5 files changed, 56 insertions, 10 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index e518d6d..24fbc57 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,14 +1,20 @@
 Package: mkin
 Type: Package
 Title: Routines for fitting kinetic models with one or more state
-        variables to chemical degradation data
-Version: 0.7-3
-Date: 2010-05-20
+  variables to chemical degradation data
+Version: 0.7-4
+Date: 2010-05-22
 Author: Johannes Ranke
 Maintainer: Johannes Ranke <jranke@harlan.com>
-Description: Calculation routines based on the FOCUS Kinetics Report
-        (2006)
-Depends: FME
+Description: Calculation routines based on the FOCUS Kinetics Report (2006). Includes 
+  a function for conveniently defining differential equation models, choice of
+  the optimisation methods made available by the FME package (default is a
+  Levenberg-Marquardt variant). Initial values for parameters of the differential
+  equations and time zero values of the state values can be defaults, user defined
+  or a combination of a fit for the parent compound carried out by the kinfit
+  package and defaults. DT50 and DT90 values are calculated as well as the 
+  chi2 error level as defined by the FOCUS Kinetics Group.
+Depends: FME, kinfit
 License: GPL
 LazyLoad: yes
 LazyData: yes
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 9e872fc..f8285fc 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -188,9 +188,9 @@ mkinfit <- function(mkinmod, observed,
         # FOCUS kinetics (2006), p. 60 f
         k_out_names = grep(paste("k", obs_var, "free", sep="_"), names(parms.all), value=TRUE)
         k_out_names = setdiff(k_out_names, paste("k", obs_var, "free", "bound", sep="_"))
-        k_1output = sum(parms.all[[k_out_names]])
-        k_12 = parms.all[[paste("k", obs_var, "free", "bound", sep="_")]]
-        k_21 = parms.all[[paste("k", obs_var, "bound", "free", sep="_")]]
+        k_1output = sum(parms.all[k_out_names])
+        k_12 = parms.all[paste("k", obs_var, "free", "bound", sep="_")]
+        k_21 = parms.all[paste("k", obs_var, "bound", "free", sep="_")]
 
         sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21)
         b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp
diff --git a/data/schaefer07_complex_case.RData b/data/schaefer07_complex_case.RData
index 0e3b3af..d58aedd 100644
--- a/data/schaefer07_complex_case.RData
+++ b/data/schaefer07_complex_case.RData
diff --git a/inst/unitTests/runit.mkinfit.R b/inst/unitTests/runit.mkinfit.R
new file mode 100644
index 0000000..6dbd11f
--- /dev/null
+++ b/inst/unitTests/runit.mkinfit.R
@@ -0,0 +1,35 @@
+test.mkinmod.schaefer07_complex_example <- function()
+{
+  schaefer07_complex_model <- mkinmod(
+    parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
+    A1 = list(type = "SFO", to = "A2"),
+    B1 = list(type = "SFO"),
+    C1 = list(type = "SFO"),
+    A2 = list(type = "SFO"))
+  
+  fit <- mkinfit(schaefer07_complex_model, 
+    mkin_wide_to_long(schaefer07_complex_case, time = "time"),
+    parms.ini = c(0.1, 0.1, 0.1, 0.01, 0.1, 0.1, 0.1, 0.1))
+  s <- summary(fit)
+  attach(as.list(fit$par))
+  k_parent <- sum(k_parent_A1, k_parent_B1, k_parent_C1)
+  r <- schaefer07_complex_results
+  r$mkin <- c(
+    k_parent,
+    s$distimes["parent", "DT50"],
+    k_parent_A1/k_parent,
+    sum(k_A1_sink, k_A1_A2),
+    s$distimes["A1", "DT50"],
+    k_parent_B1/k_parent,
+    k_B1_sink,
+    s$distimes["B1", "DT50"],
+    k_parent_C1/k_parent,
+    k_C1_sink,
+    s$distimes["C1", "DT50"],
+    k_A1_A2/(k_A1_A2 + k_A1_sink),
+    k_A2_sink,
+    s$distimes["A2", "DT50"])
+  r$means <- (r$KinGUI + r$ModelMaker)/2
+  r$mkin.deviation <- abs(round(100 * ((r$mkin - r$means)/r$means), digits=1))
+  checkTrue(r$mkin.deviation < 10)
+}
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 0e381af..0ec2d21 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -10,7 +10,12 @@
   values.
 }
 \usage{
-mkinfit(mkinmod, observed, parms.ini = rep(0.1, length(mkinmod$parms)), state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), lower = 0, upper = Inf, fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, ...)
+mkinfit(mkinmod, observed, 
+  parms.ini = rep(0.1, length(mkinmod$parms)), 
+  state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), 
+  lower = 0, upper = Inf, 
+  fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], 
+  plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, ...)
 }
 \arguments{
   \item{mkinmod}{