<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Adam,<br>
<br>
I can see that you have 13 states in your alphabet, and you define
only 12 colors in your palette. Indeed, brewer.pal() can define up
to 12 colors only. <br>
<br>
You have to use a "home made" color palete like: <br>
<br>
my.pal <- c("blue", "red", "yellow", ....) <br>
<br>
see colors() for available colors.<br>
<br>
Then you can pass your color palettedirectly in seqdef():<br>
<span style="font-size: 10pt; font-family: "Courier New";">fx.seq
<- seqdef(fx, 2:78, labels=fx.lab, cpal=my.pal)</span><br>
<br>
I'm pretty sure this is the problem.<br>
<br>
All the best,<br>
Alexis.<br>
<br>
Le 18. 05. 11 10:32, Matthias Studer a écrit :
<blockquote cite="mid:4DD3841D.5070906@unige.ch" type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
Hi all,<br>
<br>
I hope I understand well your question. Usually, the problem with
seqfplot is that the most frequent one are the stable sequence,
especially when sequences are long (and 77 monthes is long). This
is due to the fact that every small difference is taken into
account. To overcome this problem, you may use "representative
sequences". This procedure tries to regroup sequences that differ
only marginally and to identify a set of sequences that might
represent a given percentage of the sequences in that group (see
the help of the seqrep function). <br>
<br>
The procedure and the concept of representative sequence is
described in this reference: Gabadinho A, Ritschard G, Studer M,
Müller NS (2011). "Extracting and Rendering Representative
Sequences", In A Fred, JLG Dietz, K Liu, J Filipe (eds.), <em>Knowledge
Discovery, Knowledge Engineering and Knowledge Management</em>,
volume 128 of <em>Communications in Computer and Information
Science (CCIS)</em>, pp. 94-106. Springer-Verlag. <br>
<br>
I have another suggestion regarding your code. You may use the
group argument (available in all seq*plot) to automatically draw a
distinct plot of each group of sequences.<br>
<br>
seqdplot(fx.seq, group=pam.best.fx$clustering)<br>
<br>
<br>
Hope this helps.<br>
Matthias Studer<br>
<br>
Le 17.05.2011 19:19, Kleinbaum, Adam M. a écrit :
<blockquote
cite="mid:AC6EEF6CB9A72348B9F7D228C937211C258D431924@email.tucknt.dartmouth.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 12 (filtered
medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.Section1
{page:Section1;}
-->
</style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="Section1">
<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">fx <-
read.csv(file="Seq_function.txt", header=FALSE)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">fx.lab <-
c("AD", "CO", "FI", "GM", "HR", "LE", "MF", "MK", "OT",
"RD", "SC", "SL", "SV")<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">fx.seq <-
seqdef(fx, 2:78, labels=fx.lab)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">attr(fx.seq,"cpal")
<- c(brewer.pal(n=12, name="Set3"), "cyan", "white")<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">fx <-
fx[!is.na(fx[,78]), ]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">fx.seq <-
fx.seq[seqlength(fx.seq)==77,] <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">for (i in
1:k.best.om.fx)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">{<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">
seqdplot(fx.seq[pam.best.fx$clustering==i,], withlegend=F,
title=paste("Cluster ", i))<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">
seqfplot(fx.seq[pam.best.fx$clustering==i,], withlegend=F,
title=paste("Cluster ", i))<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;
font-family: "Courier New";">seqlegend(fx.seq)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">where fx.seq contains my sequences, as
shown above; pam.best.fx is the pam object that came out of
the clustering algorithm and pam.best.fx$clustering contains
the index of each actor’s cluster assignment.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The seqdplot command produces a series of
9 beautiful distribution plots, one for each cluster. No
problem.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">All the best,<o:p></o:p></p>
<p class="MsoNormal">Adam<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">--<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size: 10pt;">Adam M.
Kleinbaum<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;">Assistant
Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;">Tuck
School of Business<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;">Dartmouth
College<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;"><a
moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://bit.ly/kleinbaum">http://bit.ly/kleinbaum</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 10pt;">603.646.6447<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
Traminer-users mailing list
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Traminer-users@lists.r-forge.r-project.org">Traminer-users@lists.r-forge.r-project.org</a>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/traminer-users">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/traminer-users</a>
</pre>
</blockquote>
<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
Traminer-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Traminer-users@lists.r-forge.r-project.org">Traminer-users@lists.r-forge.r-project.org</a>
<a class="moz-txt-link-freetext" href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/traminer-users">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/traminer-users</a>
</pre>
</blockquote>
<br>
</body>
</html>