# Simulation of ecological (and other) dynamic systems

## Documentation for package ‘simecol’ version 0.6-9

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A C D E F G I L M N O P R S T U

## -- --

simecol-package | General Information about the 'simecol' Package

## -- A --

addtoenv | Add Functions from a Non-nested List of Named Functions to a Common Environment
alpha2rho | Generate Plackett Bivariate Random Numbers
approxTime | Linear Interpolation with Complete Matrices or Data Frames
approxTime1 | Linear Interpolation with Complete Matrices or Data Frames
as.list,simObj-method | Coerce simObj Objects to Lists and Vice-Versa
as.simObj | Coerce simObj Objects to Lists and Vice-Versa
as.simObj,list-method | Coerce simObj Objects to Lists and Vice-Versa

## -- C --

CA | Stochastic Cellular Automaton
chemostat | Chemostat Model
coerce,list,simObj-method | Coerce simObj Objects to Lists and Vice-Versa
coerce,simObj,list-method | Coerce simObj Objects to Lists and Vice-Versa
conway | The Classical Coway's Game of Life

## -- D --

diffusion | A Random Walk Particle Diffusion Model

## -- E --

eightneighbors | Count Number of Neighbours in a Rectangular Cellular Grid.
eightneighbours | Count Number of Neighbours in a Rectangular Cellular Grid.
equations | Accessor Functions for 'simObj' Objects
equations,simObj-method | Accessor Functions for 'simObj' Objects
equations-methods | Accessor Functions for 'simObj' Objects
equations<- | Accessor Functions for 'simObj' Objects
equations<-,simObj-method | Accessor Functions for 'simObj' Objects
equations<--methods | Accessor Functions for 'simObj' Objects

## -- F --

fitOdeModel | Parameter Fitting for odeModel Objects
fixInit | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fixInit,simObj-method | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fixInit-methods | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fixParms | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fixParms,simObj-method | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fixParms-methods | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fixTimes | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fixTimes,simObj-method | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fixTimes-methods | Fix 'parms', 'init' or ''imes' Slot of 'simecol' Objects
fromtoby | Create Regular Sequence from 'from-to-by' Vector
functionOrcharacter-class | Helpful Union Classes
functionOrNULL-class | Helpful Union Classes

## -- G --

gridModel | Generating-functions (Constructors) to Create Objects of Classes 'odeModel', 'rwalkModel' and 'gridModel'.
gridModel-class | General Information about the 'simecol' Package

## -- I --

indbasedModel | Generating-functions (Constructors) to Create Objects of Classes 'odeModel', 'rwalkModel' and 'gridModel'.
indbasedModel-class | General Information about the 'simecol' Package
init | Accessor Functions for 'simObj' Objects
init,simObj-method | Accessor Functions for 'simObj' Objects
init-methods | Accessor Functions for 'simObj' Objects
init<- | Accessor Functions for 'simObj' Objects
init<-,gridModel,ANY-method | Accessor Functions for 'simObj' Objects
init<-,gridModel,matrix-method | Accessor Functions for 'simObj' Objects
init<-,simObj,ANY-method | Accessor Functions for 'simObj' Objects
init<--methods | Accessor Functions for 'simObj' Objects
initfunc | Accessor Functions for 'simObj' Objects
initfunc,simObj-method | Accessor Functions for 'simObj' Objects
initfunc-methods | Accessor Functions for 'simObj' Objects
initfunc<- | Accessor Functions for 'simObj' Objects
initfunc<-,simObj-method | Accessor Functions for 'simObj' Objects
initfunc<--methods | Accessor Functions for 'simObj' Objects
initialize,simObj-method | Methods for Function 'initialize' in Package 'simecol'
initialize-methods | Methods for Function 'initialize' in Package 'simecol'
inputs | Accessor Functions for 'simObj' Objects
inputs,simObj-method | Accessor Functions for 'simObj' Objects
inputs-methods | Accessor Functions for 'simObj' Objects
inputs<- | Accessor Functions for 'simObj' Objects
inputs<-,simObj-method | Accessor Functions for 'simObj' Objects
inputs<--methods | Accessor Functions for 'simObj' Objects
iteration | Discrete Simulation
iteration,gridModel-method | Discrete Simulation
iteration,numeric-method | Discrete Simulation
iteration,odeModel-method | Discrete Simulation
iteration,simObj-method | Discrete Simulation
iteration-methods | Discrete Simulation

## -- L --

listOrdata.frame-class | Helpful Union Classes
listOrNULL-class | Helpful Union Classes
lv | Lotka-Volterra Predator-Prey Model
lv3 | Lotka-Volterra-Type Model with Resource, Prey and Predator

## -- M --

main | Accessor Functions for 'simObj' Objects
main,simObj-method | Accessor Functions for 'simObj' Objects
main-methods | Accessor Functions for 'simObj' Objects
main<- | Accessor Functions for 'simObj' Objects
main<-,simObj-method | Accessor Functions for 'simObj' Objects
main<--methods | Accessor Functions for 'simObj' Objects
mixNamedVec | Mix Two Named Vectors, Resolving Name Conflicts

## -- N --

neighbors | Count Number of Neighbours in a Rectangular Cellular Grid.
neighbours | Count Number of Neighbours in a Rectangular Cellular Grid.
numericOrlist-class | Helpful Union Classes

## -- O --

observer | Accessor Functions for 'simObj' Objects
observer,simObj-method | Accessor Functions for 'simObj' Objects
observer-methods | Accessor Functions for 'simObj' Objects
observer<- | Accessor Functions for 'simObj' Objects
observer<-,simObj-method | Accessor Functions for 'simObj' Objects
observer<--methods | Accessor Functions for 'simObj' Objects
odeModel | Generating-functions (Constructors) to Create Objects of Classes 'odeModel', 'rwalkModel' and 'gridModel'.
odeModel-class | General Information about the 'simecol' Package
out | Accessor Functions for 'simObj' Objects
out,gridModel-method | Accessor Functions for 'simObj' Objects
out,odeModel-method | Accessor Functions for 'simObj' Objects
out,simObj-method | Accessor Functions for 'simObj' Objects
out-methods | Accessor Functions for 'simObj' Objects
out<- | Accessor Functions for 'simObj' Objects
out<-,simObj-method | Accessor Functions for 'simObj' Objects
out<--methods | Accessor Functions for 'simObj' Objects

## -- P --

p.constrain | Transform Data Between Unconstrained and Box-constrained Scale
p.unconstrain | Transform Data Between Unconstrained and Box-constrained Scale
parms | Accessor Functions for 'simObj' Objects
parms,simObj-method | Accessor Functions for 'simObj' Objects
parms-methods | Accessor Functions for 'simObj' Objects
parms<- | Accessor Functions for 'simObj' Objects
parms<-,simObj-method | Accessor Functions for 'simObj' Objects
parms<--methods | Accessor Functions for 'simObj' Objects
pcu | Generate Plackett Bivariate Random Numbers
pcuseries | Generate Plackett Bivariate Random Numbers
peaks | Find Peaks Within xy-Data
plot,ANY,ANY-method | Methods for Function plot in Package 'simecol'
plot,gridModel,missing-method | Methods for Function plot in Package 'simecol'
plot,odeModel,missing-method | Methods for Function plot in Package 'simecol'
plot,rwalkModel,missing-method | Methods for Function plot in Package 'simecol'
plot,simObj,missing-method | Methods for Function plot in Package 'simecol'
plot-methods | Methods for Function plot in Package 'simecol'
print,ANY-method | Methods for Function 'print' in Package 'simecol'
print,simObj-method | Methods for Function 'print' in Package 'simecol'
print-methods | Methods for Function 'print' in Package 'simecol'

## -- R --

rho2alpha | Generate Plackett Bivariate Random Numbers
rwalkModel | Generating-functions (Constructors) to Create Objects of Classes 'odeModel', 'rwalkModel' and 'gridModel'.
rwalkModel-class | General Information about the 'simecol' Package

## -- S --

sEdit | Simple editing
seedfill | Color Fill Algorithm
show,simObj-method | Methods for Function 'print' in Package 'simecol'
sim | Simulation of 'simObj' model objects
sim,gridModel-method | Simulation of 'simObj' model objects
sim,odeModel-method | Simulation of 'simObj' model objects
sim,simObj-method | Simulation of 'simObj' model objects
sim-methods | Simulation of 'simObj' model objects
simecol | General Information about the 'simecol' Package
simObj | General Information about the 'simecol' Package
simObj-class | General Information about the 'simecol' Package
solver | Accessor Functions for 'simObj' Objects
solver,simObj-method | Accessor Functions for 'simObj' Objects
solver-methods | Accessor Functions for 'simObj' Objects
solver<- | Accessor Functions for 'simObj' Objects
solver<-,simObj-method | Accessor Functions for 'simObj' Objects
solver<--methods | Accessor Functions for 'simObj' Objects
ssqOdeModel | Sum of Squares Between odeModel and Data

## -- T --

times | Accessor Functions for 'simObj' Objects
times,simObj-method | Accessor Functions for 'simObj' Objects
times-methods | Accessor Functions for 'simObj' Objects
times<- | Accessor Functions for 'simObj' Objects
times<-,simObj-method | Accessor Functions for 'simObj' Objects
times<--methods | Accessor Functions for 'simObj' Objects

## -- U --

upca | The Uniform Period Chaotic Amplitude Model