[Basta-users] post-fledging survival - Julian day or capture days for input format?

[maren]

Hi Diederik,

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 (which is equivalent to the 
time of birth and goes into the matrix for times of birth and death). 
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.

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.

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.


When you run BaSTA studyStart will be 1 and studyEnd will be 61.

You can find more information on the input matrix and how to create it 
in the vignette of the BaSTA-package 
(https://cran.r-project.org/web/packages/BaSTA/vignettes/BaSTAoverview.pdf).

I hope this response is helpful. If you have further questions, don’t 
hesitate to ask.

Cheers,

Maren



Am 03.08.2015 um 12:54 schrieb Diederik Strubbe:
> Dear all,
>
> Apologies but it has been brought to my attention that one sentence in 
> my previous e-mail is not complete. I mean to write "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".
>
> Cheers,
>
> Diederik
>
> On 8/3/2015 12:45 PM, Diederik Strubbe wrote:
>> Dear all,
>>
>> Apologies but it has been brought to my attention that one sentence 
>> in my previous e-mail is not complete. I mean to write "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".
>>
>> Cheers,
>>
>> Diederik
>>
>>
>> On 8/3/2015 11:39 AM, Diederik Strubbe wrote:
>>>
>>> Dear BaSTA community,
>>>
>>> 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.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.
>>>
>>> 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^th day of tracking] 
>>> refers to November 17^th for birds that fledged on November 2^nd , 
>>> but to November 29^th for birds that fledged on November 14^th .
>>>
>>> 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]?
>>>
>>> Many thanks in advance for any comments or suggestions.
>>>
>>> Best wishes,
>>>
>>> Diederik
>>>
>>> -- 
>>> 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
>>
>>
>> -- 
>> 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
>
>
>
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