funFEM (version 1.2)

funFEM: The funFEM algorithm for the clustering of functional data.

Description

The funFEM algorithm allows to cluster time series or, more generally, functional data. It is based on a discriminative functional mixture model which allows the clustering of the data in a unique and discriminative functional subspace. This model presents the advantage to be parsimonious and can therefore handle long time series.

Usage

funFEM(fd, K=2:6, model = "AkjBk", crit = "bic", init = "kmeans", Tinit = c(), maxit = 50,
  eps = 1e-06, disp = FALSE, lambda = 0, graph = FALSE)

Arguments

fd

a functional data object produced by the fda package.

K

an integer vector specifying the numbers of mixture components (clusters) among which the model selection criterion will choose the most appropriate number of groups. Default is 2:6.

model

a vector of discriminative latent mixture (DLM) models to fit. There are 12 different models: "DkBk", "DkB", "DBk", "DB", "AkjBk", "AkjB", "AkBk", "AkBk", "AjBk", "AjB", "ABk", "AB". The option "all" executes the funFEM algorithm on the 12 models and select the best model according to the maximum value obtained by model selection criterion.

crit

the criterion to be used for model selection ('bic', 'aic' or 'icl'). 'bic' is the default.

init

the initialization type ('random', 'kmeans' of 'hclust'). 'kmeans' is the default.

Tinit

a n x K matrix which contains posterior probabilities for initializing the algorithm (each line corresponds to an individual).

maxit

the maximum number of iterations before the stop of the Fisher-EM algorithm.

eps

the threshold value for the likelihood differences to stop the Fisher-EM algorithm.

disp

if true, some messages are printed during the clustering. Default is false.

lambda

the l0 penalty (between 0 and 1) for the sparse version. See (Bouveyron et al., 2014) for details. Default is 0.

graph

if true, it plots the evolution of the log-likelhood. Default is false.

Value

A list is returned:

model

the model name.

K

the number of groups.

cls

the group membership of each individual estimated by the Fisher-EM algorithm.

P

the posterior probabilities of each individual for each group.

prms

the model parameters.

U

the orientation of the functional subspace according to the basis functions.

aic

the value of the Akaike information criterion.

bic

the value of the Bayesian information criterion.

icl

the value of the integrated completed likelihood criterion.

loglik

the log-likelihood values computed at each iteration of the FEM algorithm.

ll

the log-likelihood value obtained at the last iteration of the FEM algorithm.

nbprm

the number of free parameters in the model.

call

the call of the function.

plot

some information to pass to the plot.fem function.

crit

the model selction criterion used.

References

C. Bouveyron, E. C<U+00F4>me and J. Jacques, The discriminative functional mixture model for the analysis of bike sharing systems, Preprint HAL n.01024186, University Paris Descartes, 2014.

Examples

# NOT RUN {
# Clustering the well-known "Canadian temperature" data (Ramsay & Silverman)
basis <- create.bspline.basis(c(0, 365), nbasis=21, norder=4)
fdobj <- smooth.basis(day.5, CanadianWeather$dailyAv[,,"Temperature.C"],basis,
        fdnames=list("Day", "Station", "Deg C"))$fd
res = funFEM(fdobj,K=4)

# Visualization of the partition and the group means
par(mfrow=c(1,2))
plot(fdobj); lines(fdobj,col=res$cls,lwd=2,lty=1)
fdmeans = fdobj; fdmeans$coefs = t(res$prms$my)
plot(fdmeans); lines(fdmeans,col=1:max(res$cls),lwd=2)

# Visualization in the discriminative subspace (projected scores)
par(mfrow=c(1,1))
plot(t(fdobj$coefs) %*% res$U,col=res$cls,pch=19,main="Discriminative space")

# }
# NOT RUN {
###############################################################################
# Analysis of the Velib data set

# Load the velib data and smoothing
data(velib)
basis<- create.fourier.basis(c(0, 181), nbasis=25)
fdobj <- smooth.basis(1:181,t(velib$data),basis)$fd

# Clustrering with FunFEM
res = funFEM(fdobj,K=6,model='AkjBk',init='kmeans',lambda=0,disp=TRUE)

# Visualization of group means
fdmeans = fdobj; fdmeans$coefs = t(res$prms$my)
plot(fdmeans); lines(fdmeans,col=1:res$K,lwd=2,lty=1)
axis(1,at=seq(5,181,6),labels=velib$dates[seq(5,181,6)],las=2)

# # Choice of K (may be long!)
# res = funFEM(fdobj,K=2:20,model='AkjBk',init='kmeans',lambda=0,disp=TRUE)
# plot(2:20,res$plot$bic,type='b',xlab='K',main='BIC')

# Computation of the closest stations from the group means
par(mfrow=c(3,2))
for (i in 1:res$K) {
  matplot(t(velib$data[which.max(res$P[,i]),]),type='l',lty=i,col=i,xaxt='n',
          lwd=2,ylim=c(0,1))
  axis(1,at=seq(5,181,6),labels=velib$dates[seq(5,181,6)],las=2)
  title(main=paste('Cluster',i,' - ',velib$names[which.max(res$P[,i])]))
}

# Visualization in the discriminative subspace (projected scores)
par(mfrow=c(1,1))
plot(t(fdobj$coefs) %*% res$U,col=res$cls,pch=19,main="Discriminative space")
text(t(fdobj$coefs) %*% res$U)

# # Spatial visualization of the clustering (with library ggmap)
# library(ggmap)
# Mymap = get_map(location = 'Paris', zoom = 12, maptype = 'terrain')
# ggmap(Mymap) + geom_point(data=velib$position,aes(longitude,latitude),
#                           colour = I(res$cl), size = I(3))

# FunFEM clustering with sparsity
res2 = funFEM(fdobj,K=res$K,model='AkjBk',init='user',Tinit=res$P,
              lambda=0.01,disp=TRUE)

# Visualization of group means and the selected functional bases
split.screen(c(2,1))
fdmeans = fdobj; fdmeans$coefs = t(res2$prms$my)
screen(1); plot(fdmeans,col=1:res2$K,xaxt='n',lwd=2) 
axis(1,at=seq(5,181,6),labels=velib$dates[seq(5,181,6)],las=2)
basis$dropind = which(rowSums(abs(res2$U))==0)
screen(2); plot(basis,col=1,lty=1,xaxt='n',xlab='Disc. basis functions')
axis(1,at=seq(5,181,6),labels=velib$dates[seq(5,181,6)],las=2)
close.screen(all=TRUE)
# }