# Simulation of Ecological (and Other) Dynamic Systems

## Documentation for package ‘simecol’ version 0.9-2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

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

simecol-package | Simulation of Ecological (and Other) Dynamic Systems

## -- 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-method | Coerce simObj Objects to Lists and Vice-Versa
as.simObj | Coerce simObj Objects to Lists and Vice-Versa
as.simObj-method | Coerce simObj Objects to Lists and Vice-Versa

## -- C --

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

## -- D --

deviance-method | Show Results of Model Fits
diffusion | A Random Walk Particle Diffusion Model

## -- E --

editInit | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
editInit-method | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
editInit-methods | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
editParms | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
editParms-method | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
editParms-methods | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
editTimes | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
editTimes-method | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
editTimes-methods | Edit 'parms', 'init' or 'times' Slot of 'simecol' Objects
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-method | Accessor Functions for 'simObj' Objects
equations-methods | Accessor Functions for 'simObj' Objects
equations<- | Accessor Functions for 'simObj' Objects
equations<--method | Accessor Functions for 'simObj' Objects
equations<--methods | Accessor Functions for 'simObj' Objects

## -- F --

fitOdeModel | Parameter Fitting for odeModel 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 | Simulation of Ecological (and Other) Dynamic Systems

## -- I --

indbasedModel | Generating-functions (Constructors) to Create Objects of Classes 'odeModel', 'rwalkModel' and 'gridModel'.
indbasedModel-class | Simulation of Ecological (and Other) Dynamic Systems
init | Accessor Functions for 'simObj' Objects
init-method | Accessor Functions for 'simObj' Objects
init-methods | Accessor Functions for 'simObj' Objects
init<- | Accessor Functions for 'simObj' Objects
init<--method | Accessor Functions for 'simObj' Objects
init<--methods | Accessor Functions for 'simObj' Objects
initfunc | Accessor Functions for 'simObj' Objects
initfunc-method | Accessor Functions for 'simObj' Objects
initfunc-methods | Accessor Functions for 'simObj' Objects
initfunc<- | Accessor Functions for 'simObj' Objects
initfunc<--method | Accessor Functions for 'simObj' Objects
initfunc<--methods | Accessor Functions for 'simObj' Objects
initialize-method | Methods for Function 'initialize' in Package 'simecol'
initialize-methods | Methods for Function 'initialize' in Package 'simecol'
inputs | Accessor Functions for 'simObj' Objects
inputs-method | Accessor Functions for 'simObj' Objects
inputs-methods | Accessor Functions for 'simObj' Objects
inputs<- | Accessor Functions for 'simObj' Objects
inputs<--method | Accessor Functions for 'simObj' Objects
inputs<--methods | Accessor Functions for 'simObj' Objects
iteration | Discrete Simulation
iteration-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-method | Accessor Functions for 'simObj' Objects
main-methods | Accessor Functions for 'simObj' Objects
main<- | Accessor Functions for 'simObj' Objects
main<--method | Accessor Functions for 'simObj' Objects
main<--methods | Accessor Functions for 'simObj' Objects
mixNamedVec | Mix Two Named Vectors, Resolving Name Conflicts
modelFit-class | Class of Fitted Model Parameters

## -- N --

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

## -- O --

observer | Get or Set an Observer Functions to an 'simObj' Object
observer-method | Get or Set an Observer Functions to an 'simObj' Object
observer-methods | Get or Set an Observer Functions to an 'simObj' Object
observer<- | Get or Set an Observer Functions to an 'simObj' Object
observer<--method | Get or Set an Observer Functions to an 'simObj' Object
observer<--methods | Get or Set an Observer Functions to an 'simObj' Object
odeModel | Generating-functions (Constructors) to Create Objects of Classes 'odeModel', 'rwalkModel' and 'gridModel'.
odeModel-class | Simulation of Ecological (and Other) Dynamic Systems
out | Accessor Functions for 'simObj' Objects
out-method | Accessor Functions for 'simObj' Objects
out-methods | Accessor Functions for 'simObj' Objects
out<- | Accessor Functions for 'simObj' Objects
out<--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-method | Accessor Functions for 'simObj' Objects
parms-methods | Accessor Functions for 'simObj' Objects
parms<- | Accessor Functions for 'simObj' Objects
parms<--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-method | Methods for Function plot in Package 'simecol'
plot-methods | Methods for Function plot in Package 'simecol'
print-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 | Simulation of Ecological (and Other) Dynamic Systems

## -- S --

sEdit | Simple editing
seedfill | Color Fill Algorithm
show-method | Methods for Function 'print' in Package 'simecol'
sim | Simulation of 'simObj' model objects
sim-method | Simulation of 'simObj' model objects
sim-methods | Simulation of 'simObj' model objects
simecol | Simulation of Ecological (and Other) Dynamic Systems
simObj | Simulation of Ecological (and Other) Dynamic Systems
simObj-class | Simulation of Ecological (and Other) Dynamic Systems
solver | Accessor Functions for 'simObj' Objects
solver-method | Accessor Functions for 'simObj' Objects
solver-methods | Accessor Functions for 'simObj' Objects
solver<- | Accessor Functions for 'simObj' Objects
solver<--method | Accessor Functions for 'simObj' Objects
solver<--methods | Accessor Functions for 'simObj' Objects
ssqOdeModel | Sum of Squares Between odeModel and Data
summary-method | Show Results of Model Fits

## -- T --

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

## -- U --

upca | The Uniform Period Chaotic Amplitude Model

## -- misc --

$ | Show Results of Model Fits
$-method | Show Results of Model Fits
[ | Show Results of Model Fits
[-method | Show Results of Model Fits
[[ | Show Results of Model Fits
[[-method | Show Results of Model Fits