<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:x="urn:schemas-microsoft-com:office:excel" 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=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (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:"Segoe UI";
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:"Times New Roman \(Body CS\)";
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Aptos;
panose-1:2 11 0 4 2 2 2 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:10.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="en-DK" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;mso-fareast-language:EN-US">Hi Luisa,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;mso-fareast-language:EN-US"> Quick question, which version of BaSTA are you using? There is a new version at
<a href="https://github.com/fercol/basta2.0">https://github.com/fercol/basta2.0</a> that uses an improve method to construct the life table (based on product limit estimators). It also allows using the model on census data as well. Unfortunately, BaSTA is temporarily
off CRAN due to some issues when checking the package on some platforms, which do not affect functionality, but they need to be solved. You can still find version 1.9.5 in
<a href="https://github.com/fercol/BaSTA">https://github.com/fercol/BaSTA</a>.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;mso-fareast-language:EN-US"> About your project, you can certainly change the time units to months and then interpret the results as such. Still, I don’t think that’s going to solve your problem.
If I understand correctly, you know the time of birth of all the individuals, and then, after releasing them, you don’t see them until they are about 2 years old, isn’t it?
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;mso-fareast-language:EN-US">I believe that what you are doing of conditioning your analysis to a minimum age of 2 is correct. In that case, BaSTA uses a constant mortality function for all ages
up to that minimum age, and then the model you chose from that age onwards. Still, the life table is built for all ages. I suspect that maybe the model is having a hard time with the 0 recapture probabilities between ages 0 and 2. Could you send me a subset
of the data so I can run some tests? <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt"> Fernando<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">-----------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">Fernando Colchero</span></b><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">Associate Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">Department of Mathematics and Computer Sciences (IMADA)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">and Interdisciplinary Center on Population Dynamics (CPop)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">Tlf. +45 65 50 46 35<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">Email </span><span lang="DA" style="font-family:"Tahoma",sans-serif;color:black"><a href="mailto:colchero@imada.sdu.dk" title="mailto:colchero@imada.sdu.dk"><span lang="EN-US" style="color:#0563C1">colchero@imada.sdu.dk</span></a></span><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">Web www.sdu.dk/staff/colchero<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">Pers. web www.colchero.com<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">Adr. Campusvej 55, 5230, Odense, Dk<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black">University of Southern Denmark</span></b><span lang="EN-US" style="font-family:"Tahoma",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DA" style="font-size:11.0pt">------------------------------------------------------</span><span lang="EN-US" style="font-size:11.0pt"> <o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:14.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Basta-users <basta-users-bounces@lists.r-forge.r-project.org> on behalf of Luisa Fitzpatrick <luisa.fitzpatrick@utas.edu.au><br>
<b>Date: </b>Tuesday, 23 April 2024 at 09.13<br>
<b>To: </b>basta-users@lists.r-forge.r-project.org <basta-users@lists.r-forge.r-project.org><br>
<b>Subject: </b>[Basta-users] juvenile survival<o:p></o:p></span></p>
</div>
<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" align="left" width="100%" style="width:100.0%;display:table;border-collapse:seperate;float:none">
<tbody>
<tr>
<td style="background:#A6A6A6;padding:5.25pt 1.5pt 5.25pt 1.5pt"></td>
<td width="100%" style="width:100.0%;background:#EAEAEA;padding:5.25pt 3.75pt 5.25pt 11.25pt">
<div>
<p class="MsoNormal" style="mso-element:frame;mso-element-frame-hspace:2.25pt;mso-element-wrap:around;mso-element-anchor-vertical:paragraph;mso-element-anchor-horizontal:column;mso-height-rule:exactly">
<span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#212121">You don't often get email from luisa.fitzpatrick@utas.edu.au.
<a href="https://aka.ms/LearnAboutSenderIdentification">Learn why this is important</a><o:p></o:p></span></p>
</div>
</td>
<td width="75" style="width:56.25pt;background:#EAEAEA;padding:5.25pt 3.75pt 5.25pt 3.75pt">
</td>
</tr>
</tbody>
</table>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Hi everyone,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">I have used Basta to model mortality curves in two populations of a lizard species. I have mark-recapture data for around 22 years with all individuals born in the
lab, and then recaptured at maturity (age 2 or 3 if they survived) and every subsequent year that they reproduce (max lifespan 13 years). <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><br>
My question is on how to incorporate survival from birth to maturity (or until first observation). Basta doesn't allow me to include observations before birth and I ran into issues for having birth dates with no observations present. I was thinking I could
possibly use time intervals other than year. e.g. all the individuals that are born I can include as observations at age 1 month. Then instead of age 2,3,4 I can have observations at age 24, 36, 48.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">As it is, I have conditioned the analyses to survival beyond age 2 to examine patterns in adult/reproductive life. This gives me mortality trajectories that start
at mortality rate 0 at age 0 and shoot up, which gives the impression early mortality is low. The life table for ages 2-3 has a death rate of 0, and for ages 3-4 has a death rate of 0.002. When in fact I know from the dataset that survival rates from birth
to maturity are approximately 20% and from age 2-3 are around 50%. <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Does anyone have any feedback on the idea of using months instead of years or any suggestions for another way to address this issue? <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Thanks in advance,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Luisa <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black;background:white">Dr Luisa Fitzpatrick (she/her)</span></b><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black;background:white">Postdoctoral Fellow Life History Evolution and Ageing</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<div id="Signature">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black;background:white">Behavioural and Evolutionary Ecology Research Group</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black;background:white">University of Tasmania, Sandy Bay TAS 7005 </span><span style="font-size:11.5pt;color:black;background:white"><br>
</span><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:black;background:white"><a href="https://beergrouputas.wordpress.com/"><span style="color:black">https://beergrouputas.wordpress.com/</span></a></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p style="line-height:12.65pt;background:white"><i><span style="font-size:11.0pt;color:#242424">I acknowledge Aboriginal people as the traditional owners of this Land and respect their culture and identity which has been bound up with the Land, Sea, Waterways
and Sky for generations.</span></i><span style="font-size:11.0pt;color:#242424"><o:p></o:p></span></p>
</div>
<p style="line-height:10.0pt"><br>
<br>
This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained
in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.<o:p></o:p></p>
</div>
</div>
</body>
</html>