Simulation of Ecological (and Other) Dynamic Systems

An object oriented framework to simulate ecological (and other) dynamic systems. It can be used for differential equations, individual-based (or agent-based) and other models as well. It supports structuring of simulation scenarios (to avoid copy and paste) and aims to improve readability and re-usability of code.


0.8-10 o vignette updates

0.8-9 o register native routines o "fix..."-methods removed to fulfil CRAN policy, footnote in vignette

0.8-8 o correct omegahat web link o replace "fix..." . methods with workspace independent "edit"-methods

0.8-7 o enable newuoa and bobyqa optimizers from package minqa o small updates to help files and vignette

0.8-6 o use tcltk::-calls o enable automatic vignette index o add new model "diffusion_barrier.R" to doc/examples

0.8-5 o requireNamespace instead of require for tcltk

0.8-4 o addtoenv for parameters (experimental and only for class indbasedModel)

0.8-3 o double buffering for animation plots

0.8-2 o removed obsolete files in installation o moved vignette source files to /vignettes o update of package help page

0.8-1 o fix bug in seedfill function

0.8 o periodic boundary conditions in neighbours o compatibility tweaks o updated examples

0.7-2 o remove two other obsolete files from inst/doc

0.7-1 o fix documentation notes and a warning

0.7 o "inputs" is now passed explicitly to sim "odeModel" o fix namespace issue

0.6-11 o fixed NOTE about missing depends on lattice in one of the examples

0.6-10 o moved examples to /doc/examples o improve documentation of 'observer' o fixed bug that "time" was called "times" in out of iteration solver o documentation updates and fixes


o documentation fixes

0.6-8 o remove dependency on FME (until FME is released) o documentation improvements o release

0.6-7 o fixed bug in documentation example for iteration-solver o fixed documentation warning for plot-methods

0.6-6 o tested on Linux x64 with gcc and Sun Studio 12 compilers o vignette improvements

0.6-5 o changed: simecol.cpp to simecol.c to avoid C++ (we didn't need it yet)

0.6-4 o try to fix comptibility issue with Sun Studio compiler

0.6-3 o remove Rdversion, back compatibility with R 2.8.1 o submitted to CRAN

0.6-2 o fitOdeModel supports now PORT algorithm (nlminb) o documentation improvements o first version of "simecol-howto" o new utility mixNamedVec o submitted to CRAN

0.6-1 o start writing new vignette "simecol-howto" o data frame conversion for outputs of class odeModel now only for matrices and in out, not in sim.

0.6 o new class indbasedModel o new slot "observer" o .Rdata files re-generated (with observer slot) o simulation re-initializes objects that have an initfunc o example of an ODE model that passes compiled code directly to the solver o this is the useR!2008 (Dortmund) release

0.5-7 o the package uses now deSolve instead of odesolve o euler is now imported from deSolve and removed from simecol o allow solver slot to contain not only character but also function o plain version of JSS publication added as vignette

0.5-6 o small improvements and updates

0.5-5 o reworked ODE solvers, rk4 and lsoda generics removed, solvers are now called directly from sim, ensures compatibility with the deSolve package without the need to write generics for all possible (and future) ode solvers o rehabilitation of addtoenv() o documentation updates o replacement functions now delete slot "out"

0.5-4 o experimental code for parameter fitting of ODE models

0.5-3 o added citation of JSS article about simecol o removed obsolete \non_function{} entry from documentation o conversion of simObj to and from lists, as.list and as.simObj o bivariate uniform random numbers (Plackett distribution)

0.5-2 o tcltk is now Suggested again (possible due to relaxed package check conditions)

0.5-1 o fixed obsolete braces in .Rd's

0.5 o tcltk is now mandatory (in Depends), to solve issue with package check under R 2.6.0 (under development) o check for empty out-slot in plot methods o obsolete comments removed o small documentation updates

  • addtoenv may be removed in the future o version 0.5 is used in the upcoming JSS article

0.4-3 o addtoenv() is no longer used in the solver functions o standard conform accessor functions --> Attention: old applications may need adaptions! o added demo("jss", package="simecol") o new examples, small code and documentation improvements

0.4-2 o helper classes: listOrNULL and functionOrNULL o new slot initfunc, initialize method and complete rewrite of constructors o new print and show methods o general code cleanup and several bugfixes o documentation improvements

0.4-1 o general code cleanup o iteration is now a generic function o ... argument added to get-functions o argument "last" in out()

0.3-14 o euler method for numerical integration

0.3-11 - 0.3-13 several bugfixes and documentation improvements

0.3-10 o some bug fixes and error checking in the accessor functions

0.3-9 o documentation improvements

0.3-8 o made rk4 a generic. This required to include a copy of the original rk4 from the odesolve package but this cosmetic issue will be fixed as soon as possible o improvements of documentation

0.3-7 o renamed class rndwalkModel to rwalkModel o code cleanup and error checking o changed implementation of 'selfrefer' and renamed to 'addtoenv' o documentation issues o bugfixes

0.3-6 o version presented at useR-2006 o slot 'equations' renamed to 'main' o new slot 'equations' holding sub-equations callable in main

0.3.1 ... 0.3.5 o complete rewrite using S4 classes instead of S3 lists o rename of classes and several functions o several examples and utility functions removed, they will appear again in future versions, separate packages or as downloadable examples on WWW. o the 0.3 branch is incompatible to 0.2.x versions of simecol o if you have problems porting old models, please ask me for assistance.

Reference manual

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0.8-14 by Thomas Petzoldt, 2 months ago

Browse source code at

Authors: Thomas Petzoldt [aut, cre]

Documentation:   PDF Manual  

Task views: Chemometrics and Computational Physics, Differential Equations, Analysis of Ecological and Environmental Data

GPL (>= 2) license

Imports graphics, grDevices, stats, utils, minqa

Depends on deSolve, methods

Suggests tcltk, FME, lattice

See at CRAN