To use openMSE or any of its component packages you must have:

1. A recent version of the R software installed on your machine;
2. While not essential, we highly recommend using an integrated development environment (IDE) such as RStudio;
3. The latest version of openMSE or the individual component packages installed.

Installing R

The R statistical language and environment can be freely downloaded from the CRAN website and is available for all operating systems. Updated versions of R are released frequently, and it is recommended that you have the latest version installed.

If you are using Windows OS, you can uses the installr package and the installr::updateR() function to update and install the latest version. Alternatively, head to the CRAN website to download the latest version of R.

You can check your version of R by typing version into the R console.

RStudio

RStudio is a freely available integrated development environment (IDE) for R. It is not essential that you use RStudio, but it can make things a lot easier, especially if you are new to R. We assume throughout the openMSE documentation that you are using RStudio.

It is important to be aware that RStudio and R are two different pieces of software that must be installed separately. We recommend installing the R software before downloading and installing RStudio.

Installing the Packages

Installing openMSE

All component packages in the openMSE collection can be installed with:

install.packages('openMSE')

and loaded into the R session with:

library('openMSE')

This will load the openMSE package, and make all functions in MSEtool, DLMtool, and SAMtool available.

Installing the component packages

To install only the core MSE functions, install and load the Management Strategy Evaluation toolkit with: install.packages('MSEtool') and library('MSEtool').

To install and load the Data-Limited Methods toolkit use: install.packages('DLMtool') and library('DLMtool'). Note that this will also install and load the dependency MSEtool.

To install and load the Stock Assessment Methods toolkit use: install.packages('SAMtool') and library('SAMtool'). Note that this will also install and load the dependency MSEtool.

Assumed Knowledge

The openMSE packages have been designed to be accessible for all users and do not assume a high level of knowledge of R. The functions and help documentation material have been constructed in such a way that a user with little experience with R should be able to run the MSE and apply the methods to their data.

Little programming experience is required to use the package. However, users of the openMSE packages should have some familiarity with R, and be comfortable with using the command line. The help documentation attempts to explain the use of the openMSE functions and features in easy to follow steps, but familiarity with the most common R functions is assumed.

The package is fully extensible, and more experienced R users are able to design their own management procedures, develop new plotting functions, and other customizations.