simecol: 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. The package helps to organize scenarios (to avoid copy and paste) and aims to improve readability and usability of code.

AuthorThomas Petzoldt
Date of publication2016-11-19 18:30:18
MaintainerThomas Petzoldt <thomas.petzoldt@tu-dresden.de>
LicenseGPL (>= 2)
Version0.8-8
http://www.simecol.de/

View on R-Forge

Man pages

addtoenv: Add Functions from a Non-nested List of Named Functions to a...

approxTime: Linear Interpolation with Complete Matrices or Data Frames

as.simObj: Coerce simObj Objects to Lists and Vice-Versa

CA: Stochastic Cellular Automaton

chemostat: Chemostat Model

conway: The Classical Coway's Game of Life

diffusion: A Random Walk Particle Diffusion Model

editParms: Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects

eightneighbours: Count Number of Neighbours in a Rectangular Cellular Grid.

fitOdeModel: Parameter Fitting for odeModel Objects

fixParms: Fix 'parms', 'init' or 'times' Slot of 'simecol' Objects

fromtoby: Create Regular Sequence from 'from-to-by' Vector

initialize-methods: Methods for Function 'initialize' in Package 'simecol'

iteration: Discrete Simulation

listOrNULL: Helpful Union Classes

lv: Lotka-Volterra Predator-Prey Model

lv3: Lotka-Volterra-Type Model with Resource, Prey and Predator

mixNamedVec: Mix Two Named Vectors, Resolving Name Conflicts

modelFit: Class of Fitted Model Parameters

modelFit-methods: Show Results of Model Fits

neighbours: Count Number of Neighbours on a Rectangular Grid.

observer: Get or Set an Observer Functions to an 'simObj' Object

odeModel: Generating-functions (Constructors) to Create Objects of...

parms: Accessor Functions for 'simObj' Objects

p.constrain: Transform Data Between Unconstrained and Box-constrained...

pcuseries: Generate Plackett Bivariate Random Numbers

peaks: Find Peaks Within xy-Data

plot-methods: Methods for Function plot in Package 'simecol'

print-methods: Methods for Function 'print' in Package 'simecol'

sEdit: Simple editing

seedfill: Color Fill Algorithm

sim: Simulation of 'simObj' model objects

simecol-package: The 'simecol' Package

ssqOdeModel: Sum of Squares Between odeModel and Data

upca: The Uniform Period Chaotic Amplitude Model

Functions

[ Man page
[[ Man page
$ Man page
addtoenv Man page
alpha2rho Man page
approxTime Man page
approxTime1 Man page
as.list Man page
as.list,simObj-method Man page
as.simObj Man page
as.simObj,list-method Man page
CA Man page
chemostat Man page
coef,modelFit-method Man page
coerce,list,simObj-method Man page
coerce,simObj,list-method Man page
conway Man page
deviance,modelFit-method Man page
diffusion Man page
editInit Man page
editInit-methods Man page
editInit,simObj-method Man page
editParms Man page
editParms-methods Man page
editParms,simObj-method Man page
editTimes Man page
editTimes-methods Man page
editTimes,simObj-method Man page
eightneighbors Man page
eightneighbours Man page
equations Man page
equations<- Man page
equations<--methods Man page
equations-methods Man page
equations<-,simObj-method Man page
equations,simObj-method Man page
fitOdeModel Man page
fixInit Man page
fixInit-methods Man page
fixInit,simObj-method Man page
fixParms Man page
fixParms-methods Man page
fixParms,simObj-method Man page
fixTimes Man page
fixTimes-methods Man page
fixTimes,simObj-method Man page
fromtoby Man page
functionOrcharacter-class Man page
functionOrNULL-class Man page
gridModel Man page
gridModel-class Man page
indbasedModel Man page
indbasedModel-class Man page
init Man page
init<- Man page
initfunc Man page
initfunc<- Man page
initfunc<--methods Man page
initfunc-methods Man page
initfunc<-,simObj-method Man page
initfunc,simObj-method Man page
init<-,gridModel,ANY-method Man page
init<-,gridModel,matrix-method Man page
initialize Man page
initialize-methods Man page
initialize,simObj-method Man page
init<--methods Man page
init-methods Man page
init<-,simObj,ANY-method Man page
init,simObj-method Man page
inputs Man page
inputs<- Man page
inputs<--methods Man page
inputs-methods Man page
inputs<-,simObj-method Man page
inputs,simObj-method Man page
iteration Man page
iteration,gridModel-method Man page
iteration-methods Man page
iteration,numeric-method Man page
iteration,odeModel-method Man page
iteration,simObj-method Man page
listOrdata.frame-class Man page
listOrNULL-class Man page
lv Man page
lv3 Man page
main Man page
main<- Man page
main<--methods Man page
main-methods Man page
main<-,simObj-method Man page
main,simObj-method Man page
mixNamedVec Man page
modelFit-class Man page
[,modelFit-method Man page
[[,modelFit-method Man page
$,modelFit-method Man page
neighbors Man page
neighbours Man page
numericOrlist-class Man page
observer Man page
observer<- Man page
observer<--methods Man page
observer-methods Man page
observer<-,simObj-method Man page
observer,simObj-method Man page
odeModel Man page
odeModel-class Man page
out Man page
out<- Man page
out,gridModel-method Man page
out<--methods Man page
out-methods Man page
out,odeModel-method Man page
out<-,simObj-method Man page
out,simObj-method Man page
parms Man page
parms<- Man page
parms<--methods Man page
parms-methods Man page
parms<-,simObj-method Man page
parms,simObj-method Man page
p.constrain Man page
pcu Man page
pcuseries Man page
peaks Man page
plot Man page
plot,ANY,ANY-method Man page
plot,gridModel,missing-method Man page
plot-methods Man page
plot,odeModel,missing-method Man page
plot,odeModel,odeModel-method Man page
plot,rwalkModel,missing-method Man page
plot,simObj,missing-method Man page
print Man page
print,ANY-method Man page
print-methods Man page
print,simObj-method Man page
p.unconstrain Man page
rho2alpha Man page
rwalkModel Man page
rwalkModel-class Man page
sEdit Man page
seedfill Man page
show,simObj-method Man page
sim Man page
simecol Man page
simecol-package Man page
sim,gridModel-method Man page
sim-methods Man page
simObj Man page
simObj-class Man page
sim,odeModel-method Man page
sim,simObj-method Man page
solver Man page
solver<- Man page
solver<--methods Man page
solver-methods Man page
solver<-,simObj-method Man page
solver,simObj-method Man page
ssqOdeModel Man page
summary,modelFit-method Man page
times Man page
times<- Man page
times<--methods Man page
times-methods Man page
times<-,simObj-method Man page
times,simObj-method Man page
upca Man page

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/aaa_classes.R R/accessors.R R/addtoenv.R R/approxTime.R R/approxTime1.R R/coerce.R R/constructors.R R/edit.R R/fitOdeModel.R R/fromtoby.R R/iteration.R R/mixNamedVec.R R/modelFit.R R/neighbours.R R/p.constrain.R R/pcuseries.R R/peaks.R R/plot.R R/print.R R/sEdit.R R/seedfill.R R/sim.R R/ssqOdeModel.R
build
build/vignette.rds
data
data/CA.rda
data/chemostat.rda
data/conway.rda
data/diffusion.rda
data/lv.rda
data/lv3.rda
data/upca.rda
demo
demo/00Index
demo/jss.R
inst
inst/CITATION
inst/FAQ.txt
inst/NEWS
inst/THANKS
inst/doc
inst/doc/a-simecol-introduction.R
inst/doc/a-simecol-introduction.Rnw
inst/doc/a-simecol-introduction.pdf
inst/doc/b-simecol-howtos.R
inst/doc/b-simecol-howtos.Rnw
inst/doc/b-simecol-howtos.pdf
inst/doc/examples
inst/doc/examples/CA.R inst/doc/examples/chemostat.R inst/doc/examples/conway.R inst/doc/examples/diffusion_A.R inst/doc/examples/diffusion_B.R inst/doc/examples/diffusion_barrier.R
inst/doc/examples/dynload
inst/doc/examples/dynload/clotka.c
inst/doc/examples/dynload/simecol_clotka.R inst/doc/examples/dynload/test_clotka.R
inst/doc/examples/fitOdeModel
inst/doc/examples/fitOdeModel/initval.R inst/doc/examples/fitOdeModel/weighted.R inst/doc/examples/ibm_daphnia.R inst/doc/examples/logist.R inst/doc/examples/lv.R inst/doc/examples/lv3.R inst/doc/examples/lv3_approxfun.R inst/doc/examples/stoch_ca.R inst/doc/examples/stoch_ca_simple.R inst/doc/examples/upca.R
man
man/CA.Rd man/addtoenv.Rd man/approxTime.Rd man/as.simObj.Rd man/chemostat.Rd man/conway.Rd man/diffusion.Rd man/editParms.Rd man/eightneighbours.Rd man/fitOdeModel.Rd man/fixParms.Rd man/fromtoby.Rd man/initialize-methods.Rd man/iteration.Rd man/listOrNULL.Rd man/lv.Rd man/lv3.Rd man/mixNamedVec.Rd man/modelFit-methods.Rd man/modelFit.Rd man/neighbours.Rd man/observer.Rd man/odeModel.Rd man/p.constrain.Rd man/parms.Rd man/pcuseries.Rd man/peaks.Rd man/plot-methods.Rd man/print-methods.Rd man/sEdit.Rd man/seedfill.Rd man/sim.Rd man/simecol-package.Rd man/ssqOdeModel.Rd man/upca.Rd
src
src/simecol.c
vignettes
vignettes/a-simecol-introduction.Rnw
vignettes/a4wide.sty
vignettes/b-simecol-howtos.Rnw
vignettes/ca.pdf
vignettes/classes.pdf
vignettes/ibm_daphnia.R
vignettes/simecol.bib
vignettes/statespace.pdf
vignettes/vignette.cls

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.