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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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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><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;
text-align: start; text-indent: 0px; text-transform:
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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-webkit-text-stroke-width: 0px; orphans: 2; widows:
2;"><b><i><br>
</i></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;
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;
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;">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;
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;">Adr. Campusvej 55, 5230, Odense, Dk</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;"><br>
</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;"><b>University of Southern Denmark</b></div>
</div>
<br>
<div>
<div>On 16 Aug 2014, at 13:27, Caroline <<a
moz-do-not-send="true"
href="mailto:yfcaroline@gmail.com">yfcaroline@gmail.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div dir="auto">
<div>Hello, thanks Mirre-</div>
<div>you're correct about the excessive cpus for
four sims- we realised that when analysing
different model settings.</div>
<div><br>
</div>
<div>We're currently assessing if the thinning
fixes the issues and will report back on the
outcomes as soon as we can.</div>
<div><br>
</div>
<div>Fernando, on the covariate names issue that
you mentioned is in fact a bug - can we look out
for the next version of basta with this fix
included, or secondarily can you suggest any
naming workarounds?</div>
<div><br>
</div>
<div>thanks muchly for your help,</div>
<div>caroline<br>
<br>
Sent from my i</div>
<div><br>
On 16/08/2014, at 1:03 PM, Mirre Simons <<a
moz-do-not-send="true"
href="mailto:mirresimons@gmail.com">mirresimons@gmail.com</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>An why 16 cpu for 4 sim? I dont think it
distributes a single sim across multiple cpu..<br>
<br>
Sent from my iPhone</div>
<div><br>
On 6 Aug 2014, at 14:08, caroline chong <<a
moz-do-not-send="true"
href="mailto:yfcaroline@gmail.com">yfcaroline@gmail.com</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">Dear Fernando,
<div><br>
</div>
<div>Thanks so much for your response. I'm
excited to hear that the covariate bug has
been able to be isolated. Looking forward to
the fix - could you suggest a timeline when
we can anticipate the next updated version
of BaSTA to be released?</div>
<div><br>
</div>
<div>On the memory issue, I am currently
running burnins of between 1000-8000 (as
below, speciesout <- basta(object =
iM.spec.basta$newData, studyStart =
1, studyEnd = 109, model = "GO", shape=
"simple", nsim = 4, parallel =
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
<div>TRUE, ncpus = 16, updateJumps = TRUE,
niter = 2000000, burnin=
8001, lifeTable=TRUE) and encountering
the memory problems. Is this where you
meant the burnin to be specified?</div>
<div><br>
</div>
<div>Thanks again for your help,</div>
<div>Caroline.</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div>
<div>On 05/08/2014, at 10:41 AM, Fernando
Colchero wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break:
after-white-space;">Hi Caroline,
<div><br>
</div>
<div> Sorry for the late reply.
Actually, about your first enquiry,
we found a bug that produced that
error. We need to update the version
of BaSTA that fixes that bug. About
the memory problem, based on the
information you sent us I think the
issue is that you have a very large
dataset and that you are running the
model for many iterations. I quick
fix will be to specify the argument
burnin = 200 or even larger, the
default value is 20. The advantage
is that you will keep much fewer
iterations, reducing the amount of
memory you use, while you’ll also
reduce serial autocorrelation. Let
us know if this solves the issue.</div>
<div><br>
</div>
<div> Best,</div>
<div><br>
</div>
<div> Fernando</div>
<div>
<div>
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<div>
<div>On 03 Aug 2014, at 01:46,
Caroline Chong <<a
moz-do-not-send="true"
href="mailto:caroline.chong@anu.edu.au">caroline.chong@anu.edu.au</a>>
wrote:</div>
<br
class="Apple-interchange-newline">
<blockquote type="cite"><br>
<blockquote type="cite">
<blockquote type="cite"><br>
Thanks Owen, Fernando<br>
<br>
We are encountering problems
with memory usage when
running basta<br>
analyses (using the latest
version), and would be most
grateful for<br>
your suggestions on how to
resolve the following
situation. We're<br>
running basta on a 64-bit
linux and are able to
commence basta runs<br>
successfully (both in serial
and parallel), but rapidly
occupy 128 GB<br>
RAM and all available swap
(90 GB). The number of
iterations is<br>
currently set to 2 million
but we have also attempted 1
million. We<br>
are keen to run the final
analyses, and will look
forward to your<br>
feedback (and from the basta
community) with great
anticipation.<br>
<br>
- All iterations are
currently stored in the PAR
matrix. Is it<br>
possible to store only the
thinned chain in memory and
write the full<br>
chain to disc every (for
example) 100000 iterations?<br>
<br>
- If so, would this be a
reasonably straightforward
alteration to<br>
implement in the current
basta version, and what
would this look like?<br>
<br>
- Alternatively, could you
please advise of any other
methods to<br>
reduce memory useage?<br>
<br>
Example of basta commands
are below. I am aiming to
compare model<br>
types (exponential,
gompertz, logistic) run for
each of 30 or more<br>
species:<br>
<br>
for (s in
1:length(species.list))<br>
{<br>
<br>
### iterate through species
list, read input matrix file<br>
species <-
species.list[s] <br>
iM.spec <-
read.delim(paste("inputmatg.",
species, ".txt", sep=""),<br>
header=T, sep=",")
colnames(iM.spec)[4:112]<-
1:109<br>
<br>
iM.spec[,4:112] <-
sapply(iM.spec[,4:112],
as.character)<br>
iM.spec[,4:112] <-
sapply(iM.spec[,4:112],
as.numeric)<br>
<br>
### perform data check on
imput matrix<br>
iM.spec.basta <-
DataCheck(iM.spec,
studyStart = 1, studyEnd =
109,<br>
autofix = rep(1, 7), silent
= FALSE)<br>
<br>
### basta<br>
speciesout <-
basta(object =
iM.spec.basta$newData,
studyStart = 1,<br>
studyEnd = 109, model =
"GO", shape= "simple", nsim
= 4, parallel =<br>
TRUE, ncpus = 16,
updateJumps = TRUE, niter =
2000000, burnin= 8001,<br>
lifeTable=TRUE)<br>
}<br>
Example input matrix showing
data for the first three
individuals of<br>
species1 only, for brevity:<br>
<br>
"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","108","109"<br>
"1",1,0,68,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0<br>
"2",2,0,68,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0<br>
"3",3,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0<br>
<br>
<br>
My second query is as per
last week regarding the
"Error in FUN(newX[,<br>
i], ...) : invalid 'type'
(character) of argument"
error encountered<br>
when attempting to include a
single or multiple
covariates<br>
(particularly of type
categorical), but re-posted
here to the mailing<br>
list in case the community
can also help out. Do you
have any<br>
suggestions on how to code
or name categorical
covariates to<br>
circumvent this error?<br>
<br>
Many thanks for your help,<br>
best regards<br>
Caroline.<br>
<br>
<br>
<br>
On 21 Jul 2014, at 23:52,
caroline <<a
moz-do-not-send="true"
href="mailto:caroline.chong@anu.edu.au">caroline.chong@anu.edu.au</a>>
wrote:<br>
<br>
Dear Owen/Fernando,<br>
<br>
I was wondering whether you
had any updated advice on
how to code a<br>
single or multiple
categorical covariates to
avoid the "FUN(newX[,i])"<br>
error (similarly reported by
Richard on 30 May 2014). I
have checked<br>
that the covariate names do
not start with the same
characters and<br>
have also tried simplified
names (a, b, c) to no avail
so far. I would<br>
be most happy to provide you
with some of my data set if
that would be<br>
helpful for more context and
to find the solution. I also
intend to<br>
use basta with both
categorical and numeric
covariates so would<br>
appreciate any suggestions
you may have on covariate
naming.<br>
<br>
Also, I would be grateful
for your advice on
deciphering the following<br>
(run on a cluster with 32
cpus available):<br>
<br>
iM.spec.basta <-
DataCheck(iM.spec,
studyStart = 1, studyEnd =
109,<br>
autofix = rep(1, 7), silent
= FALSE)<br>
<br>
exspeciesout <-
basta(object =
iM.spec.basta$newData,
studyStart = 1,<br>
studyEnd = 109, model =
"EX", shape= "simple", nsim
= 4, parallel =<br>
TRUE, ncpus = 16,
updateJumps = TRUE, niter =
2000000, burnin= 8001,<br>
lifeTable=TRUE)<br>
<br>
Total MCMC computing time:
10.48 hours.<br>
<br>
Survival parameters
converged appropriately.<br>
DIC was calculated.<br>
Error: cannot allocate
vector of size 109.5 Gb<br>
Execution halted<br>
Warning message:<br>
system call failed: Cannot
allocate memory<br>
<br>
Warmest thanks for your
assistance,<br>
with best regards,<br>
Caroline.<br>
<br>
<br>
<br>
On 01/11/2013, at 8:54 AM,
Owen Jones wrote:<br>
<br>
<blockquote type="cite">Dear
Caroline,<br>
<br>
This is a possible bug in
one of the sub-functions
in basta that<br>
deals with the covariates.
<br>
<br>
We're investigating and
will get back to you
shortly.<br>
<br>
Best wishes,<br>
Owen<br>
<br>
<br>
<br>
<br>
On 1 Nov 2013, at 14:01,
caroline <<a
moz-do-not-send="true"
href="mailto:caroline.chong@anu.edu.au">caroline.chong@anu.edu.au</a>>
wrote:<br>
<br>
<blockquote type="cite">Dear
All,<br>
<br>
I am running a simple
Gompertz model with one
categorical<br>
covariate, species
(coded as species SPEC =
a, b, c.... ah for<br>
simplicity). After
running DataCheck with
autofix set to on, I<br>
encounter the following
error "in
FUN(newX[,i]...)" -
would you<br>
have any experience with
a similar situation, and
could provide any<br>
help or suggestions on
how to interpret and
trouble-shoot the<br>
problem? I am unsure as
to how to decipher where
the error lies.<br>
N.b. this data set seems
to run ok when I do not
include the<br>
covariate matrix.<br>
<br>
Very grateful for your
help,<br>
best regards<br>
Caroline.<br>
<br>
Caroline Chong<br>
Postdoctoral Fellow<br>
Research School of
Biology<br>
Australian National
University, Canberra ACT<br>
<br>
speciesout <-
basta(object =
inputMat2$newData,
studyStart = 1,<br>
studyEnd = 109,
covarsStruct =
"all.in.mort", nsim = 4,
parallel =<br>
TRUE, ncpus = 4,
updateJumps = TRUE,
niter = 100000) No
problems<br>
were detected with the
data.<br>
<br>
Error in FUN(newX[, i],
...) : invalid 'type'
(character) of<br>
argument<br>
</blockquote>
</blockquote>
<br>
<br>
<br>
</blockquote>
</blockquote>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<blockquote type="cite"><span>_______________________________________________</span><br>
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