<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jelle,<div><br></div><div> Well, in that case I believe that the mistake might be in the BaSTA plotting function. Let me check and see if that's the case. Thanks for pointing this out!</div><div><br></div><div> Best,</div><div><br></div><div> Fernando<br><div apple-content-edited="true">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div><span style="font-size: 12px; "><br class="Apple-interchange-newline"><br></span></div><div><span style="font-size: 12px; "><br></span></div><div><b style="font-size: 12px; ">Fernando Colchero</b></div><div><span style="font-size: 12px; ">Assistant Professor</span></div><div><span style="font-size: 12px; ">Department of Mathematics and Computer Sciences</span></div><div><span style="font-size: 12px; ">Max Planck Odense Center on the Biodemography of Aging</span></div><div><b><i style="font-size: 12px; "><br></i></b></div><div><span style="font-size: 12px; ">Tlf. +45 65 50 46 35</span></div><div><span style="font-size: 12px; ">Email <a href="mailto:colchero@imada.sdu.dk">colchero@imada.sdu.dk</a></span></div><div><span style="font-size: 12px; ">Web <a href="http://www.sdu.dk/staff/colchero">www.sdu.dk/staff/colchero</a></span></div><div><span style="font-size: 12px; ">Pers. web <a href="http://www.sdu.dk/staff/colchero">www.colchero.com</a></span></div><div><span style="font-size: 12px; ">Adr. Campusvej 55, 5230, Odense, Dk</span></div><div><span style="font-size: 12px; "><br></span></div><div><div><b>University of Southern Denmark</b></div><div><b><i style="font-size: 12px; "><br></i></b></div></div></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span style="font-size: 12px; "><br></span></div><br class="Apple-interchange-newline" style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><br class="Apple-interchange-newline">
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<br><div><div>On Feb 20, 2013, at 11:51 AM, Jelle Boonekamp <<a href="mailto:jjboonekamp@gmail.com">jjboonekamp@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div>
Hi Fernando,
</div><div><br></div><div>That is exactly what I am doing. I get the following parameter estimates from the BaSTA function.</div><div><br></div><div><br></div><div><div>b0<span class="Apple-tab-span" style="white-space:pre"> </span>-2.389 </div><div>b1 <span class="Apple-tab-span" style="white-space:pre"> </span> 0.478 </div><div>gamma<span class="Apple-tab-span" style="white-space:pre"> </span>-0.159</div><div><br></div></div>
<div><div><br></div><div>Then I used these like this: mu(x | z) = exp(b0 + b1x + gamma) for plotting mortality rate. Upon visual comparison, this gave me a slightly higher mortality rate than what BaSTA is actually plotting. Now that I am thinking about this, I am probably making a mistake, because BaSTA is plotting an average mortality curve for both groups. What would be the equation (concerning the gamma parameter) for the average curve? Is it like this: mu(x | z) = exp(b0 + b1x + gamma/2)? Probably not, because that still seems to be off.</div><div><br></div><div>Best, Jelle</div><div><br></div><div><br></div><div>-- </div><div>Jelle Boonekamp</div><div>Behavioural Biology<br>University of Groningen<br>P.O. Box 11103<br>9700 CC Groningen<br>The Netherlands<br><br>tel: +31.50.363 7853</div><div>Sent with <a href="http://www.sparrowmailapp.com/?sig">Sparrow</a></div><div><br></div></div><p style="color: #A0A0A8;">On Wednesday, 20 February 2013 at 10:48, Fernando Colchero wrote:</p>
<blockquote type="cite" style="border-left-style:solid;border-width:1px;margin-left:0px;padding-left:10px;">
<span>Hi Jelle,<div><br></div><div> I think I know what the problem was. The proportional hazards model would fix b0 and b1 and add an additional parameter for one of the two groups. So the equation becomes: mu(x | z) = exp(b0 + b1x + b2z), where z will assign 1 to group 1 and 0 otherwise. In this case, you can interpret b2 as a deviation from b0. Is that what you're trying to do? Now, the reason why the plots are different is a bit puzzling, unless we are missing something. We'll double check the plotting function to make sure that we haven't made a mistake there.</div><div><br></div><div> Best,</div><div><br></div><div> Fernando<br><div apple-content-edited="true">
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: 13px; "><div><span style="font-size: 12px; "><br><br></span></div><div><span style="font-size: 12px; "><br></span></div><div><b style="font-size: 12px; ">Fernando Colchero</b></div><div><span style="font-size: 12px; ">Assistant Professor</span></div><div><span style="font-size: 12px; ">Department of Mathematics and Computer Sciences</span></div><div><span style="font-size: 12px; ">Max Planck Odense Center on the Biodemography of Aging</span></div><div><b><i style="font-size: 12px; "><br></i></b></div><div><span style="font-size: 12px; ">Tlf. +45 65 50 46 35</span></div><div><span style="font-size: 12px; ">Email <a href="mailto:colchero@imada.sdu.dk">colchero@imada.sdu.dk</a></span></div><div><span style="font-size: 12px; ">Web <a href="http://www.sdu.dk/staff/colchero">www.sdu.dk/staff/colchero</a></span></div><div><span style="font-size: 12px; ">Pers. web <a href="http://www.sdu.dk/staff/colchero">www.colchero.com</a></span></div><div><span style="font-size: 12px; ">Adr. Campusvej 55, 5230, Odense, Dk</span></div><div><span style="font-size: 12px; "><br></span></div><div><div><b>University of Southern Denmark</b></div><div><b><i style="font-size: 12px; "><br></i></b></div></div></div><div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: 13px; "><span style="font-size: 12px; "><br></span></div><br style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: 13px; "><br>
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<br><div><div>On Feb 20, 2013, at 10:36 AM, Jelle Boonekamp <<a href="mailto:jjboonekamp@gmail.com">jjboonekamp@gmail.com</a>> wrote:</div><br><blockquote type="cite"><div>
Hi BaSTA users,
</div><div><br></div><div>I ran into something peculiar. When I manually plot the survivor function (2par Gompertz in my case) using the posterior mean parameter estimations, I get a slightly different survival curve/shape compared with the curve that BaSTA draws. Shouldn't these be exactly similar, or am I missing something? For the plotting I used the equation from table 3 on p16 of the cran manual, with proportional hazard implementation following equation 7b on page 19. The aim of this exercise was to estimate the effects of the Gompertz parameters on mean lifespan separately.</div><div><br></div><div>Best, Jelle</div><div><br></div>
<div><div><br></div><div>-- </div><div>Jelle Boonekamp</div><div>Behavioural Biology<br>University of Groningen<br>P.O. Box 11103<br>9700 CC Groningen<br>The Netherlands<br><br>tel: +31.50.363 7853</div><div>Sent with <a href="http://www.sparrowmailapp.com/?sig">Sparrow</a></div><div><br></div></div>
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