rtmbGMACS is an R package that, when completed, will provide a RTMB-based implementation of the Generalized Model for Assessing Crustacean Stocks (GMACS) modeling framework that was developed using AD Model Builder (ADMB). The ADMB version of GMACS is currently used to in stock assessment models for a number of crab species in the Bering Sea and Aleutian Islands to determine reference points for fishery management to the North Pacific Fishery Management Council (NPFMC) (see, for example, the stock assessment reports for Bristol Bay red king crab and snow crab). RTMB (R Bindings for Template Model Builder) is an R package that provides a native R interface to Template Model Builder (TMB), an R package that allows the user to develop and run C++-based statistical models (similar to ADMB) using automatic differentiation in the R framework.
UNDER CONSTRUCTION: DON’T TRY THIS YET!! You can install the current (at present, development) version of rtmbGMACS from GitHub with:
# install.packages("devtools")
devtools::install_github("wStockhausen/rtmbGMACS")The purpose of rtmbGMACS is to provide a population modeling and stock assessment framework for, in particular, federally-managed commercially-fished crab stocks in the US Bering Sea and Aleutian Islands, although the software should be more widely applicable to (at least) other crustacean stocks. Here, the modeling framework is referred to as “gmacs” while the R package is referred to “rtmbGMACS”. The R package will provide functionality to:
- set up data inputs to a gmacs model
- define associated likelihood functions
- select functional forms for various population processes
- define estimable parameters and associated priors or penalties
- run the model to estimate parameters and stock status
- determine required management-related quantities under different harvest strategies
- create plots and tables from a fitted model
- perform standard diagnostic analyses (e.g., retrospective analyses, likelihood profiling, MCMC)
- and compare results from multiple models.
The package website provides a more detailed discussion (under construction).
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