[Traminer-users] dendrogram

[so.bellit]

Thanks a lot




> Message du 02/08/12 12:25
> De : "Gilbert Ritschard"
> A : "Users questions"
> Copie à :
> Objet : Re: [Traminer-users] dendrogram
>
> 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
> > >
> >
> >
> > >
> >
> >
> > >
> >
> >
> > >
> >
> >
> > >
> >
> > _______________________________________________
> > >
> >
> > Traminer-users mailing list
> > >
> >
> > Traminer-users at lists.r-forge.r-project.org
> >
> > >
> >
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/traminer-users
> > >
> >
> >
> > >
> >
> > _______________________________________________
> > >
> >
> > Traminer-users mailing list
> > >
> >
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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
> > > -----------------------------------------
> > >
> > > _______________________________________________
> > > Traminer-users mailing list
> > > Traminer-users at lists.r-forge.r-project.org
> >
> > >
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/traminer-users
> > >
> > >
> >
> >
> > >
> >
> > >
> > > [ (pas de nom de fichier) (0.2 Ko) ]
> >
> > >
> > > [ (pas de nom de fichier) (0.2 Ko) ]
> >
> >
> >
> > _______________________________________________
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>
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