README.md

In StrathE2E2: End-to-End Marine Food Web Model

StrathE2E2

R package containing the Strath End-to-end ecosystem model.

General Requirements

StrathE2E2 runs on the following platforms:

• Mac OS X
• Linux (64-bit)
• Windows (64-bit, Windows 10 recommended)

with the following minimum runtime:

• R 3.6 or later
• R packages deSolve, NetIndices

Installation

There is a source package for Linux and binary packages for Windows 10 and Mac OS X in our CRAN compatible R package repository.

To install StrathE2E2, use install.packages() function and specify our repository:

install.packages("StrathE2E2", repos="https://marineresourcemodelling.gitlab.io/sran")

which will install either the source or binary package (depends on your OS).

Quick Start

To run the model:

library(StrathE2E2)
model <- e2e_read("North_Sea","1970-1999")
results <- e2e_run(model, nyears=5)
e2e_plot_ts(model,results)

Within R, type help.start() and navigate to the package documentation for various user and technical guides,

Building from source

The source package can be built on all platforms, and is the only way to install on Linux.

Download latest version from Strath E2E2 GitLab repository (use the repository download button).

In addition to the standard requirements, some additional R packages are required to build the package documentation (vignettes):

• knitr
• rmarkdown

For each platform there are some additional software requirements - see the individual platform build sections below.

Linux build

Full requirements for Linux build:

| Requirement | URL/Comment | |---------------|-----------------------------------------------| | R | https://cran.r-project.org/bin/windows/ | | R packages | deSolve, NetIndices, knitr, rmarkdown | | pandoc | https://pandoc.org/ | | Texlive | https://www.tug.org/texlive/ |

Usually Linux distributions will have everything either already installed, or available for install via the system package manager.

At a terminal prompt, try:

> R CMD INSTALL StrathE2E2-master.tar.gz

The package will be installed in your local R library folder (often ~/R).

Windows build

Full requirements for Windows build:

| Requirement | URL/Comment | |---------------|-----------------------------------------------| | R | https://cran.r-project.org/bin/windows/ | | R packages | deSolve, NetIndices, knitr, rmarkdown | | Rtools | https://cran.r-project.org/bin/windows/Rtools | | pandoc | https://pandoc.org/ | | MikTeX | https://miktex.org/ | | pdfpages | https://ctan.org/pkg/pdfpages |

Install Rtools as administrator and make sure the box to Add rtools to the system PATH is checked.

Add the R bin folder to the system PATH as well. Go to Control Panel->System and Security->System then select Advanced system settings. Click on the Environment Variables button edit the PATH variable, adding the path to the R bin folder, something like:

> C:\Program Files\R\R-3.6.1\bin

If you upgrade R at a later date you must remember to update this PATH setting as well.

In a cmdtool navigate to working folder where the unpacked source code resides in a sub-folder.

Start R and run:

> library(devtools)
> document("StrathE2E2")

Then on command line:

> R CMD build StrathE2E2
> R CMD INSTALL --build StrathE2E2_3.3.0.tar.gz

This will build the binary package StrathE2E2_3.3.0.zip

MacOS X build

Full requirements for MacOS build:

| Requirement | URL/Comment | |---------------|-----------------------------------------------| | R | https://cran.r-project.org/bin/macosx | | R packages: | deSolve, NetIndices, knitr, rmarkdown | | X11 Quartz | https://www.xquartz.org/ | | pandoc | https://pandoc.org/ | | MacTeX | https://www.tug.org/mactex |

make sure to restart any terminal applications after installing these packages.

Within a Terminal, unpack the downloaded source package and install/build:

tar zxvf StrathE2E2_3.3.0.tar.gz
R CMD INSTALL --build StrathE2E2

If the command line developer tools are missing you should accept the offer of installing them.

A successful build will install the package in R, and there will also be a binary package file StrathE2E2_3.3.0.tgz created.

StrathE2E2 documentation built on Jan. 23, 2021, 1:07 a.m.