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)
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# 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
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:
- Origin of the model (previous versions)
- Overview of the model concepts and design
- Ecology model description
- Fishing fleet model description
- Parameter optimization, sensitivity and Monte Carlo methodology
How to cite the package:
citation("StrathE2E2")
'StrathE2E2' in publications use:
To cite package
R. (2021).
Heath, M.R., Speirs, D.C., Thurlbeck, I. and Wilson, : an R package for modelling the dynamics of marine food
StrathE2E2in Ecology and Evolution, 12, 280-287.
webs and fisheries. Methods
for LaTeX users is
A BibTeX entry
@Article{,
= {StrathE2E2: an R package for modelling the dynamics of marine food webs
title
and fisheries},= {Michael R. Heath and Douglas C. Speirs and Ian Thurlbeck and Robert Wilson},
author = {Methods in Ecology and Evolution},
journal = {12},
volume = {280-287},
pages = {2021},
year = {2041-210X},
issn = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13510},
url = {food web, dynamic model, ecosystem, fisheries,
keywords
ordinary differential equations, optimization, -Carlo, R},
sensitivity analysis, Monte }