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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">Hi
Diederik,</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">If you are purely
interested in
survival after fledging as a function of time after fledgling
you first have to
create a mark-recapture matrix the way you suggested. The day of
fledgling is day
one and you make a table with 0s (bird not seen) and 1s (bird
seen) for days 2
to 61. For day one you always put a 0 in that table </span><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">(which is
equivalent to the time of birth and goes
into the matrix for times of birth and death). </span>This
table is the recapture matrix needed as part of the input for
BaSTA and has one column for the individual identification and
then one column for each day from 1 to 61.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">If you have your
data in a format
with one column giving the individual identification and the
other column
listing all the days you have seen the bird, you can use the
function
CensusToCaptHist() to create the recapture matrix.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">In addition to the
recapture matrix,
you create a matrix for times of birth and death. Since day of
fledgling is
always assigned as the start of the time of interest, the
entries in the column
birth will always be day 1. Since you don’t observe any deaths,
the entries in
the column death will always be 0 (standing for not known). You
have to merge this matrix with the recapture matrix to create
the input matrix for BaSTA in a way that you first have a column
for the individual identification, then a column for birth, then
death and then the recapture matrix.<br>
</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
When you run BaSTA studyStart will be 1 and studyEnd will be 61.<br>
<span style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">You can find more
information on the
input matrix and how to create it in the vignette of the
BaSTA-package
(<a class="moz-txt-link-freetext" href="https://cran.r-project.org/web/packages/BaSTA/vignettes/BaSTAoverview.pdf">https://cran.r-project.org/web/packages/BaSTA/vignettes/BaSTAoverview.pdf</a>).<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">I hope this
response is helpful. If
you have further questions, don’t hesitate to ask.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><span
style="mso-ansi-language:EN-GB" lang="EN-GB">Maren<o:p></o:p></span></p>
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<br>
<div class="moz-cite-prefix">Am 03.08.2015 um 12:54 schrieb Diederik
Strubbe:<br>
</div>
<blockquote cite="mid:55BF484F.50505@uantwerpen.be" type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
<div class="moz-cite-prefix">Dear all,<br>
<br>
Apologies but it has been brought to my attention that one
sentence in my previous e-mail is not complete. I mean to write
"<span style="mso-ansi-language:EN-GB"> I assume the most
conservative manner to treat this is to set all ‘deaths’ [i.e.
independence of juveniles = end of tracking period] to 0 -
i.e. death unknown, as we don't have hard evidence that these
birds have actually deceased".<br>
<br>
Cheers,<br>
<br>
Diederik</span><br>
<br>
On 8/3/2015 12:45 PM, Diederik Strubbe wrote:<br>
</div>
<blockquote
cite="mid:74bebea9b3b642bea071f5fcfb2557c6@xmail103.UGent.be"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div class="moz-cite-prefix">Dear all,<br>
<br>
Apologies but it has been brought to my attention that one
sentence in my previous e-mail is not complete. I mean to
write "<span style="mso-ansi-language:EN-GB"> I assume the
most conservative manner to treat this is to set all
‘deaths’ [i.e. independence of juveniles = end of tracking
period] to 0 - i.e. death unknown, as we don't have hard
evidence that these birds have actually deceased".<br>
<br>
Cheers,<br>
<br>
Diederik<br>
</span><br>
<br>
On 8/3/2015 11:39 AM, Diederik Strubbe wrote:<br>
</div>
<blockquote cite="mid:55BF3477.1050207@uantwerpen.be"
type="cite">
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span lang="NL-BE">Dear BaSTA community,<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span lang="NL-BE"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB">I am
involved in a radio-tracking study on survival rates of
tropical birds after fledging. Birds were followed from
fledging until independence (about two months for each
bird). My main question is about how to organize a data
frame for input. As not all birds fledge at the same
moment, when using Julian days as input, after 60 days of
tracking, birds are assigned a 0 value – because we
stopped looking for that bird.<span
style="mso-spacerun:yes"> </span>So, for example, on
Julian day 312 a 0 can indicate either that we did not
find the bird on that day, or that we had stopped
searching for it. <o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB">Can I
arrange that data so that ‘birth’ (here: day of fledging)
=1 for all birds, and all following days are numbered from
2 to 61. So, for example, in this arrangement, day 15 [the
15<sup>th</sup> day of tracking] refers to November 17<sup>th</sup>
for birds that fledged on November 2<sup>nd</sup>, but to
November 29<sup>th</sup> for birds that fledged on
November 14<sup>th</sup>.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB">I should
also note that although about half of the birds have only
been seed at fledging (on day 1, but no observations in
the following 60 days), we did not find any dead birds
either. I assume the most conservative manner to treat
this is to set all ‘deaths’ [i.e. independence of
juvelines = end of tracking period]?<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB">Many thanks
in advance for any comments or suggestions.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB">Best
wishes,<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;text-align:
justify"> <span style="mso-ansi-language:EN-GB">Diederik<o:p></o:p></span></p>
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<pre class="moz-signature" cols="72">--
Dr.Diederik Strubbe
Evolutionary Ecology Group
Department of Biology
University of Antwerp
Middelheimcampus GV310
Groenenborgerlaan 171
2020 Antwerpen, Belgium
office: +32 3 265 34 69
mobile phone: +32 477445568
skype user name: lakrinn</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Dr.Diederik Strubbe
Terrestrial Ecology Unit
Department of Biology
Ghent University
K. L. Ledeganckstraat 35
B-9000 Ghent
Belgium
mobile phone: +32 477445568
skype user name: lakrinn</pre>
</blockquote>
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<pre wrap="">_______________________________________________
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