
  K,
  seeds = NULL,
  nonempty = 0,
  lambda = 0,
  showplot = TRUE,
  smooth_data = FALSE,
  sparam = 25,
  parallel = FALSE,
  alignment = TRUE,
  omethod = "DP",
  MaxItr = 50,
  thresh = 0.01
)

Arguments

`f`	matrix (N x M) of M functions with N samples
`time`	vector of size N describing the sample points
`K`	number of clusters
`seeds`	indexes of cluster center functions (default = NULL)
`nonempty`	minimum number of functions per cluster in assignment step of k-means. Set it as a positive integer to avoid the problem of empty clusters (default = 0)
`lambda`	controls the elasticity (default = 0)
`showplot`	shows plots of functions (default = T)
`smooth_data`	smooth data using box filter (default = F)
`sparam`	number of times to apply box filter (default = 25)
`parallel`	enable parallel mode using `foreach` and `doParallel` package (default=F)
`alignment`	whether to perform alignment (default = T)
`omethod`	optimization method (DP,DP2,RBFGS)
`MaxItr`	maximum number of iterations
`thresh`	cost function threshold

Value

Returns a fdakma object containing

`f0`	original functions
`fn`	aligned functions - matrix (N x M) of M functions with N samples which is a list for each cluster
`qn`	aligned SRSFs - similar structure to fn
`q0`	original SRSFs
`labels`	cluster labels
`templates`	cluster center functions
`templates.q`	cluster center SRSFs
`gam`	warping functions - similar structure to fn
`qun`	Cost Function Value

References

Srivastava, A., Wu, W., Kurtek, S., Klassen, E., Marron, J. S., May 2011. Registration of functional data using fisher-rao metric, arXiv:1103.3817v2 [math.ST].

Tucker, J. D., Wu, W., Srivastava, A., Generative Models for Function Data using Phase and Amplitude Separation, Computational Statistics and Data Analysis (2012), 10.1016/j.csda.2012.12.001.

Sangalli, L. M., et al. (2010). "k-mean alignment for curve clustering." Computational Statistics & Data Analysis 54(5): 1219-1233.

Examples

## Not run: 
data("growth_vel")
out <- kmeans_align(growth_vel$f,growth_vel$time, K=2)

## End(Not run)

[Package fdasrvf version 1.9.7 Index]