Introduction

This package contains functions to run the Length-based Integrated Mixed Effects (LIME) fisheries stock assessment method. The LIME package can be used in two ways: 1) simulating the expected age-structured population dynamics, length composition, catch data, and an abundance index using LIME and 2) fitting to empirical length data at a minimum and any available catch and/or abundance index data to provide an estimate of the spawning potential ratio (SPR).

LIME has been developed for data-limited fisheries, where few data are available other than a representative sample of the size structure of the vulnerable portion of the population (i.e., the catch) and an understanding of the life history of the species. LIME relaxes the equilibrium assumptions of other length-based methods by estimating annual fishing mortality and recruitment variation (among other parameters), deriving annual recruitment as a random effect.

See Rudd and Thorson (2017) in the reference list for full details of the model, including simulation testing to evaluate performance across life history types, population variability scenarios, and data availability scenarios, as well as violations of the model assumptions.

Bug Reports

Please alert me to any bugs or issues by using GitHub.

Comments and suggestions for additional features are welcome and we can discuss via email at [email protected]. GitHub pull requests are also welcome.

Finally, please make sure you understand the data and the biological parameters (and how the model treats these) and critically evaluate any output of LIME.

First Steps

Installing the Package

1. devtools: You can install the development version of the package from GitHub using the devtools package:

install.packages("devtools", repos='http://cran.us.r-project.org')

2. Make sure you have the latest Rtools installed and in your system path. Install Rtools at: https://cran.r-project.org/bin/windows/Rtools/ Download and run the latest .exe file. During installation, make sure you check a box that allows Rtools to be written into your system path.

3. Install LIME:

devtools::install_github("merrillrudd/LIME")

The installation may produce error messages requiring other packages. You can download those from CRAN if they are not automatically downloaded in the LIME installation process, and then start from the step that produced the error. Again, please use the contact info in Bug Reports if this doesn't work, as you may have discovered a new installation error... congratulations!