Estimation functions and diagnostic tools for mean length-based total mortality estimators based on Gedamke and Hoenig (2006)
MLZ is a R package that facilitates data preparation and estimation of mortality with statistical diagnostics using the mean length-based mortality estimator and several extensions.
After installation, an overview of the main features of the package can be found in the vignette:
Currently, the package is in active development, version 0.1.0. Testing, reporting issues, and pull requests are welcome.
The estimation models are written in TMB. As a result, Rtools is required if running the package on a Windows machine. Rtools can be downloaded here: https://cran.r-project.org/bin/windows/Rtools/index.html
The MLZ package can then be installed using the
Gedamke, T. and Hoenig, J.M. 2006. Estimating mortality from mean length data in nonequilibrium situations, with application to the assessment of goosefish. Transactions of the American Fisheries Society 135:476-487.
Huynh, Q.C, Gedamke, T., Hoenig, J.M, and Porch C. 2017. Multispecies Extensions to a Nonequilibrium Length-Based Mortality Estimator. Marine and Coastal Fisheries 9:68-78.
Huynh, Q.C., Gedamke, T., Porch, C.E., Hoenig, J.M., Walter, J.F, Bryan, M., and Brodziak, J. 2017. Estimating Total Mortality Rates from Mean Lengths and Catch Rates in Non-equilibrium Situations. Transactions of the American Fisheries Society 146:803-815.
Then, A.Y, Hoenig, J.M, and Huynh, Q.C. In press. Estimating fishing and natural mortality rates, and catchability coefficient, from a series of observations on mean length and fishing effort. ICES Journal of Marine Science.