From 6168089ac43664c10ca2dc1281c8648fbf3b35a9 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Sun, 14 Apr 2013 12:42:06 +0000
Subject: - Update the TODO list, setting some requirements for version 1.0 -
 Check that initial values specified using parms.ini are actually needed for
 the model, stop otherwise - List all formation fractions in the same place in
 the summary, also if they were fitted in the model - Include an FOMC model
 coupled to two metabolites in the unit tests - Some updates needed because of
 the above - Update of static documentation including the vignettes - Update
 of the mkin vignettes in the vignettes directory

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@82 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 R/mkinfit.R | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

(limited to 'R/mkinfit.R')

diff --git a/R/mkinfit.R b/R/mkinfit.R
index b80be97..cf018f0 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -28,6 +28,8 @@ mkinfit <- function(mkinmod, observed,
   fixed_parms = NULL,
   fixed_initials = names(mkinmod$diffs)[-1],
   solution_type = "auto",
+  method.modFit = "Marq",
+  control.modFit = list(),
   plot = FALSE, quiet = FALSE,
   err = NULL, weight = "none", scaleVar = FALSE,
   atol = 1e-8, rtol = 1e-10, n.outtimes = 100,
@@ -45,6 +47,13 @@ mkinfit <- function(mkinmod, observed,
 
   # Define starting values for parameters where not specified by the user
   if (parms.ini[[1]] == "auto") parms.ini = vector()
+
+  # Prevent inital parameter specifications that are not in the model
+  wrongpar.names <- setdiff(names(parms.ini), mkinmod$parms)
+  if (length(wrongpar.names) > 0) {
+    stop("Initial parameter(s) ", paste(wrongpar.names, collapse = ", "), " not used in the model")
+  }
+
   defaultpar.names <- setdiff(mkinmod$parms, names(parms.ini))
   for (parmname in defaultpar.names) {
     # Default values for rate constants, depending on the parameterisation
@@ -168,7 +177,7 @@ mkinfit <- function(mkinmod, observed,
     }
     return(mC)
   }
-  fit <- modFit(cost, c(state.ini.optim, parms.optim), ...)
+  fit <- modFit(cost, c(state.ini.optim, parms.optim), method = method.modFit, control = control.modFit, ...)
 
   # We need to return some more data for summary and plotting
   fit$solution_type <- solution_type
@@ -203,6 +212,7 @@ mkinfit <- function(mkinmod, observed,
   fit$data <- data[order(data$variable, data$time), ]
   fit$atol <- atol
   fit$rtol <- rtol
+
   # Return all backtransformed parameters for summary
   fit$bparms.optim <- bparms.optim 
   fit$bparms.fixed <- bparms.fixed
@@ -239,7 +249,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
   dimnames(param) <- list(pnames, c("Estimate", "Std. Error", "Lower", "Upper"))
 
   blci <- buci <- numeric()
-  # Only use lower end of CI for one parameter at a time
+  # Only transform boundaries of CI for one parameter at a time
   for (pname in pnames) {
     par.lower <- par.upper <- object$par
     par.lower[pname] <- param[pname, "Lower"]
-- 
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