Best way to format data input files to censor individuals

posts related to the RMark library, which may not be of general interest to users of 'classic' MARK

Best way to format data input files to censor individuals

Postby amela22 » Sun Jan 07, 2018 1:24 pm

Hi,

I am hoping to get some advice on the proper way to format data input files for Mark/RMark that censor individuals based on certain criteria. Specifically, I am using multistate models to estimate survival and transcience probabilities 5 different geographical states. Using acoustic telemetry, I've tagged/detected 135 individuals across a 2-year period (25 sampling occasions).

I would like to censor individuals on a specific encounter occasion if the tag battery life has expired (according the the manufacturer's estimated tag life).

I know this is normally done by setting the frequency to -1 which tells Mark that after the last encounter (or detection) the fish should be removed from the study. However, the problem I am running into is that there are true absences (0's) prior to the encounter occasion that should be censored so I'm not sure how to distinguish these true 0's from the 0's that should be censored.

For example, assume I have 5 sampling occasions across 3 strata and a transmitter expires on the fourth occasion, then the encounter history would look something like,

A0000

where the first two 0's are true absences (the fish was not detected) and the last two zeroes are absences as a result of the tag expiring. If I assign a frequency of -1 to this encounter history, then the model will ignore everything after the initial encounter (the first two zeroes will not enter the model likelihood although they are true values and should be treated as such).

Can anyone recommend the best way to approach this?
amela22
 
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Re: Best way to format data input files to censor individual

Postby jhines » Sun Jan 07, 2018 4:47 pm

You can enter "." for missing data after the mfr. expiration date for each individual. This will provide no information on capture or survival rates for those occasions. However, make sure you stick to that protocol and change both the 0's and 1's after the predefined date, otherwise you could bias the survival and/or capture rate estimates.
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Re: Best way to format data input files to censor individual

Postby amela22 » Tue Jan 09, 2018 10:08 am

Thank you very much for the help. I figured it was something simple that I was overlooking.
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