<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div apple-content-edited="true" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="" style="font-size: 12px; orphans: 2; widows: 2;"><b class="">Fernando Colchero</b></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Associate Professor</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Department of Mathematics and Computer Science</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Max-Planck Odense Center on the Biodemography of Aging</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;"><b class=""><i class=""><br class=""></i></b></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Tlf. +45 65 50 23 24</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Email <a href="mailto:colchero@imada.sdu.dk" class="">colchero@imada.sdu.dk</a></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Web <a href="http://www.sdu.dk/staff/colchero" class="">www.sdu.dk/staff/colchero</a></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Pers. web <a href="http://www.sdu.dk/staff/colchero" class="">www.colchero.com</a></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Adr. Campusvej 55, 5230, Odense, Dk</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;"><br class=""></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;"><b class="">University of Southern Denmark</b></div></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On 27 Feb 2018, at 18:49, Ken Honeycutt <<a href="mailto:rkenhoneycutt@gmail.com" class="">rkenhoneycutt@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class=""><div class="">Fernando,</div><div class=""><br class=""></div><div class="">Thanks for your response and for sending along the latest BaSTA version, especially the bit about using "recaptTrans." I tried that and it worked well. </div><div class=""><br class=""></div><div class=""><span class="">I do have a couple more questions.</span></div><div class=""><span class=""> </span></div><div class=""><span class="">First, is your R-code to simulate populations (as in your 2012 J of Animal Ecology paper) publicly available somewhere? I'm thinking simulating populations would help with confidence in my results.</span></div><div class=""><span class=""><br class=""></span></div><div class=""><span class="">Second, I'm having a little trouble interpreting the meanings of parameters from the Gompertz bathtub model (I believe there are alpha0, alpha1, beta0, beta1, and c). I see these are described mathematically in the BaSTA MME supporting information, but I'm having trouble visualizing the meanings. Specifically, I'm wondering at what values would these parameters represent a bathtub shape for mortality.</span></div><div class=""><span class=""><br class=""></span></div><div class=""><span class="">Thanks,</span></div><div class=""><span class="">Ken</span></div><span class=""><p class=""><br class=""></p><p class=""><br class=""></p><p class=""><br class=""></p><p class=""><br class=""></p><span class=""><p class=""><br class=""></p><span class=""><p class=""><br class=""></p><span class=""><p class=""><br class=""></p><div class=""><br class=""></div></span></span></span></span><div class=""><span class=""><br class=""></span></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Sat, Feb 24, 2018 at 12:58 AM, Fernando Colchero <span dir="ltr" class=""><<a href="mailto:colchero@imada.sdu.dk" target="_blank" class="">colchero@imada.sdu.dk</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="-ms-word-wrap: break-word;" class="">Hi Ken,<div class=""><br class=""></div><div class=""> Sorry for the late reply. You can use months, just bearing in mind that the parameters correspond then to the distribution of ages at death in months, not in years. There is an argument that you can use for the recapture probability changes during the months you didn’t sample, which is “recaptTrans”. That argument takes a vector of times during which recapture probabilities have changed. </div><div class=""><br class=""></div><div class=""> About the lack of information on birth and death, in principle BaSTA can handle it, but of course, the less information, the higher the uncertainty in the estimation. We have tested the package on datasets without birth and death information and it works, but your setup is quite particular… Please let us know if you need more assistance. Also, I would recommend that you install the latest version of BaSTA. It is not in cran, but you can donwnload it from:</div><div class=""><br class=""></div><div class=""> <a href="https://github.com/fercol/BaSTA/blob/master/latestBuild/BaSTA_1.9.5.tar.gz" target="_blank" class="">https://github.com/fercol/<wbr class="">BaSTA/blob/master/latestBuild/<wbr class="">BaSTA_1.9.5.tar.gz</a></div><div class=""><div class="">
<div style="text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><div style="text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><div style="text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><div style="text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><div style="text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><div style="text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><br class="m_2390374109760895622Apple-interchange-newline">Best,</div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><br class=""></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 16px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Fernando<br class="m_2390374109760895622Apple-interchange-newline">______________________________<wbr class="">___</div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><b class=""><br class=""></b></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><b class="">Fernando Colchero</b></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Associate Professor</div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Department of Mathematics and Computer Science</div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Biodemography Unit</div><div style="text-transform: none; line-height: normal; text-indent: 0px; letter-spacing: normal; font-family: Helvetica; font-size: 12px; font-variant: normal; word-spacing: 0px; white-space: normal;" class=""><br class=""></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Tlf. <a href="tel:+45%2065%2050%2023%2024" target="_blank" value="+4565502324" class="">+45 65 50 23 24</a></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Email <a href="mailto:colchero@imada.sdu.dk" target="_blank" class="">colchero@imada.sdu.dk</a></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Web <a href="http://www.sdu.dk/staff/colchero" target="_blank" class="">www.sdu.dk/staff/colchero</a></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Pers. web <span class="m_2390374109760895622Apple-converted-space"> </span><a href="http://www.sdu.dk/staff/colchero" target="_blank" class="">www.colchero.com</a></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class="">Adr. <a href="https://maps.google.com/?q=Campusvej+55,+5230,+Odense,+Dk&entry=gmail&source=g" class="">Campusvej 55, 5230, Odense, Dk</a></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><br class=""></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><b class="">University of Southern Denmark</b></div><div style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; text-transform: none; text-indent: 0px; letter-spacing: normal; word-spacing: 0px; white-space: normal;" class=""><div style="font-size:16px" class="">______________________________<wbr class="">___</div><div class=""><br class=""></div></div></div></div></div></div></div></div><br class="m_2390374109760895622Apple-interchange-newline"><br class="m_2390374109760895622Apple-interchange-newline">
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<br class=""><div class=""><blockquote type="cite" class=""><div class=""><div class="h5"><div class="">On 23 Feb 2018, at 22:36, Ken Honeycutt <<a href="mailto:rkenhoneycutt@gmail.com" target="_blank" class="">rkenhoneycutt@gmail.com</a>> wrote:</div><br class="m_2390374109760895622Apple-interchange-newline"></div></div><div class=""><div class=""><div class="h5"><div dir="ltr" class="">Hi BaSTA users,<div class=""><br class=""></div><div class="">I just noticed the partial capture history I posted for example did not appear as I expected; and the text continues after many many rows of 0s and 1s. Here's the capture history again in csv. Hopefully this is better.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Ken</div><div class=""><br class=""></div><div class=""><div class="">ID,Birth,Death,6,7,8,9,...,17,<wbr class="">18,19,20</div><div class="">1,0,0,1,0,1,0,0,0,1,1,1</div><div class="">2,0,0,0,1,0,0,0,0,0,1,0</div><div class="">3,0,0,1,0,1,0,0,0,0,0,1</div><div class="">4,0,0,0,1,0,0,0,0,1,0,1</div><div class="">…,0,0,1,0,1,0,0,0,0,1,1</div><div class="">1544,0,0,0,1,0,0,0,0,0,1,0</div></div></div></div></div>
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