- Fitting and summaries now work with the new parameter transformations.

- The SFORB models with metabolites is broken (see TODO)
- Moved the vignette to the location recommended since R 2.14
- Added the missing documentation
- Commented out the schaefer_complex_case test, as this version of
  mkin is not able to fit a model without sink and therefore 
  mkin estimated parameters are quite different




git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@22 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 0 insertions, 89 deletions

diff --git a/R/predict.mkinmod.R b/R/predict.mkinmod.R
deleted file mode 100644
index 279fa525..00000000
--- a/R/predict.mkinmod.R
+++ /dev/null
@@ -1,89 +0,0 @@
-predict.mkinmod <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_output = TRUE, atol = 1e-6) {
-
-  # Get the names of the state variables in the model
-  mod_vars <- names(mkinmod$diffs)
-
-  # Create function for evaluation of expressions with ode parameters and initial values
-  evalparse <- function(string)
-  {
-    eval(parse(text=string), as.list(c(odeparms, odeini)))
-  }
-
-  # Create a function calculating the differentials specified by the model
-  # if necessary
-  if (solution_type == "analytical") {
-    parent.type = names(mkinmod$map[[1]])[1]  
-    parent.name = names(mkinmod$diffs)[[1]]
-    o <- switch(parent.type,
-      SFO = SFO.solution(outtimes, 
-          evalparse(parent.name),
-          evalparse(paste("k", parent.name, sep="_"))),
-      FOMC = FOMC.solution(outtimes,
-          evalparse(parent.name),
-          evalparse("alpha"), evalparse("beta")),
-      DFOP = DFOP.solution(outtimes,
-          evalparse(parent.name),
-          evalparse("k1"), evalparse("k2"),
-          evalparse("g")),
-      HS = HS.solution(outtimes,
-          evalparse(parent.name),
-          evalparse("k1"), evalparse("k2"),
-          evalparse("tb")),
-      SFORB = SFORB.solution(outtimes,
-          evalparse(parent.name),
-          evalparse(paste("k", parent.name, "bound", sep="_")),
-          evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")),
-          evalparse(paste("k", parent.name, sep="_")))
-    )
-    out <- cbind(outtimes, o)
-    dimnames(out) <- list(outtimes, c("time", sub("_free", "", parent.name)))
-  }
-  if (solution_type == "eigen") {
-    coefmat.num <- matrix(sapply(as.vector(mkinmod$coefmat), evalparse), 
-      nrow = length(mod_vars))
-    e <- eigen(coefmat.num)
-    c <- solve(e$vectors, odeini)
-    f.out <- function(t) {
-      e$vectors %*% diag(exp(e$values * t), nrow=length(mod_vars)) %*% c
-    }
-    o <- matrix(mapply(f.out, outtimes), 
-      nrow = length(mod_vars), ncol = length(outtimes))
-    dimnames(o) <- list(mod_vars, outtimes)
-    out <- cbind(time = outtimes, t(o))
-  } 
-  if (solution_type == "deSolve") {
-    mkindiff <- function(t, state, parms) {
-
-      time <- t
-      diffs <- vector()
-      for (box in names(mkinmod$diffs))
-      {
-        diffname <- paste("d", box, sep="_")      
-        diffs[diffname] <- with(as.list(c(time, state, parms)),
-          eval(parse(text=mkinmod$diffs[[box]])))
-      }
-      return(list(c(diffs)))
-    } 
-    out <- ode(
-      y = odeini,
-      times = outtimes,
-      func = mkindiff, 
-      parms = odeparms,
-      atol = atol
-    )
-  }
-  if (map_output) {
-    # Output transformation for models with unobserved compartments like SFORB
-    out_mapped <- data.frame(time = out[,"time"])
-    for (var in names(mkinmod$map)) {
-      if((length(mkinmod$map[[var]]) == 1) || solution == "analytical") {
-        out_mapped[var] <- out[, var]
-      } else {
-        out_mapped[var] <- rowSums(out[, mkinmod$map[[var]]])
-      }
-    }
-    return(out_mapped) 
-  } else {
-    return(out)
-  }
-}