[Traminer-users] seqfplot issue

[Kleinbaum, Adam M.]

Hi all,

I'm having an issue with seqfplot I'm hoping you can help me with.  I have a series of career sequences over a 77-month observation period for a group of 15,000 or so individuals.  I use the following code to read in my data (including labels), define a color palette, and drop any observations with missing data:

fx <- read.csv(file="Seq_function.txt", header=FALSE)
fx.lab <- c("AD", "CO", "FI", "GM", "HR", "LE", "MF", "MK", "OT", "RD", "SC", "SL", "SV")
fx.seq <- seqdef(fx, 2:78, labels=fx.lab)
attr(fx.seq,"cpal") <- c(brewer.pal(n=12, name="Set3"), "cyan", "white")
fx <- fx[!is.na(fx[,78]), ]
fx.seq <- fx.seq[seqlength(fx.seq)==77,]

Then I use TraMineR to calculate the substitution cost matrix and do optimal matching.  Next I use the "cluster" package to do a cluster analysis and I find that there are 9 prototypical sequences.  I'd like to do a bit of graphing for each of the 9 clusters, so I run the following code:

for (i in 1:k.best.om.fx)
{
  seqdplot(fx.seq[pam.best.fx$clustering==i,], withlegend=F, title=paste("Cluster ", i))
  seqfplot(fx.seq[pam.best.fx$clustering==i,], withlegend=F, title=paste("Cluster ", i))
}
seqlegend(fx.seq)

where fx.seq contains my sequences, as shown above; pam.best.fx is the pam object that came out of the clustering algorithm and pam.best.fx$clustering contains the index of each actor's cluster assignment.

The seqdplot command produces a series of 9 beautiful distribution plots, one for each cluster.  No problem.

What I want seqfplot to do is, for each cluster, graph out the frequency of sequences within each cluster, from most frequent on down the list.  To take one example, the medoid of one cluster is 77 observations of all the same job function - people who stay in sales and don't move.  People assigned to that cluster should have spent nearly all 77 periods in that function.  The output should look like a long sequence of blocks that are mostly the same color, with another sequence above it that's a little bit different, but also mostly all the same color.  But instead, every single block is a different color from the one next to it.  There's obviously some problem with either how I'm calling the function or how I'm defining my color palette, but I can't figure out what it is.  I'm especially perplexed that seqdplot works properly while an identical call to seqfplot does not.  Any ideas?  Thanks in advance,

All the best,
Adam

--
Adam M. Kleinbaum
Assistant Professor
Tuck School of Business
Dartmouth College
http://bit.ly/kleinbaum
603.646.6447

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