Multichannel sequence analysis through WeightedCluster package

Question

I would like to apply the functions available in the WeightedCluster package to analyze multichannel sequences I obtained through TraMineR. I am trying so, but due to the fact that multichannel sequences are lists composed by each channel separatedly, I get errors in functions like seqtreedisplay() and all those which require a sequence object.

This is an example:

fullsequences <- list(
  work_sequence2 = work_sequence[which(rownames(work_sequence) %in% commonid),],
  educ_sequence2 = educ_sequence[which(rownames(educ_sequence) %in% commonid),],
  part_sequence2 = part_sequence[which(rownames(part_sequence) %in% commonid),],
  kid_sequence2 = kid_sequence[which(rownames(kid_sequence) %in% commonid),]
)  # a total of 926 with complete sequences on all channels

multidist <- seqdistmc(
          channels = fullsequences,
          method = "OM", 
          norm = FALSE, 
          sm = list("TRATE","TRATE","TRATE","TRATE"), 
          with.missing=FALSE, 
          full.matrix=TRUE, 
          link="sum")  

clusterward <- hclust(as.dist(multidist), method = "ward")  

seqtreedisplay(as.seqtree(clusterward, ncluster = 5,
           seqdata = fullsequences , diss = multidist))

Error in seqlegend(seqdata, fontsize = legend.fontsize, title = "Legend",  : 
  data is not a sequence object, use seqdef function to create one

Is there a method to use the functionalities of WeightedCluster package upon a multichannel-type object (list of sequences). I am specially interested in using the Partition Around Medioids algorithm with initial ward clusters (function wcKMedioids()). If it is not possible, which is the best alternative to cluster multichannels in R? Thanks a lot in advance!

Gilbert Gilbert · Accepted Answer · 2015-09-16T13:47:26

The as.seqtree function (from WeightedCluster) requires an object of class stslist (as produced by the TraMineR seqdef function) as seqdata argument. In your case, fullsequences is a list of such objects (the list of parallel sequences), which is NOT itself of class stslist. This causes the error.

Even if you would be able to define a tree of parallel sequences, the problem would be that the seqtreedisplay does not know how to plot parallel sequences. This means that you would have to define a plot function for a list of state sequences and, using the more general disstreedisplay function instead of seqtreedisplay, pass the plot function as imagefunc argument.

To summarize, there are two problems. First you need some as.disstree equivalent of as.seqtree that would work for hierarchical clustering of non-stslist objects. Second, you need a plot function for parallel sequences. The first problem is purely technical and should be easily solved. The second is more conceptual.

Multichannel sequence analysis through WeightedCluster package

1 Answers