examples/case_study/README.md

In quantifish/TagGrowth: Mixed effects model of capture-mark-recapture-age data

Case Study - Antarctic toothfish

Antarctic toothfish are large Nototheniids native to the Southern Ocean. They can grow to be more than 2m in length, weighing over 100kg, and can live for up to 50 years of age. The exploratory toothfish fishery in the Ross Sea region began in 1997 and is managed by The Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR). Since then the fishery has increased to about 3000 tonnes per year. Fishing is restricted to the summer months (December usually until to March), once the ice shelf recedes allowing vessels access to the region. The Antarctic toothfish tagging programme was initiated in the 2001 fishing season by New Zealand vessels involved in the fishery. In 2004, toothfish tagging was made compulsory for all vessels participating in the fishery. Currently toothfish are required to be double tagged at a rate of 1 fish per tonne landed. The tagging programme records information on the date, depth, location, sex, and size of each tagged/recaptured fish. A small subset of the recaptured fish are aged by reading their otolith. The otoliths are assumed to be aged without error, a reasonable assumption for this species.

Methods

We identified those fish that had been tagged...

Results

This folder contains all the code requied to fit a model. Model outputs are placed in each of the version folders depending on which random-effects are being fitted. The models run, if they were positive definitive Hessian (pdH) and the folders they are stored in is summarised in the table below.

| Random effects | pdH | Folder | | -------------- |:---:|:------:| | None | Yes | v0 | | k | Yes | v1 | | z | Yes | v2 | | y | No | v3 | | k, z | Yes | v4 | | k, y | - | v5 | | z, y | Yes | v6 | | k, z, y | - | v7 |

No variation (v0)

Random effects: None pdH: Yes Directory: v0

Variation in k (v1)

Random effects: k pdH: Yes Directory: v1

Variation in z (v2)

Random effects: z pdH: Yes Directory: v2

v3

Random effects: y pdH: No Directory: v3

Variation in k and z (v4)

Random effects: k, z pdH: Yes Directory: v4

v5

Random effects: k, y pdH: Failed to fit Directory: v5

v6

Random effects: z, y pdH: Yes Directory: v6

v7

Random effects: k, z, y pdH: Failed to fit Directory: v7

quantifish/TagGrowth documentation built on May 26, 2019, 12:36 p.m.