CJS inp file formatting with individual covariates & morts

questions concerning analysis/theory using program MARK

CJS inp file formatting with individual covariates & morts

Postby pfishsurv » Wed May 21, 2025 7:44 pm

After a careful read of chapter 2 and high/low search for examples, I'm posing a question about formatting input file data when there are (1) known removals/mortalities and (2) rows are individual capture histories (and covariates), rather than capture histories with frequencies across a number individuals. In the latter case, aggregating removals with common capture histories and entering frequencies as negative values is a straightforward solution; but I'm hitting a wall (e.g., model not running) on figuring out how to denote a known removal/mort when rows represent individuals with categorical or continuous covariates. Should I be including a frequency (with 1 or -1) or coding using a -1 for the capture occasion coincident with the removal?

And if I've missed a post or chapter content that speaks to this, apologies in advance. This was the only entry that I could locate that was close (viewtopic.php?f=21&t=3583&hilit=censor) and it didn't quite address the question. Thank you!
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Re: CJS inp file formatting with individual covariates & mor

Postby jlaake » Wed May 21, 2025 8:05 pm

Use -1 as frequency for a loss on capture.
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Re: CJS inp file formatting with individual covariates & mor

Postby jhines » Wed May 21, 2025 8:09 pm

Each input line should include the capture-history, frequency and (optionally) covariates. Use 1 for the frequency for animals which were released on last capture and -1 for animals not released on last capture. The Mark program will know that all 0's after the last capture in the history are not to be used in estimation of survival and/or detection if the frequency is -1 (or anything < 0).
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