version 0.5-7

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: simecol 
-Version: 0.5-5
-Date: 2008-04-05 
+Version: 0.5-7
+Date: 2008-06-25 
 Title: Simulation of ecological (and other) dynamic systems
 Author: Thomas Petzoldt
-Depends: R (>= 2.3.0), odesolve, methods
+Depends: R (>= 2.3.0), deSolve, methods
 Suggests: tcltk
 LazyLoad: yes
 Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de> 
 Description: Object oriented framework to simulate ecological (and other) dynamic systems
 License: GPL (>= 2)  
 URL: http://www.simecol.de/
-Packaged: Tue Apr  8 04:58:01 2008; theussl
+Packaged: Tue Jul  1 04:49:08 2008; theussl

NAMESPACE

@@ -4,10 +4,10 @@ useDynLib(simecol, .registration = TRUE)
 
 importFrom(graphics, plot)
 
-import(odesolve)
+import(deSolve)
 
 exportClasses(simObj, odeModel, gridModel, rwalkModel)
-exportClasses(numericOrlist,listOrNULL,functionOrNULL,listOrdata.frame)
+exportClasses(numericOrlist,listOrNULL,functionOrNULL,listOrdata.frame,functionOrcharacter)
 
 exportMethods(sim, parms, "parms<-", init, "init<-", times, "times<-")
 exportMethods(inputs, "inputs<-", main, "main<-", equations, "equations<-")
@@ -27,8 +27,8 @@ export(simObj, odeModel, gridModel, rwalkModel)
 export(addtoenv, fromtoby)
 export(neighbours, neighbors, eightneighbours, eightneighbors, seedfill)
 export(approxTime, approxTime1, sEdit, peaks)
-export(euler, iteration)
-#export(rk4, lsoda)
+export(iteration)
+#export(euler, rk4, lsoda) # from deSolve
 
 ## parameter fitting
 export(ssqOdeModel, fitOdeModel)

R/aaa_classes.R

@@ -4,6 +4,7 @@
 
 ## helper classes
 setClassUnion("functionOrNULL", c("NULL", "function"))
+setClassUnion("functionOrcharacter", c("character", "function"))
 setClassUnion("listOrNULL", c("NULL", "list"))
 setClassUnion("numericOrlist", c("numeric", "list"))
 setClassUnion("listOrdata.frame", c("list", "data.frame"))
@@ -17,7 +18,7 @@ setClass("simObj",
            init      = "ANY",
            parms     = "ANY",
            inputs    = "ANY",
-           solver    = "character",
+           solver    = "functionOrcharacter",
            out       = "ANY",
            initfunc  = "functionOrNULL"
          )

R/accessors.R

@@ -37,6 +37,7 @@ setMethod("parms", "simObj",
 setMethod("parms<-", "simObj", 
     function(obj, value) {
       obj@parms <- value
+      obj@out <- NULL
       invisible(obj)
     }
 )
@@ -65,6 +66,7 @@ setMethod("times<-", "simObj",
           print("Warning: Ignored. Invalid (or incomplete) names in right hand side of assignment.")
         }
       }
+      obj@out <- NULL
       invisible(obj)
     }
 )
@@ -78,13 +80,15 @@ setMethod("init", "simObj",
 setMethod("init<-", "simObj",
     function(obj, value) {
       obj@init <- value
+      obj@out <- NULL
       invisible(obj)
     }
 )
 
 setMethod("init<-", c("gridModel", "matrix"),
     function(obj, value) {
       obj@init <- value
+      obj@out <- NULL      
       invisible(obj)
     }
 )
@@ -103,6 +107,7 @@ setMethod("inputs", "simObj",
 setMethod("inputs<-", "simObj",
     function(obj, value) {
       obj@inputs <- value
+      obj@out <- NULL      
       invisible(obj)
     }
 )
@@ -114,6 +119,7 @@ setMethod("main", "simObj",
 setMethod("main<-", "simObj",
     function(obj, value) {
       obj@main <- value
+      obj@out <- NULL      
       invisible(obj)
     }
 )
@@ -125,6 +131,7 @@ setMethod("equations", "simObj",
 setMethod("equations<-", "simObj",
     function(obj, value) {
       obj@equations <- value
+      obj@out <- NULL      
       invisible(obj)
     }
 )
@@ -136,6 +143,7 @@ setMethod("initfunc", "simObj",
 setMethod("initfunc<-", "simObj",
     function(obj, value) {
       obj@initfunc <- value
+      obj@out <- NULL      
       invisible(obj)
     }
 )
@@ -147,6 +155,7 @@ setMethod("solver", "simObj",
 setMethod("solver<-", "simObj",
     function(obj, value) {
       obj@solver <- value
+      obj@out <- NULL      
       invisible(obj)
     }
 )
@@ -162,6 +171,7 @@ setMethod("out", "simObj",
 setMethod("out<-", "simObj",
     function(obj, value) {
       if(!is.null(value)) stop("``out'' can only be set to NULL")
+      obj@out <- NULL      
       obj@out <- value
       invisible(obj)
     }

R/iteration.R

@@ -18,7 +18,6 @@ setMethod("iteration", "numeric",
     if (!is.numeric(y))     stop("`y' must be numeric")
     if (!is.numeric(times)) stop("`times' must be numeric")
     if (!is.function(func)) stop("`func' must be a function")
-    # if (!is.numeric(parms)) stop("`parms' must be numeric")
 
     n     <- length(y)
     parms <- c(parms, DELTAT = 0)
@@ -51,8 +50,6 @@ setMethod("iteration", "simObj",
     inputs            <- y@inputs
     equations         <- y@equations
     environment(func) <- environment()
-    #attach(equations)
-    #on.exit(detach(equations))
     equations               <- addtoenv(equations)
     parms$DELTAT <- 0
     out <- list(func(times[1], init, parms))
@@ -81,8 +78,6 @@ setMethod("iteration", "odeModel",
     equations         <- y@equations
     environment(func) <- environment()
     equations         <- addtoenv(equations)
-    #attach(equations)
-    #on.exit(detach(equations))
     n   <- length(init)
     parms <- c(parms, DELTAT = 0)
     nm  <- c("time", if (!is.null(attr(init, "names")))

R/sim.R

@@ -8,39 +8,21 @@ setMethod("sim", "simObj",
   }
 )
 
-#setMethod("sim", "odeModel",
-#  function(obj, ...) {
-#    times <- fromtoby(obj@times)
-#    #if (obj@solver == "lsoda") {
-#    #  out <- wraplsoda(obj, ...)
-#    #} else {
-#      out <- do.call(obj@solver, list(obj, ...))
-#    #}
-#    obj@out <- as.data.frame(out)
-#    invisible(obj)
-#  }
-#)
-
 setMethod("sim", "odeModel",
   function(obj, ...) {
     times             <- fromtoby(obj@times)
     func              <- obj@main
     inputs            <- obj@inputs
     equations         <- obj@equations
-    #parms             <- obj@parms
     environment(func) <- environment()
 
     equations        <- addtoenv(equations)
     out <- do.call(obj@solver, list(obj@init, times, func, obj@parms, ...))
-
-    #out <- do.call(obj@solver, list(obj, ...))
     obj@out <- as.data.frame(out)
     invisible(obj)
   }
 )
 
-
-
 setMethod("sim", "gridModel",
   function(obj, ...) {
     times <- fromtoby(obj@times)

inst/NEWS

@@ -1,3 +1,14 @@
+0.5-7
+
+o the package uses now deSolve instead of odesolve
+o euler is now imported from deSolve and removed from simecol
+o allow solver slot to contain not only character but also function
+o plain text version of JSS publication added as vignette
+
+0.5-6
+
+o small improvements and updates 
+
 0.5-5
 
 o reworked ODE solvers, rk4 and lsoda generics removed,
@@ -7,6 +18,7 @@ o reworked ODE solvers, rk4 and lsoda generics removed,
   ode solvers
 o rehabilitation of addtoenv()
 o documentation updates
+o replacement functions now delete slot "out"
 
 0.5-4
 

inst/ToDo.txt

@@ -0,0 +1,5 @@
+2008-05-21
+ - switch from odesolve to deSolve
+ - remove euler (is now in deSolve)
+ - r-initialize during sim if initfunc  exists
+