set up an OM,
use an OEM to generate length data,
estimate empirical LBIs,
simple model based estimates using FLR
wrappers for 3rd party methods
evaluate robustness to uncertainty

Introduction

This tutorial describes how to simuation test data limited methods in FLR using a variety of other packages.

Required packages

To follow this tutorial you should have installed the following packages:

FLR: FLCore, FLBRP, FLasher, FLife

for example

Operating Model

Turbot

Figure 1 Time series relative to MSY benchmarks.

Length Based Methods

Based on Beverton and Holt $L_{F} = \frac{L\infty +\frac{F+M}{K}L_c}{1+\frac{F+M}{K}}$

$L_{current}/L_{F=M}$
$M/(Z_{current}-M)$
$F_{0.1}/(Z_{current}-M)$
$LBSPR$ Length-based spawning potential ratio (Hordyk et al. 2015)
$Lime$ (Rudd and Thorson, 2018) mixed effects non-equilibrium

MLZ

MLZ is a package that facilitates data preparation and estimation of mortality with statistical diagnostics using the mean length-based mortality estimator and several extensions.

Figure 2 Mean length of catch turbot.

         iter   Estimate   Std. Error
Z[1]        1  0.8506783 1.693855e-02
Z[2]        1  0.9991248 1.022041e-02
Z[3]        1  0.7294890 8.740152e-03
yearZ[1]    1 41.5477473 5.847062e-01
yearZ[2]    1 52.2059039 2.099466e-01
sigma       1  2.3176293 1.089313e-14

LB-SPR

LBSPR is a R package for simulation and estimation using life-history ratios and length composition data

Figure 3 Observation error model for turbot.

Figure 4 Estimates of SPR for turbot.

Figure 5 Estimates of $F/M$ for turbot.

References

More information

You can submit bug reports, questions or suggestions on this tutorial at https://github.com/flr/doc/issues.
Or send a pull request to https://github.com/flr/doc/
For more information on the FLR Project for Quantitative Fisheries Science in R, visit the FLR webpage, http://flr-project.org.

Software Versions

R version 4.0.3 (2020-10-10)
FLCore: 2.6.18.9002
FLasher: 0.6.8
Compiled: Wed Dec 1 13:45:38 2021

License

This document is licensed under the Creative Commons Attribution-ShareAlike 4.0 International license.

Author information

Laurence KELL. laurie@seaplusplus.co.uk

Acknowledgements

This vignette and the methods documented in it were developed under the MyDas project funded by the Irish exchequer and EMFF 2014-2020. The overall aim of MyDas is to develop and test a range of assessment models and methods to establish Maximum Sustainable Yield (MSY) reference points (or proxy MSY reference points) across the spectrum of data-limited stocks.

Simulation Testing Data Limited Methods FLife

01 December, 2021