Various improvements, the most prominent being the addition of the

test dataset from the original KinGUI Piacenza paper.



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@10 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

2 files changed, 49 insertions, 1 deletions

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 640207c..0e381af 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -10,7 +10,7 @@
   values.
 }
 \usage{
-mkinfit(mkinmod, observed, parms.ini = rep(0.1, length(mkinmod$parms)), state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), 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}{
@@ -37,6 +37,15 @@ mkinfit(mkinmod, observed, parms.ini = rep(0.1, length(mkinmod$parms)), state.in
     \code{\link{mkinmod}}). The default is to set the initial value of the first model
     variable to 100 and all others to 0.
   }
+  \item{lower}{
+    Lower bounds for the parameters, passed to \code{\link{modFit}}. Defaults to 0 because
+    negative values to not make sense for the models currently created by \code{\link{mkinmod}}.
+  }
+  \item{upper}{
+    Upper bounds for the parameters, passed to \code{\link{modFit}}. Defaults to \code{Inf}. Setting
+    non-infinite upper bounds has a strong impact on performance, and using a method like "L-BFGS-B" (by 
+    specifying an additional \code{method} argument) is recommended.
+  }
   \item{fixed_parms}{
     The names of parameters that should not be optimised but rather kept at the values
     specified in \code{parms.ini}.
diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd
new file mode 100644
index 0000000..2978e25
--- /dev/null
+++ b/man/schaefer07_complex_case.Rd
@@ -0,0 +1,39 @@
+\name{schaefer07_complex_case}

+\alias{schaefer07_complex_case}

+\encoding{latin1}

+\docType{data}

+\title{

+  Metabolism data set used for checking the software quality of KinGUI

+}

+\description{

+  This dataset was used for a comparison of KinGUI and ModelMaker to check the

+  software quality of KinGUI in the original publication (Schäfer et al., 2007).

+}

+\usage{data(schaefer07_complex_case)}

+\format{

+  A data frame with 8 observations on the following 6 variables.

+  \describe{

+    \item{\code{time}}{a numeric vector}

+    \item{\code{parent}}{a numeric vector}

+    \item{\code{A1}}{a numeric vector}

+    \item{\code{B1}}{a numeric vector}

+    \item{\code{C1}}{a numeric vector}

+    \item{\code{A2}}{a numeric vector}

+  }

+}

+\source{

+  Schäfer D, Mikolasch M, Rainbird P and Harvey B (2007). KinGUI: a new kinetic

+  software tool for evaluations according to FOCUS degradation kinetics. In: Del

+  Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII

+  Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.  }

+\examples{

+data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")

+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"))

+\dontrun{mkinfit(model, data, plot=TRUE)}

+}

+\keyword{datasets}