How to model mixed cohort + individual capture histories?

[Jmackay]

Hello!

I'm looking for advice on how to best model data from 1 season of mark-recapture of juvenile coho salmon. My primary goal is to estimate abundance, and hopefully survival, to explore some hypotheses. My problem is that I have a mix of individual and cohort-based capture histories:

Fish were sampled in one closed mark-recapture event per month (2 secondary events) for each of 5 months (5 primary occasions) over the 2025 season. Individual fish received cohort-based VIE tags until/unless they grew large enough to be PIT tagged (and thus, gain an individual capture history). As such, my dataset is a mix of VIE tagging (both secondary events have the same mark; cannot discern individual capture history) and individual PIT tagged fish (which may have VIE tags from previous occasions). I've appended a small example of capture histories for clarity at the end.

I was initially hoping to conduct a robust-design model to estimate abundance and survival, though at this point I'm unable to incorporate the VIE data. I could use only the PIT data (individual histories), but I fear the sparse early-season PIT data (smaller fish = high proportion of VIE marks) and low overall recapture rates would result in poor estimates.

A couple of alternative options have occurred to me: 1. Collapse the secondary occasions and form pseudo capture histories for a Jolly-Seber model, or 2. Use two separate models - a robust model using only the PIT data to estimate survival/capture probability, and multiple closed capture models using PIT and VIE data for each secondary occasion to estimate abundance. However, I worry that this would be compromised by the low recapture rates.

Is there a way to format the data to use both VIE and PIT data for a robust model? Is it be better to run separate open/closed models? Is there another approach I could consider?

Advice is greatly appreciated! I'm happy to provide more information if needed.

Many thanks,

Jamie


P.S. some example capture histories:

___________|---P1---|---P2---|---P3---|---P4---|---P5---|
___________|-S1-S2-|-S1-S2--|-S1-S2-|-S1-S2-|-S1-S2--|
fish 1 (PIT): ---0--1-----0---0-----1---1-----0---1----0---0---
fish 2 (VIE): ----1----------0---------1----------1--------0-----
fish 3 (both):---0----------1-------1---0-----0---1----1---1---