[Traminer-users] Traminer-users Digest, Vol 35, Issue 2
Jeremy Reynolds
jeremyr at uga.edu
Mon Nov 18 17:43:47 CET 2013
Dear Alexis and Chris,
Thank you very much for your help with the special seqrplot plot. I have
an additional question that you or someone else on the list can probably
answer easily.
In experimenting with seqrplot, I have found that when I request plots for
each cluster in a cluster solution I get a different result than when I try
to get a single plot using only the data from one cluster. I have included
an example below. Shouldn't these be the same? Am I doing something wrong
when selecting the cases to use in the second sqrplot command?
Thanks,
Jeremy
P.S. Has anyone identified a color scheme for sequence index plots that
works well when the plot has to be black & white or grey scale?
############
# My example code
############
data(mvad)
mvad.labels <- c("employment", "further education", "higher education",
"joblessness", "school", "training")
mvad.scode <- c("EM", "FE", "HE", "JL", "SC", "TR")
mvad.seq <- seqdef(mvad, 17:86, states = mvad.scode, labels = mvad.labels,
xtstep = 6)
ccost <- seqsubm(mvad.seq, method = "CONSTANT", cval = 2)
seq.om <- seqdist(mvad.seq, method = "OM", sm = ccost)
clusterward <- agnes(seq.om, diss = TRUE, method = "ward")
cluster3 <- cutree(clusterward, k = 3)
cluster3 <- factor(cluster3, labels = c("Type 1", "Type 2", "Type 3"))
table(cluster3)
#representative sequences for each cluster
seqrplot(mvad.seq, group = cluster3, dist.matrix = seq.om, border = NA)
#representative sequences for a particular cluster (here cluster 1)
#why are the results not the same as when done by group in the previous
seqrplot? (# of sequences and coverage do not match output from above)
clust1 <- which(cluster3=="Type 1")
seqrplot(mvad.seq[clust1,], dist.matrix = seq.om, border = NA)
############
# The output
############
> #representative sequences for each cluster
> seqrplot(mvad.seq, group = cluster3, dist.matrix = seq.om, border = NA)
[>] number of objects (sum of weights): 295
[>] max. distance: 140
[>] neighborhood radius: 14
[>] 1 representative(s) selected, coverage=32% (threshold=25%)
[>] 186 distinct sequence(s)
[>] number of objects (sum of weights): 164
[>] max. distance: 140
[>] neighborhood radius: 14
[>] 2 representative(s) selected, coverage=39% (threshold=25%)
[>] 98 distinct sequence(s)
[>] number of objects (sum of weights): 253
[>] max. distance: 140
[>] neighborhood radius: 14
[>] 3 representative(s) selected, coverage=30% (threshold=25%)
[>] 206 distinct sequence(s)
> #representative sequences for a particular cluster (here cluster 1)
> #why are the results not the same as when done by group in the previous
seqrplot? (# of sequences and coverage do not match output from above)
> clust1 <- which(cluster3=="Type 1")
> seqrplot(mvad.seq[clust1,], dist.matrix = seq.om, border = NA)
[>] number of objects (sum of weights): 295
[>] max. distance: 140
[>] neighborhood radius: 14
[>] 3 representative(s) selected, coverage=27% (threshold=25%)
[>] 186 distinct sequence(s)
> Today's Topics:
>
> 1. Plot of Representative Sequences (Jeremy Reynolds)
> 2. Re: Plot of Representative Sequences (Chris Cameron)
> 3. Re: Plot of Representative Sequences (Alexis Gabadinho)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 14 Nov 2013 16:15:49 -0500
> From: Jeremy Reynolds <jeremyr at uga.edu>
> To: traminer-users at lists.r-forge.r-project.org
> Subject: [Traminer-users] Plot of Representative Sequences
> Message-ID:
> <CABicVB9xs7V33HQ=
> vFYYKjOxULd5fzZjgFBOZOeTmqkVYragQQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear TraMineR Users,
>
> Does anyone know how Gabadinho and Ritschard produced figure 5 of their
> paper (see link below)? For each group, it has one plot showing three
> different sequences: the sequence that is most frequent, the sequence with
> the highest neighborhood density, and the sequence that is most central.
>
> I can do a plot with one of the three sequences for each group, but I'm not
> sure how to combine the three into a single plot.
>
> Thanks,
>
> Jeremy
>
> Gabadinho A, Ritschard G (2013). "Searching for typical life trajectories
> applied to child birth histories", In R L?vy, E. Widmer (eds.), *Gendered
> Life Courses*, pp. 287-312. Vienna: LIT.
>
>
> http://mephisto.unige.ch/pub/publications/gr/GabadhinoRitschard-TypicalTrajectories2013.pdf
>
> --
> ********************
> Dr. Jeremy Reynolds
> Associate Professor
> Undergraduate Coordinator
> Department of Sociology
> 116 Baldwin Hall
> University of Georgia
> Athens, GA 30602-1611
> Phone: (706) 583-8072
> Web: http://uga.edu/soc/people/faculty/reynolds_jeremy.php
> Fax: (706) 542-4320
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> ------------------------------
>
> Message: 2
> Date: Thu, 14 Nov 2013 16:35:43 -0500
> From: Chris Cameron <cjc73 at cornell.edu>
> To: Users questions <traminer-users at r-forge.wu-wien.ac.at>
> Subject: Re: [Traminer-users] Plot of Representative Sequences
> Message-ID: <0996DFC3-86BB-4629-8F7C-9EC42255217A at cornell.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Jeremy
>
> I think you would create a new input sequences set with only the desired
> sequences and then use seqiplot.
> You can also just plot particular values using indexing. Does this work
> for your case?
>
> seqiplot(morn.dss[c(1,6,10),])
>
> Chris Cameron
> PhD Candidate
> Dept of Sociology
> Cornell University
>
>
> On Nov 14, 2013, at 4:15 PM, Jeremy Reynolds <jeremyr at uga.edu> wrote:
>
> > Dear TraMineR Users,
> >
> > Does anyone know how Gabadinho and Ritschard produced figure 5 of their
> paper (see link below)? For each group, it has one plot showing three
> different sequences: the sequence that is most frequent, the sequence with
> the highest neighborhood density, and the sequence that is most central.
> >
> > I can do a plot with one of the three sequences for each group, but I'm
> not sure how to combine the three into a single plot.
> >
> > Thanks,
> >
> > Jeremy
> >
> > Gabadinho A, Ritschard G (2013). "Searching for typical life
> trajectories applied to child birth histories", In R L?vy, E. Widmer
> (eds.), Gendered Life Courses, pp. 287-312. Vienna: LIT.
> >
> >
> http://mephisto.unige.ch/pub/publications/gr/GabadhinoRitschard-TypicalTrajectories2013.pdf
> >
> >
> > --
> > ********************
> > Dr. Jeremy Reynolds
> > Associate Professor
> > Undergraduate Coordinator
> > Department of Sociology
> > 116 Baldwin Hall
> > University of Georgia
> > Athens, GA 30602-1611
> > Phone: (706) 583-8072
> > Web: http://uga.edu/soc/people/faculty/reynolds_jeremy.php
> > Fax: (706) 542-4320
> > _______________________________________________
> > 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
>
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> ------------------------------
>
> Message: 3
> Date: Fri, 15 Nov 2013 11:04:45 +0100
> From: Alexis Gabadinho <alexis.gabadinho at unige.ch>
> To: <traminer-users at lists.r-forge.r-project.org>
> Subject: Re: [Traminer-users] Plot of Representative Sequences
> Message-ID: <5285F1BD.5090905 at unige.ch>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Dear Jeremry,
>
> The plot is created by using the seqrep function with all three
> criteria, then retrieving the index of the representatives and using
> them to select the sequences to plot in the whole set with the tlim
> argument.
>
> Here is a code example, where
> - "seq.object" is the sequence object,
> - "dist" is the pairwise distance matrix
> - "max.dist" is the maximum theoretical distance between two sequences
> (it is provided because it is not sure wether the maximum observed
> distance equal the theoretical maximum)
>
> ## Sequences representatives
> medoid <- seqrep(seq.object, criterion="dist", nrep=1, dist.matrix=dist,
> dmax=max.dist)
> freq <- seqrep(seq.object, criterion="freq", nrep=1, dist.matrix=dist,
> dmax=max.dist)
> density <- seqrep(seq.object, criterion="density", nrep=1,
> dist.matrix=dist, dmax=max.dist)
>
> rep.idx <- c(attr(freq,"Index")[1], attr(density,"Index")[1],
> attr(medoid,"Index")[1])
> seqiplot(seq.object, tlim=rep.idx, withlegend=FALSE, title="Title",
> border=NA)
>
> Best regards,
> Alexis
>
>
> Le 14. 11. 13 22:15, Jeremy Reynolds a ?crit :
> > Dear TraMineR Users,
> >
> > Does anyone know how Gabadinho and Ritschard produced figure 5 of
> > their paper (see link below)? For each group, it has one plot showing
> > three different sequences: the sequence that is most frequent, the
> > sequence with the highest neighborhood density, and the sequence that
> > is most central.
> >
> > I can do a plot with one of the three sequences for each group, but
> > I'm not sure how to combine the three into a single plot.
> >
> > Thanks,
> >
> > Jeremy
> >
> > Gabadinho A, Ritschard G (2013). "Searching for typical life
> > trajectories applied to child birth histories", In R L?vy, E. Widmer
> > (eds.),/Gendered Life Courses/, pp. 287-312. Vienna: LIT.
> >
> >
> http://mephisto.unige.ch/pub/publications/gr/GabadhinoRitschard-TypicalTrajectories2013.pdf
> >
> >
> > --
> > ********************
> > Dr. Jeremy Reynolds
> > Associate Professor
> > Undergraduate Coordinator
> > Department of Sociology
> > 116 Baldwin Hall
> > University of Georgia
> > Athens, GA 30602-1611
> > Phone: (706) 583-8072
> > Web: http://uga.edu/soc/people/faculty/reynolds_jeremy.php
> > Fax: (706) 542-4320
> >
> >
> > _______________________________________________
> > 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
>
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>
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> Traminer-users at lists.r-forge.r-project.org
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>
> End of Traminer-users Digest, Vol 35, Issue 2
> *********************************************
>
--
********************
Dr. Jeremy Reynolds
Associate Professor
Undergraduate Coordinator
Department of Sociology
116 Baldwin Hall
University of Georgia
Athens, GA 30602-1611
Phone: (706) 583-8072
Web: http://uga.edu/soc/people/faculty/reynolds_jeremy.php
Fax: (706) 542-4320
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