- Added the reference fit data for FOCUS 2006 datasets from the kinfit package

- Used these data in unit tests for parent only models
- Fixed SFORB data and calculation of formation fractions along the way
- Reintroduced the test for the Schaefer 2007 data
- Got rid of the mkinmod unit tests - they are too hard to maintain and the mkinfit
  tests test the model definitions as well

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@32 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

5 files changed, 159 insertions, 2 deletions

diff --git a/man/FOCUS_2006_DFOP_ref_A_to_B.Rd b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd
new file mode 100644
index 00000000..88bd4ac6
--- /dev/null
+++ b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd
@@ -0,0 +1,39 @@
+\name{FOCUS_2006_DFOP_ref_A_to_B}

+\Rdversion{1.1}

+\alias{FOCUS_2006_DFOP_ref_A_to_B}

+\docType{data}

+\title{

+Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

+}

+\description{

+A table with the fitted parameters and the resulting DT50 and DT90 values

+generated with different software packages. Taken directly from FOCUS (2006).

+The results from fitting the data with the Topfit software was removed, as

+the initial concentration of the parent compound was fixed to a value of 100

+in this fit.

+}

+\usage{data(FOCUS_2006_DFOP_ref_A_to_B)}

+\format{

+  A data frame containing the following variables.

+  \describe{

+    \item{\code{package}}{a factor giving the name of the software package}

+    \item{\code{M0}}{The fitted initial concentration of the parent compound}

+    \item{\code{f}}{The fitted f parameter}

+    \item{\code{k1}}{The fitted k1 parameter}

+    \item{\code{k2}}{The fitted k2 parameter}

+    \item{\code{DT50}}{The resulting half-life of the parent compound}

+    \item{\code{DT90}}{The resulting DT90 of the parent compound}

+    \item{\code{dataset}}{The FOCUS dataset that was used}

+  }

+}

+\source{

+  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

+  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

+  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

+  \url{http://focus.jrc.ec.europa.eu/dk} 

+}

+\examples{

+data(FOCUS_2006_DFOP_ref_A_to_B)

+}

+\keyword{datasets}

diff --git a/man/FOCUS_2006_FOMC_ref_A_to_F.Rd b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd
new file mode 100644
index 00000000..2fcc2db7
--- /dev/null
+++ b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd
@@ -0,0 +1,38 @@
+\name{FOCUS_2006_FOMC_ref_A_to_F}

+\Rdversion{1.1}

+\alias{FOCUS_2006_FOMC_ref_A_to_F}

+\docType{data}

+\title{

+Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)

+}

+\description{

+A table with the fitted parameters and the resulting DT50 and DT90 values

+generated with different software packages. Taken directly from FOCUS (2006).

+The results from fitting the data with the Topfit software was removed, as

+the initial concentration of the parent compound was fixed to a value of 100

+in this fit.

+}

+\usage{data(FOCUS_2006_FOMC_ref_A_to_F)}

+\format{

+  A data frame containing the following variables.

+  \describe{

+    \item{\code{package}}{a factor giving the name of the software package}

+    \item{\code{M0}}{The fitted initial concentration of the parent compound}

+    \item{\code{alpha}}{The fitted alpha parameter}

+    \item{\code{beta}}{The fitted beta parameter}

+    \item{\code{DT50}}{The resulting half-life of the parent compound}

+    \item{\code{DT90}}{The resulting DT90 of the parent compound}

+    \item{\code{dataset}}{The FOCUS dataset that was used}

+  }

+}

+\source{

+  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

+  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

+  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

+  \url{http://focus.jrc.ec.europa.eu/dk} 

+}

+\examples{

+data(FOCUS_2006_FOMC_ref_A_to_F)

+}

+\keyword{datasets}

diff --git a/man/FOCUS_2006_HS_ref_A_to_F.Rd b/man/FOCUS_2006_HS_ref_A_to_F.Rd
new file mode 100644
index 00000000..6fc99933
--- /dev/null
+++ b/man/FOCUS_2006_HS_ref_A_to_F.Rd
@@ -0,0 +1,39 @@
+\name{FOCUS_2006_HS_ref_A_to_F}

+\Rdversion{1.1}

+\alias{FOCUS_2006_HS_ref_A_to_F}

+\docType{data}

+\title{

+Results of fitting the HS model to Datasets A to F of FOCUS (2006)

+}

+\description{

+A table with the fitted parameters and the resulting DT50 and DT90 values

+generated with different software packages. Taken directly from FOCUS (2006).

+The results from fitting the data with the Topfit software was removed, as

+the initial concentration of the parent compound was fixed to a value of 100

+in this fit.

+}

+\usage{data(FOCUS_2006_HS_ref_A_to_F)}

+\format{

+  A data frame containing the following variables.

+  \describe{

+    \item{\code{package}}{a factor giving the name of the software package}

+    \item{\code{M0}}{The fitted initial concentration of the parent compound}

+    \item{\code{tb}}{The fitted tb parameter}

+    \item{\code{k1}}{The fitted k1 parameter}

+    \item{\code{k2}}{The fitted k2 parameter}

+    \item{\code{DT50}}{The resulting half-life of the parent compound}

+    \item{\code{DT90}}{The resulting DT90 of the parent compound}

+    \item{\code{dataset}}{The FOCUS dataset that was used}

+  }

+}

+\source{

+  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

+  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

+  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

+  \url{http://focus.jrc.ec.europa.eu/dk} 

+}

+\examples{

+data(FOCUS_2006_HS_ref_A_to_F)

+}

+\keyword{datasets}

diff --git a/man/FOCUS_2006_SFO_ref_A_to_F.Rd b/man/FOCUS_2006_SFO_ref_A_to_F.Rd
new file mode 100644
index 00000000..19650ed4
--- /dev/null
+++ b/man/FOCUS_2006_SFO_ref_A_to_F.Rd
@@ -0,0 +1,37 @@
+\name{FOCUS_2006_SFO_ref_A_to_F}

+\Rdversion{1.1}

+\alias{FOCUS_2006_SFO_ref_A_to_F}

+\docType{data}

+\title{

+Results of fitting the SFO model to Datasets A to F of FOCUS (2006)

+}

+\description{

+A table with the fitted parameters and the resulting DT50 and DT90 values

+generated with different software packages. Taken directly from FOCUS (2006).

+The results from fitting the data with the Topfit software was removed, as

+the initial concentration of the parent compound was fixed to a value of 100

+in this fit.

+}

+\usage{data(FOCUS_2006_SFO_ref_A_to_F)}

+\format{

+  A data frame containing the following variables.

+  \describe{

+    \item{\code{package}}{a factor giving the name of the software package}

+    \item{\code{M0}}{The fitted initial concentration of the parent compound}

+    \item{\code{k}}{The fitted first-order degradation rate constant}

+    \item{\code{DT50}}{The resulting half-life of the parent compound}

+    \item{\code{DT90}}{The resulting DT90 of the parent compound}

+    \item{\code{dataset}}{The FOCUS dataset that was used}

+  }

+}

+\source{

+  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

+  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

+  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

+  \url{http://focus.jrc.ec.europa.eu/dk} 

+}

+\examples{

+data(FOCUS_2006_SFO_ref_A_to_F)

+}

+\keyword{datasets}

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 0c8e48f1..5f70dae9 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -17,7 +17,8 @@ mkinfit(mkinmod, observed,
   solution_type = "auto",
   plot = FALSE, quiet = FALSE, err = NULL, weight = "none", 
   scaleVar = FALSE, 
-  atol = 1e-6, n.outtimes, ...)
+  atol = 1e-6, n.outtimes, 
+  trace_parms, ...)
 }
 \arguments{
   \item{mkinmod}{
@@ -92,6 +93,9 @@ mkinfit(mkinmod, observed,
     the numerical solver if that is used (see \code{solution} argument. 
     The default value is 100.
   }
+  \item{trace_parms}{
+    Should a trace of the parameter values be listed?
+  }
   \item{\dots}{
     Further arguments that will be passed to \code{\link{modFit}}. 
   }
@@ -101,7 +105,7 @@ mkinfit(mkinmod, observed,
     A summary can be obtained by \code{\link{summary.mkinfit}}. 
 }
 \author{
-  Johannes Ranke <jranke@{harlan.com,uni-bremen.de}>
+  Johannes Ranke <jranke@uni-bremen.de>
 }
 \examples{
 # One parent compound, one metabolite, both single first order.