Chapter 3 Installing the package

Install the package from within an R session using:

install.packages("StrathE2E2", 
                 repos="https://www.marineresourcemodelling.maths.strath.ac.uk/sran/")


Alternatively, download the installation zip file for your operating system from https://www.marineresourcemodelling.maths.strath.ac.uk/strathe2e/index.html and install into your R version.


Note that Strathe2E2 requires installation of the following additional packages which are available from any CRAN site:

  • deSolve

  • NetIndices


Further information on building the package from the source code is available at the StrathE2E GitLab site and repository


3.1 Installing the supplementary data-package

The model package has a supplementary data-package - Strathe2E2examples - which contains example outputs from the more computationally intensive functions in the package. These are provided to illustrate the performance of various post-processing and plotting functions for these analyses that are available.


Manually install the package using:

install.packages("StrathE2E2examples", 
                 repos="https://www.marineresourcemodelling.maths.strath.ac.uk/sran/")

Once installed details of the data sets are available by typing:

library(StrathE2E2examples)
help(StrathE2E2examples)


<!--chapter:end:02-installation.Rmd-->

# Initial tour of the package

**To see an overview of the StrathE2E2 package, launch an R-session and then:**    

```r
library(StrathE2E2)     # Load the package
help(StrathE2E2)        # Launch the overview document in a browser window


The package overview contains links to help and example pages for each of the available functions. These are also acessible by typing, for example:

help(e2e_run)        # Launch the help page for the e2e_run function in a browser window


Cheatsheet - quick-reference guide to StrathE2E2 functions


Reference Manual - compilation of the help pages for all the package functions generated by CRAN-check


User Manual - guide to using the package


Technical Manual - documentation on the structure of input and output R-objects and files


In addition the following supporting documents are available:




How to cite the package:

citation("StrathE2E2")

To cite package 'StrathE2E2' in publications use:

  Heath, M.R., Speirs, D.C., Thurlbeck, I. and Wilson, R. (2021).
  StrathE2E2: an R package for modelling the dynamics of marine food
  webs and fisheries. Methods in Ecology and Evolution, 12, 280-287.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {StrathE2E2: an R package for modelling the dynamics of marine food webs 
          and fisheries},
    author = {Michael R. Heath and Douglas C. Speirs and Ian Thurlbeck and Robert Wilson},
    journal = {Methods in Ecology and Evolution},
    volume = {12},
    pages = {280-287},
    year = {2021},
    issn = {2041-210X},
    url = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13510},
    keywords = {food web, dynamic model, ecosystem, fisheries, 
                 ordinary differential equations, optimization, 
                 sensitivity analysis, Monte-Carlo, R},
  }