Simulation of ecological (and other) dynamic systems

Documentation for package ‘simecol’ version 0.5-5

Help Pages

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

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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<-,simObj-method	Accessor Functions for ‘simObj’ Objects
equations<--methods	Accessor Functions for ‘simObj’ Objects
euler	Euler Integration
euler,numeric-method	Euler Integration
euler,odeModel-method	Euler Integration
euler-methods	Euler Integration

-- 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
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 --

init	Accessor Functions for ‘simObj’ Objects
init,simObj-method	Accessor Functions for ‘simObj’ Objects
init-methods	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<-,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<-,simObj-method	Accessor Functions for ‘simObj’ Objects
inputs<--methods	Accessor Functions for ‘simObj’ Objects
iteration	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<-,simObj-method	Accessor Functions for ‘simObj’ Objects
main<--methods	Accessor Functions for ‘simObj’ Objects

-- 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 --

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<-,simObj-method	Accessor Functions for ‘simObj’ Objects
out<--methods	Accessor Functions for ‘simObj’ Objects

-- P --

p.constrain	Transform data between unconstrained and box box-constrained scale
p.unconstrain	Transform data between unconstrained and box 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<-,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<-,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<-,simObj-method	Accessor Functions for ‘simObj’ Objects
times<--methods	Accessor Functions for ‘simObj’ Objects

-- U --

upca	The Uniform Period Chaotic Amplitude Model