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<div class="moz-cite-prefix">Hi Pierre,<br>
<br>
I think this is a lack of memory, a 20000x20000 distance matrix
requires a huge amount of memory. You can try the
"full.matrix=FALSE" option so that only half of the -symmetric-
distance matrix is returned by the seqdist function. Remember also
that having other big objects in your current R environment, like
other distance matrices - uses a part of the available memory. <br>
<br>
Regarding weights, these are defined once when creating a sequence
object with seqdef, and used automatically by seqdplot and other
plot and sequence analysis functions. Please see our freely
available article in the journal of statistical software and
help(seqdef) for more details.<br>
<br>
All the best, <br>
Alexis<br>
<br>
<br>
Le 11. 02. 13 13:14, Pierre Blavier a écrit :<br>
</div>
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cite="mid:CAPmyiXdmCKx8y9hZHF_Y_or6k4oYqwG_vz=TRQec6z7VCq9zHQ@mail.gmail.com"
type="cite">
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<p class="MsoNormal">
</p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">Hi
TramineR-users, </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">2
questions : </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US"><br>
</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">1)
pb of memory computing
distance matrix</span></p>
<p class="MsoNormal" style="margin-left:4.0pt;text-autospace:none"><span
style="font-family:Arial" lang="EN-US">Everything works
perfectly (</span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">couts</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US"> <- seqsubm(</span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">seq.seq</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">, </span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">method</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">=</span><span
style="font-size:11.0pt;font-family:Monaco;color:#9c0c00"
lang="EN-US">"CONSTANT"</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">, </span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">cval</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">=</span><span
style="font-size:11.0pt;font-family:Monaco;color:#10420b"
lang="EN-US">2</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">) / range(</span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">couts</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">) / round(</span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">couts</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">, </span><span
style="font-size:11.0pt;font-family:Monaco;color:#10420b"
lang="EN-US">2</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">) )</span></p>
<p class="MsoNormal" style="margin-left:4.0pt;text-autospace:none"><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">Until : </span></p>
<p class="MsoNormal"><span
style="font-size:11pt;font-family:Monaco" lang="EN-US"><a
moz-do-not-send="true" href="http://seq.om">seq.om</a></span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US"> <-seqdist(</span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">seq.seq</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">, </span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">method</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">=</span><span
style="font-size:11.0pt;font-family:Monaco;color:#9c0c00"
lang="EN-US">"OM"</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">,</span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">indel</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">=</span><span
style="font-size:11.0pt;font-family:Monaco;color:#10420b"
lang="EN-US">1.1</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">, </span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">sm</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">=</span><span
style="font-size:11pt;font-family:Monaco" lang="EN-US">couts</span><span
style="font-size:11.0pt;font-family:Monaco;color:#00008d"
lang="EN-US">)</span><span style="font-family:Arial"
lang="EN-US"></span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">I
obtain : </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">Erreur
: impossible d'allouer
un vecteur de taille 1.5 Go</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">R(351,0xac7312c0)
malloc: ***
mmap(size=1617408000) failed (error code=12)</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">***
error: can't allocate
region</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">***
set a breakpoint in
malloc_error_break to debug</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">R(351,0xac7312c0)
malloc: ***
mmap(size=1617408000) failed (error code=12)</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">***
error: can't allocate region</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">***
set a breakpoint in
malloc_error_break to debug</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">My
dataset is rather large
(43 periods, n=20 000, 6 states) but it is rather suprising,
how can I solve
the problem ? ? (I have a brand-new macintosh with 8Go of live
memory, so I think
this is not the pb). </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">2)
How can we use the weights
in TramineR, for example in order to make it take them into
account in commands
like </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">>
seqdplot(seq.seq, withlegend=T, title="1988",
weights="pond")</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">It
does not seem to work… </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">Thanks
a lot and best
regards, </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="EN-US">Pierre </span></p>
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