<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>great, thanks maren! We appreciate your help and look forward to your response.</div><div><br></div><div>Meanwhile, happy to report that increasing the thinning frequency (to 100-500) has helped with the memory usage issue.</div><div><br></div><div>best</div><div>caroline.</div><div><br></div><div><br><br>Sent from my iPhone</div><div><br>On 03/09/2014, at 11:24 AM, maren <<a href="mailto:maren.rebke@avitec-research.de">maren.rebke@avitec-research.de</a>> wrote:<br><br></div><blockquote type="cite"><div>
<meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type">
Hi Caroline,<br>
<br>
Thanks for reporting the error. We will check why the error is still
occuring and get back to you as soon as we know.<br>
<br>
Best wishes,<br>
Maren<br>
(also part of the BaSTA-team)<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 28.08.2014 17:21, schrieb caroline
chong:<br>
</div>
<blockquote cite="mid:F81E7669-2583-409C-8DD1-40E057F8A935@gmail.com" type="cite">Hi Fernando,
<div><br>
</div>
<div>I have just downloaded and tried the first model on my list
that has a single categorical covariate, corresponding to three
different groups (populations).</div>
<div><br>
</div>
<div>Following "no errors were detected with the data" I get
reported:</div>
<div>Error in FUN(newX[, i], ...) : invalid 'type' (character) of
argument.</div>
<div><br>
</div>
<div>Following is the code, specifying a Gompertz model and fused
covariate structure, and part of my input data matrix - but just
let me know if the entire data set would be helpful in
deciphering the problem and I will send that through. Many
thanks for your suggestions with this.</div>
<div><br>
</div>
<div>Meanwhile, we can report that the thinning appears to be
working as our larger model is running smoothly at the moment -
I'll keep you updated as/if it runs to completion!</div>
<div><br>
</div>
<div>Thanks and</div>
<div>best regards,</div>
<div>Caroline</div>
<div><br>
</div>
<div>
<div>#with one categorical covariate (pop), in total 3 groups</div>
<div>library(BaSTA)</div>
<div>library(snowfall)</div>
<div><br>
</div>
<div>iM.spec <- read.csv("tristecat_inputMat3.csv")</div>
<div>#colnames(iM.spec)[4:110]<- 1:107</div>
<div>iM.spec.basta <- DataCheck(iM.spec, studyStart = 1,
studyEnd = 107, autofix = rep(1, 7), silent = FALSE)</div>
<div><br>
</div>
<div>### basta</div>
<div>tristeout <- basta(object = iM.spec.basta$newData,
studyStart = 1, studyEnd = 107, nsim = 4, parallel = TRUE,
ncpus = 4, updateJumps = TRUE, model = "GO", shape = "simple",
covarsStruct = "fused", niter = 1000000, burnin= 5001,
thinning = 100, lifeTable=TRUE)</div>
<div><br>
</div>
<div>input:</div>
<div>
<div>ID,birth,death,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,pop</div>
<div>302,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>303,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>304,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>305,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>306,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>307,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>308,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>309,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>310,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>311,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>312,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>313,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>314,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>315,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>316,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>317,0,53,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>318,99,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>319,3,53,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,nariest</div>
<div>320,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,nariest</div>
</div>
<div><br>
</div>
<div>
<div>On 21/08/2014, at 4:33 PM, Fernando Colchero wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;">Hi Caroline,
<div><br>
</div>
<div> The latest version of BaSTA is not yet on CRAN
but you can download it from <a moz-do-not-send="true" href="http://basta.r-forge.r-project.org/#summary">http://basta.r-forge.r-project.org/#summary</a> and
just follow the instructions to install it. This las
version should have the fix for the error message you
were getting when adding covariates. If this does not
work, please let us know and we’ll go back to fixing it.</div>
<div><br>
</div>
<div> Could you fix the memory issue with the thinning?</div>
<div><br>
</div>
<div> Best,</div>
<div><br>
</div>
<div> Fernando<br>
<div>
<div style="color: rgb(0, 0, 0); font-family:
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none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;"><b><br class="Apple-interchange-newline">
<br>
</b></div>
<div style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal;
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none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;"><b>Fernando Colchero</b></div>
<div style="color: rgb(0, 0, 0); font-family:
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font-variant: normal; font-weight: normal;
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text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;">Assistant Professor</div>
<div style="color: rgb(0, 0, 0); font-family:
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text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;">Department of Mathematics and Computer Science</div>
<div style="color: rgb(0, 0, 0); font-family:
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none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;">Max-Planck Odense Center on the Biodemography of
Aging</div>
<div style="color: rgb(0, 0, 0); font-family:
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</i></b></div>
<div style="color: rgb(0, 0, 0); font-family:
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font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;">Tlf. +45 65 50 23 24</div>
<div style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal;
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text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;">Email <a moz-do-not-send="true" href="mailto:colchero@imada.sdu.dk">colchero@imada.sdu.dk</a></div>
<div style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;">Web <a moz-do-not-send="true" href="http://www.sdu.dk/staff/colchero">www.sdu.dk/staff/colchero</a></div>
<div style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal;
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text-align: start; text-indent: 0px; text-transform:
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-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;">Pers. web <a moz-do-not-send="true" href="http://www.sdu.dk/staff/colchero">www.colchero.com</a></div>
<div style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal;
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none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;">Adr. Campusvej 55, 5230, Odense, Dk</div>
</div></div></div></blockquote></div></div></blockquote></div></blockquote><blockquote type="cite"><div><span>_______________________________________________</span><br><span>Basta-users mailing list</span><br><span><a href="mailto:Basta-users@lists.r-forge.r-project.org">Basta-users@lists.r-forge.r-project.org</a></span><br><span><a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/basta-users">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/basta-users</a></span><br></div></blockquote></body></html>