From a4421eba19eae98a0bd00adb4e8c6d72cc49f9fb Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Thu, 20 May 2010 18:02:42 +0000
Subject: 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
---
 man/mkinfit.Rd                 | 11 ++++++++++-
 man/schaefer07_complex_case.Rd | 39 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 1 deletion(-)
 create mode 100644 man/schaefer07_complex_case.Rd

(limited to 'man')

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}
-- 
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