<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 14 (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;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","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;}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0in;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></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]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">In that case would<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal">mymodel -noest -nohess -mcmc N -mcsave M –ainp mymodel.par<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Work? <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Ian Taylor [mailto:ian.taylor@noaa.gov]
<br>
<b>Sent:</b> Tuesday, January 31, 2012 4:26 PM<br>
<b>To:</b> Mark Maunder<br>
<b>Cc:</b> Mollie Brooks; ADMB Users<br>
<b>Subject:</b> Re: [ADMB Users] mcpin<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I thought the model automatically looked in the directory for the .mcm file or whatever it's called. It works to run<o:p></o:p></p>
<div>
<p class="MsoNormal">mymodel -noest -nohess -mcmc N -mcsave M<br>
which will start at the initial values rather than those in the .pin file, but it definitely makes use of the correct Hessian matrix info.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">-Ian<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Tue, Jan 31, 2012 at 4:09 PM, Mark Maunder <<a href="mailto:mmaunder@iattc.org">mmaunder@iattc.org</a>> wrote:<o:p></o:p></p>
<p class="MsoNormal">I think there is, but not sure how to do it.<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><br>
-----Original Message-----<br>
From: Mollie Brooks [mailto:<a href="mailto:mbrooks@ufl.edu">mbrooks@ufl.edu</a>]<br>
Sent: Tuesday, January 31, 2012 3:12 PM<br>
To: Mark Maunder<br>
Cc: ADMB Users<br>
Subject: Re: [ADMB Users] mcpin<br>
<br>
Thanks Mark.<br>
I think I already estimated the variance covariance matrix in the first model run. Is there a way to give it to ADMB?<br>
<br>
<br>
<br>
On 31 Jan 2012, at 5:47 PM, Mark Maunder wrote:<br>
<br>
> You also need the variance-covariance matrix for the jumping rule. You could use<br>
><br>
> xxxx -ainp xxxx.par -mcmc 100000000<br>
><br>
> To start the model at the parameter estimates (makes it run quicker), estimate the hessian (will take some time), and run the mcmc<br>
><br>
><br>
><br>
><br>
> -----Original Message-----<br>
> From: <a href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a> [mailto:<a href="mailto:users-bounces@admb-project.org">users-bounces@admb-project.org</a>] On Behalf Of Mollie Brooks<br>
> Sent: Tuesday, January 31, 2012 2:16 PM<br>
> To: ADMB Users<br>
> Subject: [ADMB Users] mcpin<br>
><br>
> Hi,<br>
> I have already found point estimates for the parameters of my model. Now I'm interested in doing mcmc sampling.<br>
> Can I use the command line option -mcpin to start the mcmc sampling at the values stored in model.par without redoing the maximum likelihood estimation? The manual talks about using -mcpin with values from profiling, but I can't do profiling because I'm interested
in the distribution of the variance parameters of random effects.<br>
><br>
> thanks,<br>
> Mollie<br>
><br>
> Mollie Brooks<br>
> Ph.D. Candidate<br>
> NSF IGERT Fellow<br>
> Biology Department<br>
> University of Florida<br>
> <a href="mailto:mbrooks@ufl.edu">mbrooks@ufl.edu</a><br>
> <a href="http://people.biology.ufl.edu/mbrooks" target="_blank">http://people.biology.ufl.edu/mbrooks</a><br>
><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Users mailing list<br>
> <a href="mailto:Users@admb-project.org">Users@admb-project.org</a><br>
> <a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">
http://lists.admb-project.org/mailman/listinfo/users</a><br>
><br>
<br>
_______________________________________________<br>
Users mailing list<br>
<a href="mailto:Users@admb-project.org">Users@admb-project.org</a><br>
<a href="http://lists.admb-project.org/mailman/listinfo/users" target="_blank">http://lists.admb-project.org/mailman/listinfo/users</a><o:p></o:p></p>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</body>
</html>