version 0.7-1

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: simecol
-Version: 0.7
+Version: 0.7-1
 Date: 2010-12-01
 Title: Simulation of ecological (and other) dynamic systems
 Author: Thomas Petzoldt
@@ -15,6 +15,6 @@ Description: simecol is an object oriented framework to simulate
         of code.
 License: GPL (>= 2)
 URL: http://www.simecol.de/
-Packaged: 2010-11-30 09:44:02 UTC; thpe
+Packaged: 2011-03-20 19:30:01 UTC; petzoldt
 Repository: CRAN
-Date/Publication: 2010-11-30 10:14:02
+Date/Publication: 2011-03-21 06:47:44

R/addtoenv.R

@@ -1,7 +1,6 @@
 ## environment manipulation function
 ## Warning: use carefully and avoid name mangling
 ## solution provided by Gabor Grothendieck (replaces older own function)
-## --> this function is deprecated and may be removed in further versions
 
 addtoenv <- function(L, p = parent.frame()) {
   for(nm in names(L)) {

R/sEdit.R

@@ -49,7 +49,7 @@ sEdit <- function(x, title="Please enter values:") {
         row.names <- paste("var",1:length(slot),sep="")
       }
       for (i in 1:length(slot)) {
-        entries[[i]] <- tkentry(tt, textvariable=row.names[i])       
+        entries[[i]] <- tkentry(tt, textvariable=row.names[i])
         tkgrid(tklabel(tt,text=row.names[i]), entries[[i]])
       }
       reset.but  <- tkbutton(tt, text="Reset", command=reset)
@@ -82,7 +82,7 @@ sEdit <- function(x, title="Please enter values:") {
       ret  <- lapply(ret, listToNum)
     } else {
       ## default editor, e.g. data.frame or if tcltk is missing
-      ret  <- edit(x) 
+      ret  <- edit(x)
     }
     return(ret)
 }
@@ -97,9 +97,9 @@ setMethod("fixParms", "simObj",
   function(x) {
     sl   <- "parms"
     subx <- substitute(x)
-    if (is.name(subx)) 
+    if (is.name(subx))
        subx <- deparse(subx)
-    if (!is.character(subx) || length(subx) != 1) 
+    if (!is.character(subx) || length(subx) != 1)
         stop("this function requires a name")
     if (!(sl %in% slotNames(x)))
         stop(paste("'", sl, "' does not exist in ", subx, sep=""))
@@ -108,17 +108,17 @@ setMethod("fixParms", "simObj",
     slot(x, sl) <- ret
     ## interactive function is assumed to work
     ## in global environment
-    assign(subx, x, env=.GlobalEnv)
+    assign(subx, x, envir=.GlobalEnv)
   }
 )
 
 setMethod("fixTimes", "simObj",
   function(x) {
     sl <- "times"
     subx <- substitute(x)
-    if (is.name(subx)) 
+    if (is.name(subx))
        subx <- deparse(subx)
-    if (!is.character(subx) || length(subx) != 1) 
+    if (!is.character(subx) || length(subx) != 1)
         stop("this function requires a name")
     if (!(sl %in% slotNames(x)))
         stop(paste("'", sl, "' does not exist in ", subx, sep=""))
@@ -131,7 +131,7 @@ setMethod("fixTimes", "simObj",
     slot(x, sl) <- ret
     ## interactive function is assumed to work
     ## in global environment
-    assign(subx, x, env=.GlobalEnv)
+    assign(subx, x, envir=.GlobalEnv)
 
   }
 )
@@ -140,9 +140,9 @@ setMethod("fixInit", "simObj",
   function(x) {
     sl <- "init"
     subx <- substitute(x)
-    if (is.name(subx)) 
+    if (is.name(subx))
        subx <- deparse(subx)
-    if (!is.character(subx) || length(subx) != 1) 
+    if (!is.character(subx) || length(subx) != 1)
         stop("this function requires a name")
     if (!(sl %in% slotNames(x)))
         stop(paste("'", sl, "' does not exist in ", subx, sep=""))
@@ -151,11 +151,11 @@ setMethod("fixInit", "simObj",
     slot(x, sl) <- ret
     ## interactive function is assumed to work
     ## in global environment
-    assign(subx, x, env=.GlobalEnv)
+    assign(subx, x, envir=.GlobalEnv)
 
   }
 )
 
 
-    
+
 

demo/00Index

@@ -1,2 +1,2 @@
 jss	Sourcecode and demo for Petzoldt and Rinke (2007): Journal of Statistical Software, vol. 22 issue 09
-rwalk3d  Demo of a random walk model in 3D
+

inst/NEWS

@@ -1,3 +1,6 @@
+0.7-1
+o fix documentation notes and a warning 
+
 0.7
 o "inputs" is now passed explicitly to sim "odeModel"
 o fix namespace issue

inst/doc/examples/chemostat.R

@@ -1,27 +1,20 @@
 chemostat <- new("odeModel",
-    main = function(time, init, parms, inputs=NULL) {
-        vm  <- parms["vm"] # max growth rate 
-        km  <- parms["km"] # half saturation constant
-        D   <- parms["D"]  # dilution rate
-        S0  <- parms["S0"] # substrate in inflow
-        Y   <- parms["Y"]  # yield coefficient for substrate
-        X   <- init[1]     # cells (e.g. algae)
-        S   <- init[2]     # substrate (e.g. phosphorus)
-
-        mu  <- vm * S/(km + S)              # Monod equation
-        dx1 <- mu * X - D * X               # cells 
-        dx2 <-  D *(S0 - S) - 1/Y * mu * X  # substrate
-        list(c(dx1, dx2))
-    },
-    parms = c(
-        vm = 1.0,           # 1/d
-        km = 2.0,           # mumol Substrate/l
-        Y  = 100,           # cells /mumol Substrate
-        D  = 0.5,           # 1/d
-        S0 = 10             #  mumol Substrate/l
-    ),
-    times = c(from=0, to=40, by=.5),
-    init  = c(X=10, S=10), # cells/l; umol Substrate/l                     
-    solver = "lsoda"
+  main = function(time, init, parms, inputs = NULL) {
+    with(as.list(c(init, parms)), {
+      mu  <- vm * S / (km + S)            # Monod equation
+      dx1 <- mu * X - D * X               # cells, e.g. algae
+      dx2 <-  D *(S0 - S) - 1/Y * mu * X  # substrate, e.g. phosphorus
+      list(c(dx1, dx2))
+    })
+  },
+  parms = c(
+    vm = 1.0,           # max growth rate, 1/d
+    km = 2.0,           # half saturation constant, mumol / L
+    Y  = 100,           # cells /mumol Substrate
+    D  = 0.5,           # dilution rate, 1/d
+    S0 = 10             # substrate in inflow, mumol / L
+  ),
+  times = c(from = 0, to = 40, by = .5),
+  init  = c(X = 10, S = 10), # cells / L; Substrate umol / L
+  solver = "lsoda"
 )
-