Multi-Species sIZE Spectrum Modelling in R

A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.


mizer is a package that implements size-based ecological models. The package has been developed to model marine ecosystems that are subject to fishing. However, it may also be appropriate for other ecosystems.

The package contains routines and methods to allow users to set up the model community, and then project it through time under different fishing strategies.

Methods are included to explore the results, including plots and calculation of community indicators such as the slope of the size spectrum. Size-based models can be complicated so mizer contains many default options that can be easily changed by the user.

See the accompanying vignette, "mizer_vignette", for more details on how the package works including detailed examples.

News

mizer 0.4

  • Improvements made to the speed by evaluating convolution sums via fft, removing the bottlenecks in getPhiPrey() and getPredRate().
  • Using C++ for the inner loop in the project method for extra speed.
  • Minor corrections to vignette and documentation to bring them into alignment and to document the new home on github and new maintainers.

mizer 0.3

  • Improvements made to the speed of the simulations. Remaining bottle necks are the sweep statements in getPhiPrey() and getPredRate().
  • Moved tests to new suggested folder.
  • Minor changes to documentation to pass new check requirements.

mizer 0.2

  • Release to coincide with the submission of the MEE paper. No major changes. Just minor bug fixes.

mizer 0.1

  • Beta release - just about works but still some gremlins to sort out. There are a number of features I'd like to add in the coming relases.

Reference manual

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install.packages("mizer")

1.0 by Gustav Delius, 2 months ago


Browse source code at https://github.com/cran/mizer


Authors: Finlay Scott [aut, cph], Julia Blanchard [aut, cph], Ken Andersen [aut, cph], Gustav Delius [ctb, cre], Richard Southwell [ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports deSolve, ggplot2, grid, methods, plyr, progress, Rcpp, reshape2

Suggests testthat, roxygen2, knitr, shiny, shinyBS

Linking to Rcpp


See at CRAN