spict

An R-package for fittng surplus production models in continuous-time to fisheries catch data and biomass indices (either scientific or commercial). Main advantages of spict are:

1. All estimated reference points (MSY, Fmsy, Bmsy) are reported with uncertainties.

2. The model can be used for short-term forecasting and management strategy evaluation.

3. The model is fully stochastic in that observation error is included in catch and index observations, and process error is included in fishing and stock dynamics.

4. The model is formulated in continuous-time and can therefore incorporate arbitrarily sampled data.

Help files

A vignette for the package is available here, and serves as an introduction to the package and its functionality. The vignette also contains description of the more advanced features of the package.

The package also contains reasonable documentation in the form of help texts associated with each function (some may not be fully up-to-date). These can be accessed in the usual R manner by writing e.g. ?check.inp. A pdf compiling help texts for all functions can be downloaded here. A good place to start (in addition to reading the vignette) is to read ?check.inp and ?fit.spict.

Citation

The underlying model used in the package is described in a published paper. This paper is included in the package in the inst folder. To get citation information write citation(spict) in the command line.

Package requirements

The package requires TMB to be installed. TMB is now a part of CRAN and can therefore be installed using the install.packages() command. For more information about TMB click here.

Installing the spict package

To install spict from GitHub use

library(devtools)
install_github("mawp/spict/spict")            # master branch
install_github("mawp/spict/spict", ref="dev") # development branch

Windows

The above procedure using install_github() should now work on Windows (make sure to remove spict before trying to reinstall). If it doesn't work the old, but tedious, procedure can be used:

1. Start 64 bit R and change working directory to the (cloned or unzipped) spict folder.

2. From R run: source("install_windows.R")

This requires that Rtools is installed. Rtools can be obtained here. When running install_windows.R remember to set your working directory to the spict directory containing install_windows.R.