simecol: Simulation of Ecological (and Other) Dynamic Systems
Version 0.8-7

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.

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AuthorThomas Petzoldt
Date of publication2015-09-03 13:26:50
MaintainerThomas Petzoldt <thomas.petzoldt@tu-dresden.de>
LicenseGPL (>= 2)
Version0.8-7
URL http://www.simecol.de/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("simecol")

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

Files

inst
inst/CITATION
inst/NEWS
inst/FAQ.txt
inst/THANKS
inst/doc
inst/doc/examples
inst/doc/examples/diffusion_barrier.R
inst/doc/examples/lv3.R
inst/doc/examples/upca.R
inst/doc/examples/dynload
inst/doc/examples/dynload/simecol_clotka.R
inst/doc/examples/dynload/clotka.c
inst/doc/examples/dynload/test_clotka.R
inst/doc/examples/stoch_ca_simple.R
inst/doc/examples/diffusion_A.R
inst/doc/examples/ibm_daphnia.R
inst/doc/examples/CA.R
inst/doc/examples/lv.R
inst/doc/examples/fitOdeModel
inst/doc/examples/fitOdeModel/initval.R
inst/doc/examples/fitOdeModel/weighted.R
inst/doc/examples/diffusion_B.R
inst/doc/examples/logist.R
inst/doc/examples/stoch_ca.R
inst/doc/examples/conway.R
inst/doc/examples/lv3_approxfun.R
inst/doc/examples/chemostat.R
inst/doc/a-simecol-introduction.pdf
inst/doc/b-simecol-howtos.Rnw
inst/doc/a-simecol-introduction.R
inst/doc/a-simecol-introduction.Rnw
inst/doc/b-simecol-howtos.R
inst/doc/b-simecol-howtos.pdf
src
src/simecol.c
NAMESPACE
demo
demo/00Index
demo/jss.R
data
data/lv.rda
data/upca.rda
data/chemostat.rda
data/CA.rda
data/lv3.rda
data/conway.rda
data/diffusion.rda
R
R/coerce.R
R/accessors.R
R/approxTime1.R
R/sEdit.R
R/plot.R
R/seedfill.R
R/peaks.R
R/ssqOdeModel.R
R/p.constrain.R
R/mixNamedVec.R
R/approxTime.R
R/fromtoby.R
R/print.R
R/fitOdeModel.R
R/addtoenv.R
R/sim.R
R/aaa_classes.R
R/iteration.R
R/modelFit.R
R/pcuseries.R
R/neighbours.R
R/constructors.R
vignettes
vignettes/simecol.bib
vignettes/a4wide.sty
vignettes/b-simecol-howtos.Rnw
vignettes/ca.pdf
vignettes/ibm_daphnia.R
vignettes/vignette.cls
vignettes/statespace.pdf
vignettes/a-simecol-introduction.Rnw
vignettes/classes.pdf
MD5
build
build/vignette.rds
DESCRIPTION
man
man/chemostat.Rd
man/eightneighbours.Rd
man/plot-methods.Rd
man/modelFit-methods.Rd
man/modelFit.Rd
man/neighbours.Rd
man/iteration.Rd
man/sEdit.Rd
man/fitOdeModel.Rd
man/fixParms.Rd
man/seedfill.Rd
man/mixNamedVec.Rd
man/upca.Rd
man/initialize-methods.Rd
man/listOrNULL.Rd
man/pcuseries.Rd
man/lv.Rd
man/CA.Rd
man/lv3.Rd
man/conway.Rd
man/peaks.Rd
man/simecol-package.Rd
man/observer.Rd
man/diffusion.Rd
man/print-methods.Rd
man/addtoenv.Rd
man/ssqOdeModel.Rd
man/approxTime.Rd
man/as.simObj.Rd
man/p.constrain.Rd
man/fromtoby.Rd
man/sim.Rd
man/parms.Rd
man/odeModel.Rd
.Rinstignore
simecol documentation built on May 19, 2017, 4:13 p.m.