openMSE or any of its component packages you must have:
- A recent version of the R software installed on your machine;
- While not essential, we highly recommend using an integrated development environment (IDE) such as RStudio;
- The latest version of
openMSEor the individual component packages installed.
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 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
All component packages in the
openMSE collection can be installed with:
and loaded into the R session with:
This will load the
openMSE package, and make all functions in
Installing the component packages
To install only the core MSE functions, install and load the Management Strategy Evaluation toolkit with:
To install and load the Data-Limited Methods toolkit use:
library('DLMtool'). Note that this will also install and load the dependency
To install and load the Stock Assessment Methods toolkit use:
library('SAMtool'). Note that this will also install and load the dependency
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.