<div dir="ltr">Dear Fernando, <div><br></div><div>thanks for your rapid and clarifying reply. </div><div><br></div><div>About the resighting covariates. How realistic are the prospects of implementing this feature in the near future ? </div><div><br></div><div>About the large CI. According to the model output, all parameters should have converged. I have added the traces for all the parameters to <a href="https://www.dropbox.com/sh/kk1wztsftfljbw5/AAC4OHKT-pNXepioaR4qf78oa?dl=0">the dropbox folder</a>. </div><div><br></div><div>Best wishes, </div><div><br></div><div>Dries</div><div class="gmail_extra"><br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-09-17 10:46 GMT+02:00 Fernando Colchero <span dir="ltr"><<a href="mailto:colchero@imada.sdu.dk" target="_blank">colchero@imada.sdu.dk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Dear Dries,<div><br></div><div> Thanks for sending this very detailed explanation. I’ll try to answer to each of your points below:</div><div><br><div>
<div style="color:rgb(0,0,0);font-family:Helvetica;font-size:16px;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"><span class=""><blockquote type="cite"><div dir="ltr"><div style="font-size:12.8px">(i) <b>Recapture probability</b> is around 10 %. We however did not check for presence/absence of the bird every day after fledging. Usually on the 5th/6th day (range 3-9). This thus underestimates recapture probability dramatically. We noted on the BaSTA website that future versions would include covariates on recapture and recovery probabilities. We could for example add "search effort" as covariate, stating the specific days when we actually looked for that individual. Is there a possibility of trying this out already ?</div></div></blockquote><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:16px;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"><br></div></span>Fernando: Unfortunately we have not yet been able to implement this.</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:16px;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"><br></div><div style="text-align:start;text-indent:0px"><span class=""><blockquote type="cite" style="color:rgb(0,0,0);font-family:Helvetica;font-size:16px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px"><div dir="ltr"><div style="font-size:12.8px">(ii) Our <b>confidence intervals</b> on the mortality rates just after fledging are big. To that extent that it obscures the real shape of the mortality function when added to the graphs. <a href="https://www.dropbox.com/sh/kk1wztsftfljbw5/AAC4OHKT-pNXepioaR4qf78oa?dl=0" target="_blank">See PlotFancyBaSTA with CI and regular plot without CI</a>. Because we only searched for the juveniles some days after fledging, the first resightings are only done on day 3 and later. Is it possible that the particular sampling strategy is on the origin of this big CI's ? </div></div></blockquote></span><div><div dir="ltr"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px"><br></div><div>Fernando: By looking at your plots, particularly the PlotFancy, I suspect that not all your parameters had converged… Did you have a chance at checking the traces?.</div><span class=""><div><br></div><div><blockquote type="cite"><div dir="ltr"><div style="font-size:12.8px">(iii) Based on the lowest DIC from running all basic models (no covariates), we selected the WEIBULL model with a <b>Makeham</b> shape. Adding the Makeham constant avoids creating immortal individuals when having a declining mortality shape (i.e. when 0 < b0 < 1) by setting a "base mortality". How do we interpret this value when having other shapes (b0 <= 1) ? Why is this in these cases not (partially) embedded within the scale parameter (b1) ?</div></div></blockquote><div><div dir="ltr"><div style="font-size:12.8px"><br></div></div></div></div></span><div>Fernando: Actually embedding the third parameter (c) into b1 does not solve the problem of starting mortality at 0, inherent to the Weibull model, while the intended effect of the Makeham constant is to shift up or down the mortality. If it’s embebed in b1, then you are only changing mortality proportionally.</div><span class=""><div><br></div><div><blockquote type="cite"><div dir="ltr"><div style="font-size:12.8px">(iv) The <b>serial autocorrelation</b> of most coefficient estimates appears to be rather high (> 0.4). Would you recommend readjusting the thinning argument or other model settings ? Or does this not really effect our estimates and outcome ? </div></div></blockquote></div><div><br></div></span><div>Fernando: Yes, I would recommend running the model for more iterations with a large thinning argument. If you run it in parallel then you can run more chains for less iterations but with higher thinning, that’ll be even better and it would save you quite a bit of time.</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px"><br></div><div><span class=""><blockquote type="cite" style="color:rgb(0,0,0);font-family:Helvetica;font-size:16px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px"><div dir="ltr"><div style="font-size:12.8px">NB : we noticed a discrepancy between the default values in the package versus the ones listed in the BaSTA vignette (niter = 11000, burnin = 1001 and thinning = 20 vs. niter = 50000, burnin = 5001 and thinning = 50). Which settings to you recommend as default values ?</div></div></blockquote></span><div><div dir="ltr"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px"><br></div><div>Fernando: Thanks for spotting this! We’ll check the settings.</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12.8px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-transform:none;white-space:normal;word-spacing:0px"><br></div></div></div></div></div></div>Best,</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:16px;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"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:16px;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">Fernando<br><br></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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px"><b>Fernando Colchero</b></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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px">Assistant Professor</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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px">Department of Mathematics and Computer Science</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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px">Max-Planck Odense Center on the Biodemography of Aging</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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px"><b><i><br></i></b></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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px">Tlf. <a href="tel:%2B45%2065%2050%2023%2024" value="+4565502324" target="_blank">+45 65 50 23 24</a></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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px">Email <a href="mailto:colchero@imada.sdu.dk" target="_blank">colchero@imada.sdu.dk</a></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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px">Web <a href="http://www.sdu.dk/staff/colchero" target="_blank">www.sdu.dk/staff/colchero</a></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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px">Pers. web <a href="http://www.sdu.dk/staff/colchero" target="_blank">www.colchero.com</a></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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px">Adr. Campusvej 55, 5230, Odense, Dk</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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px"><br></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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:12px"><b>University of Southern Denmark</b></div>
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<br><div><blockquote type="cite"><div><div class="h5"><div>On 16 Sep 2015, at 15:13, Dries Van de Loock <<a href="mailto:dries.vandeloock@ugent.be" target="_blank">dries.vandeloock@ugent.be</a>> wrote:</div><br></div></div><div><div><div class="h5"><div dir="ltr"><span style="font-size:12.8px">Dear BaSTA community, </span><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">I'm involved in the same project as Diederik Strubbe on post-fledging survival of a tropical passerine (see <a href="http://lists.r-forge.r-project.org/pipermail/basta-users/2015-August/thread.html" target="_blank">archive</a>). </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Nests were monitored until fledging and juveniles were relocated every 5 to 6 days after fledging. </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Our input matrix is formatted accordingly : the birthyear is considered the point of fledging and is set to "1" for all individuals. The resighting matrix starts at day 1 and is "0" for all individuals on that day. Day 2 in the matrix is thus the first day after fledging. <a href="https://www.dropbox.com/sh/kk1wztsftfljbw5/AAC4OHKT-pNXepioaR4qf78oa?dl=0" target="_blank">See screenshot</a> from RStudio. </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">When running the models, we bumped into following questions :</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">(i) <b>Recapture probability</b> is around 10 %. We however did not check for presence/absence of the bird every day after fledging. Usually on the 5th/6th day (range 3-9). This thus underestimates recapture probability dramatically. We noted on the BaSTA website that future versions would include covariates on recapture and recovery probabilities. We could for example add "search effort" as covariate, stating the specific days when we actually looked for that individual. Is there a possibility of trying this out already ?</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">(ii) Our <b>confidence intervals</b> on the mortality rates just after fledging are big. To that extent that it obscures the real shape of the mortality function when added to the graphs. <a href="https://www.dropbox.com/sh/kk1wztsftfljbw5/AAC4OHKT-pNXepioaR4qf78oa?dl=0" target="_blank">See PlotFancyBaSTA with CI and regular plot without CI</a>. Because we only searched for the juveniles some days after fledging, the first resightings are only done on day 3 and later. Is it possible that the particular sampling strategy is on the origin of this big CI's ? </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">(iii) Based on the lowest DIC from running all basic models (no covariates), we selected the WEIBULL model with a <b>Makeham</b> shape. Adding the Makeham constant avoids creating immortal individuals when having a declining mortality shape (i.e. when 0 < b0 < 1) by setting a "base mortality". How do we interpret this value when having other shapes (b0 <= 1) ? Why is this in these cases not (partially) embedded within the scale parameter (b1) ?</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">(iv) The <b>serial autocorrelation</b> of most coefficient estimates appears to be rather high (> 0.4). Would you recommend readjusting the thinning argument or other model settings ? Or does this not really effect our estimates and outcome ? </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">NB : we noticed a discrepancy between the default values in the package versus the ones listed in the BaSTA vignette (niter = 11000, burnin = 1001 and thinning = 20 vs. niter = 50000, burnin = 5001 and thinning = 50). Which settings to you recommend as default values ?</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">We performed all analysis using BaSTA 1.9.4</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Your feedback and suggestions are greatly appreciated, </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Best wishes, </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Dries</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">-----</div><div style="font-size:12.8px"><div>Dries Van de Loock</div><div>PhD student</div><div>Terrestrial Ecology Unit</div><div>Department of Biology</div><div>Ghent University</div><div>KL Ledeganckstraat 35</div><div>B-9000 Ghent, Belgium</div><div>Phone: <a href="tel:%2B32%20%280%299%20265%2050%2039" value="+3292655039" target="_blank">+32 (0)9 265 50 39</a></div><div><a href="http://www.ecology.ugent.be/terec/" target="_blank">http://www.ecology.ugent.be/terec/</a></div></div></div></div></div>
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