Chapter 5 User guide

This section details installation guides for users. See the developer installation guide.

5.1 User Installation Guide

This section describes how to install the FIMS R package and dependencies.

5.2 Installing the package from Github

The following software is required: - R version 4.0.0 or newer (or RStudio version 1.2.5042 or newer) - the remotes R package - TMB (install instructions at are here.)

5.2.1 Windows users

Rtools4 (available from here)
- this likely requires IT support to install it on NOAA computers (or any without administrative accounts)

5.3 Installing from `R`

remotes::install_github("NOAA-FIMS/FIMS")
library(FIMS)

5.4 Running the model

This section describes how to set-up and run the model.

5.4.1 Specifying the model

5.4.1.1 Naming conventions

TODO: add description and link to naming conventions

5.4.1.2 Structuing data input

You can add components to the model using S4 classes.

#TODO: add script to demonstrate how to structure data input

5.4.1.3 Defining model specifications

#TODO: add scripts detailing how to set up different components of the model

5.4.2 How to run the model

#TODO: add script with examples on how to run the model

5.4.3 Extracting model output

Here is how you get the model output.

#Todo add code for how to extract model output