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 * Overview

 * Download
    * Prerequisites
    * Installation

 * Examples
    * Lotka-Volterra
    * Conway’s Game of Life
    * Template

 * Documentation
    * Package docs
    * Publications
    * License
    * Author
    * Support

 * Links


R PACKAGE SIMECOL



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Quick links: Author +++ R-Forge Project page +++ CRAN

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OVERVIEW

simecol (simulation of ecological systems) is a lightweight R package that
employs an object oriented paradigm for the implementation of dynamic simulation
models.

The package is intended to give users (students and scientists) an interactive
environment to implement, distribute, simulate and document basic and advanced
ecological models without the need to write long simulation programs. An object
oriented approach is used to provide a consistent but still flexible and
extensible way to implement simulation models of different types:

 * ordinary differential equation (ODE) models,
 * non-spatial individual-based models,
 * grid-oriented individual-based models,
 * particle diffusion-type / random walk models
 * and more.

A simulation model is implemented as simecol object (simObj) with components
main, holding the main model equations, rules or arbitrary program code,
equations (optional, a list of possibly nested sub-models or sub-equations ),
parms with model parameters, init with the initial state, inputs (optional) for
external input data and times to define the simulation time and the time steps
used.

simecolModels is a simulation model collection, together with additional
classes, demos and experimental code.


DOWNLOAD


PREREQUISITES

 * simecol is based on R, a freely available system for statistical computation
   and graphics. Current versions are tested with R version 3.0 or above.
 * simecol depends on the deSolve package for numerical integration.
 * optional: the tcltk package is required for the graphical parameter editing
   functions
 * Operating systems: All operating systems on which R can be installed: Linux
   and other Unixes, Windows, Mac


INSTALLATION

The packages can be installed directly from the internet within R or Rstudio via
the menu or the R command line:

Stable Version:

install.packages("simecol")

Development versions:

install.packages("simecol", repos="http://R-Forge.R-project.org")
install.packages("simecolModels", repos="http://R-Forge.R-project.org")

Subversion (svn) access:

Anonymous SVN access (read only):

svn checkout svn://svn.r-forge.r-project.org/svnroot/simecol


EXAMPLES


LOTKA-VOLTERRA

library("simecol")
data(lv, package="simecol")
plot(sim(lv))


CONWAY’S GAME OF LIFE

library("simecol")
data(conway, package="simecol")
plot(sim(conway))
m <- matrix(0, 40, 40)
m[5:35,19:21] <-1
init(conway) <- m
sim(conway, animate=TRUE, delay=100, col=c("white", "green"), axes=FALSE)


TEMPLATE

The following example shows that the structure of a model object is just a
template.

library("simecol")
conway <- new("gridModel",
    main = function(time, init, parms) {
        x   <- init
        srv <- parms$srv
        gen <- parms$gen
        n   <- nrow(x)
        m   <- ncol(x)
        nb  <- eightneighbours(x)
        ## survival rule
        xsrv <- ifelse(x > 0 & (nb %in% srv), 1, 0)
        ## generation rule
        xgen <- ifelse(x == 0 & (nb %in% gen), 1, 0)
        x    <- as.numeric((xgen + xsrv)>0)
        dim(x) <- c(n,m)
    x
    },
    parms = list(srv=c(2, 3), gen=3),
    times = c(from=1, to=10, by=1),
    init = matrix(round(runif(40*40)), nrow=40, ncol=40),
    solver = "iteration"
)

plot(sim(conway))


DOCUMENTATION


PACKAGE DOCS

 * Reference Manual
 * Introduction to the simecol package
 * Simecol-Howto: Tips, Tricks and Building Blocks


PUBLICATIONS

 * Petzoldt, T. and K. Rinke (2007). simecol: An Object-Oriented Framework for
   Ecological Modeling in R. Journal of Statistical Software, 22(9), 1–31. pdf
 * Petzoldt, T. (2003). R as a Simulation Platform in Ecological Modelling.
   R-News 3(3), 8–16. pdf
 * Petzoldt, T., Rinke, K. and Kates, L. (2006) Population ecology modelling
   with R. A Comparison of Object Oriented Approaches. The R User Conference
   2006, Vienna, 2006-06-15 to 2006-06-17 slides
 * Petzoldt, T. (2008) Objects, Clones and Collections. Dynamic (Ecological)
   Models and Scenarios with simecol. The R User Conference 2008, Dortmund,
   2008-08-12 – 2008-08-14. slides


LICENSE

simecol, like R, is free open source software licensed under the GNU Public
License (GPL 2.0 or above). The software is provided as is and comes WITHOUT
WARRANTY.


AUTHOR

Thomas Petzoldt, Technische Universität Dresden, Institute of Hydrobiology


SUPPORT

Please send your questions to the R-SiG-Dynamic-Models mailing list.

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LINKS

 * Release version of simecol (from CRAN)
   * binaries, docs, sourcecode
 * Development versions of simecol and simecolModels (from R-Forge)
   * project overview page
   * package download
   * source code
 * Related work:
   * R package deSolve
   * R package FME
 * Thomas Petzoldt.

February 25th 2017