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## initialize methods and constructors (generating functions)
## the initialize method is called by new
## simObj initialize first calls the default
## initialize and then (if available) an object (instance!) specific
## function stored in slot "initfunc" where "initfunc" has access to all
## functions stored in the equations list (see ?addtoenv)
##
## the constructors are provided for compatibility with older releases
## of simecol and may / or may not be deprecated in future versions
setMethod("initialize", signature(.Object="simObj"),
function(.Object, ...) {
.Object <- callNextMethod()
## delete outputs from former simulations
.Object@out <- NULL
if (is.function(.Object@initfunc)) {
initfunc <- .Object@initfunc
equations <- .Object@equations
environment(initfunc) <- environment()
environment(main) <- environment()
#attach(equations)
#on.exit(detach(equations))
equations <- addtoenv(equations)
.Object <- initfunc(.Object)
}
invisible(.Object)
}
)
## constructors ('generating functions')
simObj <- function(obj, main=NULL, equations=NULL,
times=c(from=0, to=10, by=1),
init=matrix(0), parms=list(), inputs=NULL,
solver="iteration", initfunc=NULL) {
if (is(obj, "simObj")) {
obj <- initialize(obj)
} else {
obj <- new("simObj", main=main,
equations=equations, times=times,
init=init, parms=parms, inputs=inputs, solver=solver,
initfunc=initfunc)
}
invisible(obj)
}
odeModel <- function(obj=NULL, main=NULL, equations=NULL,
times=c(from=0, to=10, by=1),
init=numeric(0), parms=numeric(0), inputs=NULL,
solver="rk4", initfunc=NULL) {
if (is(obj, "odeModel")) {
obj <- initialize(obj)
} else {
obj <- new("odeModel", main=main,
equations=equations, times=times,
init=init, parms=parms, inputs=inputs, solver=solver,
initfunc=initfunc)
}
invisible(obj)
}
gridModel <- function(obj=NULL, main=NULL, equations=NULL,
times=c(from=0, to=10, by=1),
init=matrix(0), parms=list(), inputs=NULL,
solver="iteration", initfunc=NULL) {
if (is(obj, "gridModel")) {
obj <- initialize(obj)
} else {
obj <- new("gridModel", main=main,
equations=equations, times=times,
init=init, parms=parms, inputs=inputs, solver=solver,
initfunc=initfunc)
}
invisible(obj)
}
rwalkModel <- function(obj=NULL, main=NULL, equations=NULL,
times=c(from=0, to=10, by=1),
init=NULL, parms=list(), inputs=NULL,
solver="iteration", initfunc=NULL) {
if (is(obj, "rwalkModel")) {
obj <- initialize(obj)
} else {
obj <- new("rwalkModel", main=main,
equations=equations, times=times,
init=init, parms=parms, inputs=inputs, solver=solver,
initfunc=initfunc)
}
invisible(obj)
}
indbasedModel <- function(obj=NULL, main=NULL, equations=NULL,
times=c(from=0, to=10, by=1),
init=NULL, parms=list(), inputs=NULL,
solver="iteration", initfunc=NULL) {
if (is(obj, "indbasedModel")) {
obj <- initialize(obj)
} else {
obj <- new("indbasedModel", main=main,
equations=equations, times=times,
init=init, parms=parms, inputs=inputs, solver=solver,
initfunc=initfunc)
}
invisible(obj)
}
## === template to derive your own initialize method ===
#setMethod("initialize",
# signature(.Object="odeModel"),
# function(.Object, ...) {
# ## ~~ put your initialization code here ~~
# callNextMethod()
# }
#)
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