[Traminer-users] dendrogram
Gilbert Ritschard
Gilbert.Ritschard at unige.ch
Thu Aug 2 12:25:47 CEST 2012
The identify.hclust function works on dendrograms obtained by plotting
the outcome of hclust. The following example works perfectly on my system:
####### start of example ###########
## generating the state sequence object (from preview on the TraMineR
web page)
library(TraMineR)
data(mvad)
mvad.alphabet <- c("employment", "FE", "HE", "joblessness", "school",
"training")
mvad.labels <- c("employment", "further education", "higher education",
"joblessness", "school", "training")
mvad.scodes <- c("EM", "FE", "HE", "JL", "SC", "TR")
mvad.seq <- seqdef(mvad, 17:86, alphabet = mvad.alphabet, states =
mvad.scodes,
labels = mvad.labels, xtstep = 6)
## OM distances
dist.om1 <- seqdist(mvad.seq, method = "OM", indel = 1, sm = "TRATE")
## generating the hierarchical clusters with hclust
hca <- hclust(as.dist(dist.om1))
plot(hca)
## now using identify on the dendrogram produced by the above plot function
(x <- identify(hca))
###### end example ########
Best,
Gilbert
On 01-Aug-12 17:54, so.bellit wrote:
>
>
> I would like to use the "identify" function in order to know how
> identify clusters in the dendogram. But it seems not work with the
> Optimal Matching Analysis.
>
> Thanks
> Sonia
>
>
>
>
>
> > Message du 01/08/12 11:29
> > De : "so.bellit"
> > A : "Users questions"
> > Copie à :
> > Objet : [Traminer-users] dendrogram
> >
> >
>
> Hi,
>
> Anyone knows if we can link the cluster or individuals with the
> dendrogram?
>
> Thanks
> Sonia
>
>
>
>
>
> > Message du 23/07/12 17:49
> > De : "Joel Schwartz"
> > A : "Users questions"
> > Copie à :
> > Objet : Re: [Traminer-users] how to sort a sequence plot
> (seqIplot) by more than one variable
> >
> > Hi Jan,
>
>
> >
>
> Yes, that worked. Using the order() function, I created a new,
> sorted version of the sequence object and got the sort order I
> wanted.
>
>
> >
>
> Thanks!
>
> Joel
>
>
> >
>
> On Jul 19, 2012, at 10:53 AM, Jan Goebel wrote:
>
>
> Dear Joel,
> >
> > the help page on plot.stslist states that sortv has to
> be a variable name:
> >
> > sortv: name of an optional variable used to sort the
> sequences
> > before plotting.
> >
> > So my guess is, that you have to create a new variable
> within your data frame and not to supply an "external" vector.
> >
> > However ?seqIplot has in my opinion at least some
> fuzziness, because here you find:
> > "The ‘sortv’ argument can be used to pass a vector of
> numerical values for sorting the sequences. See
> ‘plot.stslist’ for a complete list of optional arguments."
> >
> > Best wishes,
> >
> > Jan
> >
> > On 07/17/2012 03:25 PM, Joel Schwartz wrote:
> >
>
> Hi Alexis,
> >
>
>
> >
>
> I tried your suggestion and for some reason it's not
> working, even when I create a sorting
> >
>
> variable that uses a single variable to sort on.
> Here's what I did:
> >
>
>
> >
>
> # Original version, which works fine. See first
> attached file below, which shows plot is
> >
>
> clearly sorted by f09as.
> >
>
> seqIplot(df.seq09, border = NA, withlegend = "right",
> sortv=df09$f09as)
> >
>
>
> >
>
> # Create sorting variable
> >
>
> term.sort = order(df09$f09as)
> >
>
>
> >
>
> # Create plot again, using sorting variable. This
> version of the plot is unsorted. See second
> >
>
> attached file.
> >
>
> seqIplot(df.seq09, border = NA, withlegend = "right",
> sortv=term.sort)
> >
>
>
> >
>
> I checked the sorting variable by looking at what it
> does to the original data frame and it
> >
>
> looked exactly like it should, so the sorting variable
> doesn't seem to have a problem. Here's
> >
>
> the command I used for that: df09[order(df09$f09as), ]
> >
>
>
> >
>
> Any idea what could be going wrong? If it would help
> to look at the sequence object or
> >
>
> data.frame I'm working with, I can send those.
> >
>
>
> >
>
> Thanks again,
> >
>
> Joel
> >
>
>
> >
>
>
> >
>
> =
> >
>
>
> >
>
>
> >
>
>
> >
>
>
> >
>
>
> >
>
>
> >
>
>
> >
>
> On Jul 16, 2012, at 12:10 AM, Alexis gabadinho wrote:
> >
>
>
> >
>
> Hi Joel,
> >
>
>
> >
>
> Use first the order function to create one single
> sorting variable, and then pass this
> >
>
> variable to the seqIplot function. Here is an
> example with the biofam data frame where
> >
>
> sequences are sorted by gender and birthyr
> >
>
>
> >
>
> data(biofam)
> >
>
> biofam.seq <- seqdef(biofam, 10:25)
> >
>
> csort <- order(biofam$sex, biofam$birthyr)
> >
>
> seqIplot(biofam.seq, sortv=csort)
> >
>
>
> >
>
> All the best,
> >
>
> Alexis
> >
>
>
> >
>
>
> >
>
> Le 16. 07. 12 08:12, Joel Schwartz a écrit :
> >
>
> I'm a new TraMineR user and just ran into a
> problem while using the seqIplot function. I'm
> >
>
> making a plot of hundreds of sequences. To
> make it possible to see patterns, I'm trying to
> >
>
> sort the sequences by more than one variable.
> It works as expected when I sort by one
> >
>
> variable. But when I try to sort by more than
> one, I get the exact same result as when I
> >
>
> sort by one variable.
> >
>
>
> >
>
> Here are the two commands I'm using
> >
>
>
> >
>
> # Sort by one variable
> >
>
> seqIplot(df.seq, border=NA,
> withlegend="right", sortv=df$s09as)
> >
>
>
> >
>
> # Sort by two variables
> >
>
> seqIplot(df.seq, border = NA,
> withlegend="right", sortv=c(df$s09as, df$f09as))
> >
>
>
> >
>
> I get the exact same plot either way, and no
> warnings or errors.
> >
>
>
> >
>
> Is there a way to sort by more than one variable?
> >
>
>
> >
>
> Thanks for your help.
> >
>
>
> >
>
> Best Wishes,
> >
>
> Joel Schwartz
> >
>
>
> >
>
>
> >
>
>
> >
>
>
> >
>
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> >
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> >
>
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> >
>
> This body part will be downloaded on demand.
> >
>
>
> >
>
>
> > --
> > -----------------------------------------
> > Dr. Jan Goebel
> > Head of the Division
> > Data Operation and Research Data Center
> >
> > DIW Berlin
> > Socio-Economic Panel Study (SOEP)
> > Mohrenstr. 58
> > D-10117 Berlin -- Germany --
> > phone: +49 30 89789-377
> > -----------------------------------------
> >
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