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authorjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2012-04-24 17:33:56 +0000
committerjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2012-04-24 17:33:56 +0000
commit081b5f25cc4ef779175307d9ce20672e0573b7c9 (patch)
treee8002ab30dd8c93c7afae8b0c9075d14bac6b05e /man
parent4411ea3b88d815232eac3a3c87f7636a0bbf80f1 (diff)
- 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
Diffstat (limited to 'man')
-rw-r--r--man/FOCUS_2006_DFOP_ref_A_to_B.Rd39
-rw-r--r--man/FOCUS_2006_FOMC_ref_A_to_F.Rd38
-rw-r--r--man/FOCUS_2006_HS_ref_A_to_F.Rd39
-rw-r--r--man/FOCUS_2006_SFO_ref_A_to_F.Rd37
-rw-r--r--man/mkinfit.Rd8
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.

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