Mean Length-Based Estimators of Mortality using TMB

Estimation functions and diagnostic tools for mean length-based total mortality estimators based on Gedamke and Hoenig (2006) .


Build Status

Introduction

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:

library(MLZ)
vignette("MLZ")

Version

Currently, the package is in active development, version 0.1.0. Testing, reporting issues, and pull requests are welcome.

Installation

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 devtools package:

devtools::install_github("quang-huynh/MLZ")

Citations

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.

News

Reference manual

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install.packages("MLZ")

0.1.3 by Quang Huynh, a month ago


Browse source code at https://github.com/cran/MLZ


Authors: Quang Huynh [aut, cre] , Todd Gedamke [ctb] , Amy Then [ctb]


Documentation:   PDF Manual  


GPL-2 license


Imports methods, stats, graphics, grDevices, dplyr, gplots, ggplot2, reshape2, parallel, TMB

Suggests knitr, rmarkdown

Linking to TMB, RcppEigen


See at CRAN