diff options
| author | jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb> | 2010-03-30 19:49:44 +0000 |
|---|---|---|
| committer | jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb> | 2010-03-30 19:49:44 +0000 |
| commit | 12934520d7ec3218ce1505787b6066334a24a562 (patch) | |
| tree | e3d3439a63260dfe8fc01037ef297e09e876cc67 /man | |
Initial import of the kinfit package developed from 2008-07 to 2010-03 at
Harlan Laboratories Ltd (former RCC Ltd).
Supports fitting of parent data with the usual FOCUS kinetic models.
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@2 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
Diffstat (limited to 'man')
| -rw-r--r-- | man/DFOP.Rd | 37 | ||||
| -rw-r--r-- | man/FOCUS_2006_A.Rd | 29 | ||||
| -rw-r--r-- | man/FOCUS_2006_B.Rd | 29 | ||||
| -rw-r--r-- | man/FOCUS_2006_C.Rd | 30 | ||||
| -rw-r--r-- | man/FOCUS_2006_D.Rd | 33 | ||||
| -rw-r--r-- | man/FOCUS_2006_DFOP_ref_A_to_B.Rd | 43 | ||||
| -rw-r--r-- | man/FOCUS_2006_E.Rd | 32 | ||||
| -rw-r--r-- | man/FOCUS_2006_F.Rd | 32 | ||||
| -rw-r--r-- | man/FOCUS_2006_FOMC_ref_A_to_F.Rd | 42 | ||||
| -rw-r--r-- | man/FOCUS_2006_HS_ref_A_to_F.Rd | 43 | ||||
| -rw-r--r-- | man/FOCUS_2006_SFO_ref_A_to_F.Rd | 41 | ||||
| -rw-r--r-- | man/FOMC.Rd | 49 | ||||
| -rw-r--r-- | man/HS.Rd | 35 | ||||
| -rw-r--r-- | man/SFO.Rd | 30 | ||||
| -rw-r--r-- | man/kinerrmin.Rd | 43 | ||||
| -rw-r--r-- | man/kinfit.Rd | 77 | ||||
| -rw-r--r-- | man/kinobject.Rd | 29 | ||||
| -rw-r--r-- | man/kinobjects.Rd | 29 | ||||
| -rw-r--r-- | man/kinplot.Rd | 50 | ||||
| -rw-r--r-- | man/kinreport.Rd | 48 | ||||
| -rw-r--r-- | man/kinresplot.Rd | 49 | ||||
| -rw-r--r-- | man/kinresults.Rd | 45 | ||||
| -rw-r--r-- | man/kinwrite.KinGUI.Rd | 47 |
23 files changed, 922 insertions, 0 deletions
diff --git a/man/DFOP.Rd b/man/DFOP.Rd new file mode 100644 index 0000000..129b3b1 --- /dev/null +++ b/man/DFOP.Rd @@ -0,0 +1,37 @@ +\name{DFOP}
+\Rdversion{1.1}
+\alias{DFOP}
+\title{
+Dual First-Order in Parallel kinetics
+}
+\description{
+ Function describing decline from a defined starting value using the sum
+ of two exponential decline functions.
+}
+\usage{
+DFOP(t, parent.0, k1, k2, g)
+}
+\arguments{
+ \item{t}{ Time. }
+ \item{parent.0}{ Starting value for the response variable at time zero. }
+ \item{k1}{ First kinetic constant. }
+ \item{k2}{ Second kinetic constant. }
+ \item{g}{ Fraction of the starting value declining according to the
+ first kinetic constant.
+ }
+}
+\value{
+ The value of the response variable at time \code{t}.
+}
+\references{
+ 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}
+}
+\author{ Johannes Ranke }
+\examples{
+ \dontrun{plot(function(x) DFOP(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))}
+}
+\keyword{ manip }
diff --git a/man/FOCUS_2006_A.Rd b/man/FOCUS_2006_A.Rd new file mode 100644 index 0000000..218004e --- /dev/null +++ b/man/FOCUS_2006_A.Rd @@ -0,0 +1,29 @@ +\name{FOCUS_2006_A}
+\Rdversion{1.1}
+\alias{FOCUS_2006_A}
+\docType{data}
+\title{
+Dataset A from the FOCUS Kinetics report from 2006
+}
+\description{
+Data generated using a model and assuming some variability.
+}
+\usage{data(FOCUS_2006_A)}
+\format{
+ A data frame with 8 observations on the following 2 variables.
+ \describe{
+ \item{\code{t}}{a numeric vector containing time points}
+ \item{\code{parent}}{a numeric vector containing parent concentrations in percent of applied radioactivity}
+ }
+}
+\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_A)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_2006_B.Rd b/man/FOCUS_2006_B.Rd new file mode 100644 index 0000000..112056a --- /dev/null +++ b/man/FOCUS_2006_B.Rd @@ -0,0 +1,29 @@ +\name{FOCUS_2006_B}
+\Rdversion{1.1}
+\alias{FOCUS_2006_B}
+\docType{data}
+\title{
+Dataset B from the FOCUS Kinetics report from 2006
+}
+\description{
+Data generated using a model and assuming some variability.
+}
+\usage{data(FOCUS_2006_B)}
+\format{
+ A data frame with 8 observations on the following 2 variables.
+ \describe{
+ \item{\code{t}}{a numeric vector containing time points}
+ \item{\code{parent}}{a numeric vector containing parent concentrations in percent of applied radioactivity}
+ }
+}
+\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_B)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_2006_C.Rd b/man/FOCUS_2006_C.Rd new file mode 100644 index 0000000..a20bc82 --- /dev/null +++ b/man/FOCUS_2006_C.Rd @@ -0,0 +1,30 @@ +\name{FOCUS_2006_C}
+\Rdversion{1.1}
+\alias{FOCUS_2006_C}
+\docType{data}
+\title{
+Dataset C from the FOCUS Kinetics report from 2006
+}
+\description{
+Data taken from an \dQuote{existing dataset}.
+}
+\usage{data(FOCUS_2006_C)}
+\format{
+ A data frame with 9 observations on the following 2 variables.
+ \describe{
+ \item{\code{t}}{a numeric vector containing time points}
+ \item{\code{parent}}{a numeric vector containing parent concentrations in percent of applied radioactivity}
+ }
+}
+\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}
+}
+\note{ This dataset is just a subset of \code{\link{FOCUS_2006_E}}. }
+\examples{
+data(FOCUS_2006_C)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_2006_D.Rd b/man/FOCUS_2006_D.Rd new file mode 100644 index 0000000..c548f8d --- /dev/null +++ b/man/FOCUS_2006_D.Rd @@ -0,0 +1,33 @@ +\name{FOCUS_2006_D}
+\Rdversion{1.1}
+\alias{FOCUS_2006_D}
+\docType{data}
+\title{
+Dataset D from the FOCUS Kinetics report from 2006
+}
+\description{
+Data taken from an \dQuote{existing dataset}. At each time point two data
+points were generated, as the experiment was performed in duplicate.
+}
+\usage{data(FOCUS_2006_D)}
+\format{
+ A data frame with 10 observations on the following 2 variables.
+ \describe{
+ \item{\code{t}}{a numeric vector containing time points}
+ \item{\code{parent}}{a numeric vector containing parent concentrations
+ in percent of applied radioactivity}
+ \item{\code{m1}}{a numeric vector containing concentrations of metabolite 1
+ in percent of applied radioactivity}
+ }
+}
+\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_D)
+}
+\keyword{datasets}
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 0000000..b0b01d7 --- /dev/null +++ b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd @@ -0,0 +1,43 @@ +\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}
+ }
+}
+\note{
+ The comparison of these results with the results obtained with the
+ current version of \code{kinfit} can be found in the package vignette.
+}
+\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_E.Rd b/man/FOCUS_2006_E.Rd new file mode 100644 index 0000000..7ae905b --- /dev/null +++ b/man/FOCUS_2006_E.Rd @@ -0,0 +1,32 @@ +\name{FOCUS_2006_E}
+\Rdversion{1.1}
+\alias{FOCUS_2006_E}
+\docType{data}
+\title{
+Dataset E from the FOCUS Kinetics report from 2006
+}
+\description{
+Data taken from an \dQuote{existing dataset}.
+}
+\usage{data(FOCUS_2006_E)}
+\format{
+ A data frame with 9 observations on the following 3 variables.
+ \describe{
+ \item{\code{t}}{a numeric vector containing time points}
+ \item{\code{parent}}{a numeric vector containing parent concentrations
+ in percent of applied radioactivity}
+ \item{\code{m1}}{a numeric vector containing concentrations of metabolite 1
+ in percent of applied radioactivity}
+ }
+}
+\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_E)
+}
+\keyword{datasets}
diff --git a/man/FOCUS_2006_F.Rd b/man/FOCUS_2006_F.Rd new file mode 100644 index 0000000..87bd1af --- /dev/null +++ b/man/FOCUS_2006_F.Rd @@ -0,0 +1,32 @@ +\name{FOCUS_2006_F}
+\Rdversion{1.1}
+\alias{FOCUS_2006_F}
+\docType{data}
+\title{
+Water sediment study dataset F from the FOCUS Kinetics report from 2006
+}
+\description{
+Data taken from an \dQuote{existing dataset}.
+}
+\usage{data(FOCUS_2006_F)}
+\format{
+ A data frame with 9 observations on the following 3 variables.
+ \describe{
+ \item{\code{t}}{a numeric vector containing time points}
+ \item{\code{parent.water}}{a numeric vector containing parent
+ concentrations in water in percent of applied radioactivity}
+ \item{\code{parent.sediment}}{a numeric vector containing parent
+ concentrations in water in percent of applied radioactivity}
+ }
+}
+\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_F)
+}
+\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 0000000..8710046 --- /dev/null +++ b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd @@ -0,0 +1,42 @@ +\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}
+ }
+}
+\note{
+ The comparison of these results with the results obtained with the
+ current version of \code{kinfit} can be found in the package vignette.
+}
+\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 0000000..4ed8555 --- /dev/null +++ b/man/FOCUS_2006_HS_ref_A_to_F.Rd @@ -0,0 +1,43 @@ +\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}
+ }
+}
+\note{
+ The comparison of these results with the results obtained with the
+ current version of \code{kinfit} can be found in the package vignette.
+}
+\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 0000000..fb6b304 --- /dev/null +++ b/man/FOCUS_2006_SFO_ref_A_to_F.Rd @@ -0,0 +1,41 @@ +\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}
+ }
+}
+\note{
+ The comparison of these results with the results obtained with the
+ current version of \code{kinfit} can be found in the package vignette.
+}
+\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/FOMC.Rd b/man/FOMC.Rd new file mode 100644 index 0000000..7228b1b --- /dev/null +++ b/man/FOMC.Rd @@ -0,0 +1,49 @@ +\name{FOMC}
+\Rdversion{1.1}
+\alias{FOMC}
+\title{ First-Order Multi-Compartment kinetics }
+\description{
+ Function describing exponential decline from a defined starting value, with
+ a decreasing rate constant.
+
+ The form given here differs slightly from the original reference by Gustafson
+ and Holden (1990). The parameter \code{beta} corresponds to 1/beta in the
+ original equation.
+}
+\usage{
+FOMC(t, parent.0, alpha, beta)
+}
+\arguments{
+ \item{t}{ Time. }
+ \item{parent.0}{ Starting value for the response variable at time zero. }
+ \item{alpha}{
+ Shape parameter determined by coefficient of variation of rate constant
+ values. }
+ \item{beta}{
+ Location parameter.
+}
+}
+\note{
+ The FOMC kinetic model reduces to the \code{\link{SFO}} kinetic model for
+ large values of \code{alpha} and \code{beta} with
+ \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}.
+}
+\value{
+ The value of the response variable at time \code{t}.
+}
+\references{
+ 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}
+
+ Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A
+ new model based on spatial variability. \emph{Environmental Science and
+ Technology} \bold{24}, 1032-1038
+}
+\author{ Johannes Ranke }
+\examples{
+ \dontrun{plot(function(x) FOMC(x, 100, 10, 2), 0, 2)}
+}
+\keyword{ manip }
diff --git a/man/HS.Rd b/man/HS.Rd new file mode 100644 index 0000000..9adbd18 --- /dev/null +++ b/man/HS.Rd @@ -0,0 +1,35 @@ +\name{HS}
+\Rdversion{1.1}
+\alias{HS}
+\title{ Hockey-Stick kinetics }
+\description{
+ Function describing two exponential decline functions with a break point
+ between them.
+}
+\usage{
+HS(t, parent.0, k1, k2, tb)
+}
+\arguments{
+ \item{t}{ Time. }
+ \item{parent.0}{ Starting value for the response variable at time zero. }
+ \item{k1}{ First kinetic constant. }
+ \item{k2}{ Second kinetic constant. }
+ \item{tb}{ Break point. Before this time, exponential decline according
+ to \code{k1} is calculated, after this time, exponential decline proceeds
+ according to \code{k2}. }
+}
+\value{
+ The value of the response variable at time \code{t}.
+}
+\references{
+ 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}
+}
+\author{ Johannes Ranke }
+\examples{
+ \dontrun{plot(function(x) HS(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))}
+}
+\keyword{ manip }
diff --git a/man/SFO.Rd b/man/SFO.Rd new file mode 100644 index 0000000..e4986da --- /dev/null +++ b/man/SFO.Rd @@ -0,0 +1,30 @@ +\name{SFO}
+\Rdversion{1.1}
+\alias{SFO}
+\title{ Single First-Order kinetics }
+\description{
+ Function describing exponential decline from a defined starting value.
+}
+\usage{
+ SFO(t, parent.0, k)
+}
+\arguments{
+ \item{t}{ Time. }
+ \item{parent.0}{ Starting value for the response variable at time zero. }
+ \item{k}{ Kinetic constant. }
+}
+\value{
+ The value of the response variable at time \code{t}.
+}
+\references{
+ 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}
+}
+\author{ Johannes Ranke }
+\examples{
+ \dontrun{plot(function(x) SFO(x, 100, 3), 0, 2)}
+}
+\keyword{ manip }
diff --git a/man/kinerrmin.Rd b/man/kinerrmin.Rd new file mode 100644 index 0000000..1afddf0 --- /dev/null +++ b/man/kinerrmin.Rd @@ -0,0 +1,43 @@ +\name{kinerrmin}
+\Rdversion{1.1}
+\alias{kinerrmin}
+\title{
+Calculate the minimum error to assume in order to pass the variance test
+}
+\description{
+This function uses \code{\link{optimize}} in order to iteratively find the
+smallest relative error still resulting in passing the chi-squared test
+as defined in the FOCUS kinetics report from 2006.
+}
+\usage{
+kinerrmin(kinfits, kinmodel = "SFO", alpha = 0.05)
+}
+\arguments{
+ \item{kinfits}{
+The list of kinetic model(s) from which to select. Usually this will have been
+generated by \code{\link{kinfit}}.
+}
+ \item{kinmodel}{
+The kinetic model to be checked. Should be one of the names of the kinetic models used for generating \code{kinfits}.
+}
+ \item{alpha}{
+The confidence level chosen for the chi-squared test.
+}
+}
+\value{
+The relative error, expressed as a fraction.
+}
+\references{
+ 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}
+}
+\author{ Johannes Ranke }
+\examples{
+data(FOCUS_2006_A)
+kinfits <- kinfit(FOCUS_2006_A)
+kinerrmin(kinfits)
+}
+\keyword{ manip }
diff --git a/man/kinfit.Rd b/man/kinfit.Rd new file mode 100644 index 0000000..f0301fd --- /dev/null +++ b/man/kinfit.Rd @@ -0,0 +1,77 @@ +\name{kinfit}
+\Rdversion{1.1}
+\alias{kinfit}
+\title{
+Fit kinetic models to chemical degradation data
+}
+\description{
+ A selection of kinetic models as defined in the FOCUS kinetics report from
+ 2006 are fitted to a given dataframe of chemical degradation data.
+}
+\usage{
+kinfit(kindata, kinmodels = c("SFO"), parent.0.user = NA,
+ start.SFO = list(parent.0 = NA, k = NA),
+ start.FOMC = list(parent.0 = NA, alpha = NA, beta = NA),
+ start.DFOP = list(parent.0 = NA, k1 = NA, k2 = NA, g = NA),
+ start.HS = list(parent.0 = NA, k1 = NA, k2 = NA, tb = NA),
+ algorithm = "port")
+}
+\arguments{
+ \item{kindata}{
+ A data frame containing a time variable named \code{t} and concentration
+ data for the parent compound named \code{parent}.
+ }
+ \item{kinmodels}{
+ An array of character strings which are names of the models to be fit.
+ Possible names are \code{\link{SFO}}, \code{\link{FOMC}}, \code{\link{DFOP}}
+ and \code{\link{HS}}.
+ }
+ \item{parent.0.user}{
+ The user can give a starting estimate for parent.0 here, overriding other
+ potential sources for starting values as specified below.
+ }
+ \item{start.SFO}{
+ A list of starting parameters for fitting the \code{\link{SFO}} model,
+ containing \code{parent.0} and \code{k}.
+ }
+ \item{start.FOMC}{
+ A list of starting parameters for fitting the \code{\link{FOMC}} model,
+ containing \code{parent.0}, \code{alpha} and \code{beta}.
+ }
+ \item{start.DFOP}{
+ A list of starting parameters for fitting the \code{\link{DFOP}} model,
+ containing \code{parent.0}, \code{k1}, \code{k2} and \code{g}.
+ }
+ \item{start.HS}{
+ A list of starting parameters for fitting the \code{\link{HS}} model,
+ containing \code{parent.0}, \code{k1}, \code{k2} and \code{tb}.
+ }
+ \item{algorithm}{
+ The algorithm to use for the calls to \code{\link{nls}}.
+ }
+}
+\details{
+ Per default all starting parameters are \code{NA} and the function tries to
+ find suitable starting parameters on its own.
+}
+\value{
+ A list of models of class \code{nls} representing the models that were
+ fitted successfully.
+}
+\references{
+ 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}
+}
+\author{ Johannes Ranke }
+\examples{
+data(FOCUS_2006_A)
+(kinfits <- kinfit(FOCUS_2006_A))
+data(FOCUS_2006_B)
+(kinfits <- kinfit(FOCUS_2006_B, kinmodels=c("SFO","FOMC")))
+}
+\keyword{ models }
+\keyword{ regression }
+\keyword{ nonlinear }
diff --git a/man/kinobject.Rd b/man/kinobject.Rd new file mode 100644 index 0000000..cd6f0ca --- /dev/null +++ b/man/kinobject.Rd @@ -0,0 +1,29 @@ +\name{kinobject}
+\Rdversion{1.1}
+\alias{kinobject}
+\title{
+Creates list representing a kinetic experiment or trial
+}
+\description{
+Function to initialise an object representing a kinetic experiment or trial.
+}
+\usage{
+ kinobject(parent, type, system, layers = NA, sampling_times = NA)
+}
+\arguments{
+ \item{parent}{ The name of the parent compound }
+ \item{type}{ The type of experiment or trial, optionally with an ID }
+ \item{system}{ System name. Important if several systems were used, e.g. several soils. }
+ \item{layers}{ Optional specification of the layer names in a field trial. }
+ \item{sampling_times}{ Optional specification of the sampling time pionts. }
+}
+\value{
+ A list containing the specified information.
+}
+\author{ Johannes Ranke }
+\examples{
+ko <- kinobject("Compound XY",
+ "Degradation in the environment",
+ "System 1")
+}
+\keyword{ manip }
diff --git a/man/kinobjects.Rd b/man/kinobjects.Rd new file mode 100644 index 0000000..7c960f3 --- /dev/null +++ b/man/kinobjects.Rd @@ -0,0 +1,29 @@ +\name{kinobjects}
+\Rdversion{1.1}
+\alias{kinobjects}
+\title{
+Creates list of objects, each representing a kinetic experiment or trial
+}
+\description{
+Function to initialise several objects representing a kinetic experiment or trial at once.
+}
+\usage{
+ kinobjects(parent, type, systems, layers = NA, sampling_times = NA)
+}
+\arguments{
+ \item{parent}{ The name of the parent compound }
+ \item{type}{ The type of experiment or trial, optionally with an ID }
+ \item{systems}{ An array of the system names }
+ \item{layers}{ Optional specification of the layer names in a field trial. }
+ \item{sampling_times}{ Optional specification of the sampling time pionts. }
+}
+\value{
+ A list of lists containing the specified information.
+}
+\author{ Johannes Ranke }
+\examples{
+ko <- kinobjects("Compound XY",
+ "Degradation in the environment",
+ c("System 1", "System 2", "System 3"))
+}
+\keyword{ manip }
diff --git a/man/kinplot.Rd b/man/kinplot.Rd new file mode 100644 index 0000000..9e684b7 --- /dev/null +++ b/man/kinplot.Rd @@ -0,0 +1,50 @@ +\name{kinplot}
+\Rdversion{1.1}
+\alias{kinplot}
+\title{
+Creates a plot of the kinetic fits
+}
+\description{
+Function to create a plot for a set of fitted models
+}
+\usage{
+kinplot(kinobject, xlab = "Time [days]", ylab = "Parent [\% of applied radioactivity]", ylim = c("auto", "auto"), lpos = "topright")
+}
+\arguments{
+ \item{kinobject}{
+ A list containing the following elements:
+ The name of the parent compound to be output (\code{parent}),
+ the type of the test system (\code{type}),
+ the name of the specific test system used for generating this dataset
+ (\code{system}),
+ the list of fitted kinetic models (\code{fits}), as returned by
+ \code{\link{kinfit}}, and the list of results (\code{results})
+ as returned by \code{\link{kinresults}}.
+ Optionally also
+ the label position of the test compound (\code{label}) and
+ the source of the data (\code{source}). }
+ \item{xlab}{ Label for the x axis. }
+ \item{ylab}{ Label for the y axis. }
+ \item{ylim}{ An array of length two holding the range for values on the y axis or "auto". }
+ \item{lpos}{ Where should the legend be placed? Will be passed on to
+ \code{\link{legend}}. }
+}
+\value{
+The function is called for its side effect, namely creating a plot with
+the fitted model.
+}
+\author{ Johannes Ranke }
+\examples{
+data(FOCUS_2006_C)
+kinfits <- kinfit(FOCUS_2006_C, kinmodels = c("SFO", "FOMC", "DFOP"))
+kinobject <- list(
+ parent = "Compound XY",
+ type = "Degradation in the environment",
+ system = "System 1",
+ source = "Synthetic example data from FOCUS kinetics",
+ data = FOCUS_2006_C,
+ fits = kinfits,
+ results = kinresults(kinfits))
+\dontrun{kinplot(kinobject)}
+}
+\keyword{ hplot }
diff --git a/man/kinreport.Rd b/man/kinreport.Rd new file mode 100644 index 0000000..de7e632 --- /dev/null +++ b/man/kinreport.Rd @@ -0,0 +1,48 @@ +\name{kinreport}
+\Rdversion{1.1}
+\alias{kinreport}
+\title{
+Creates a report of the kinetic fits
+}
+\description{
+Function to create a report for a set of fitted models, passing it to the
+console as well as to a file, if specified.
+}
+\usage{
+kinreport(kinobject, file = NA, vcov = FALSE, endpoint.digits = 1)
+}
+\arguments{
+ \item{kinobject}{
+ A list containing the following elements:
+ The name of the parent compound to be output (\code{parent}),
+ the type of the test system (\code{type}),
+ the name of the specific test system used for generating this dataset
+ (\code{system}),
+ the list of fitted kinetic models (\code{fits}), as returned by
+ \code{\link{kinfit}}, and the list of results (\code{results})
+ as returned by \code{\link{kinresults}}.
+ Optionally also
+ the label position of the test compound (\code{label}) and
+ the source of the data (\code{source}). }
+ \item{file}{ The name of the file to which to write. }
+ \item{vcov}{ Should the variance-covariance matrix/matrices be reported? }
+ \item{endpoint.digits}{ How many digits should be reported for DT50 and DT90 values? }
+}
+\value{
+The function is called for its side effect, namely the report being passed
+to the R console as well as to a text file.
+}
+\author{ Johannes Ranke }
+\examples{
+data(FOCUS_2006_A)
+kinfits <- kinfit(FOCUS_2006_A)
+kinobject <- list(
+ parent = "Compound XY",
+ type = "Degradation in the environment",
+ system = "System 1",
+ source = "Synthetic example data from FOCUS kinetics",
+ fits = kinfits,
+ results = kinresults(kinfits))
+kinreport(kinobject)
+}
+\keyword{ manip }
diff --git a/man/kinresplot.Rd b/man/kinresplot.Rd new file mode 100644 index 0000000..85ec333 --- /dev/null +++ b/man/kinresplot.Rd @@ -0,0 +1,49 @@ +\name{kinresplot}
+\Rdversion{1.1}
+\alias{kinresplot}
+\title{
+Creates a plot of the residual for specified kinetic fits
+}
+\description{
+Function to create a residual plot for a specified fitted model
+}
+\usage{
+kinresplot(kinobject, kinmodel, xlab = "Time [days]", ylab = "Residual [\% of applied radioactivity]", maxabs = "auto")
+}
+\arguments{
+ \item{kinobject}{
+ A list containing the following elements:
+ The name of the parent compound to be output (\code{parent}),
+ the type of the test system (\code{type}),
+ the name of the specific test system used for generating this dataset
+ (\code{system}),
+ the list of fitted kinetic models (\code{fits}), as returned by
+ \code{\link{kinfit}}, and optionally the list of results
+ (\code{results}) as returned by \code{\link{kinresults}}.
+ Also optional is the label position of the test compound (\code{label})
+ and the source of the data (\code{source}). }
+ \item{kinmodel}{ The fitted model for which the residuals should be plotted. }
+ \item{xlab}{ Label for the x axis. }
+ \item{ylab}{ Label for the y axis. }
+ \item{maxabs}{ Maximum value of the absolute residuals, will be calculated
+ from the residuals if not specified otherwise. }
+}
+\value{
+The function is called for its side effect, namely creating a residual plot
+for the specified fit.
+}
+\author{ Johannes Ranke }
+\examples{
+data(FOCUS_2006_C)
+kinfits <- kinfit(FOCUS_2006_C)
+kinobject <- list(
+ parent = "Compound XY",
+ type = "Degradation in the environment",
+ system = "System 1",
+ source = "Synthetic example data from FOCUS kinetics",
+ data = FOCUS_2006_C,
+ fits = kinfits,
+ results = kinresults(kinfits))
+\dontrun{kinresplot(kinobject, "SFO")}
+}
+\keyword{ hplot }
diff --git a/man/kinresults.Rd b/man/kinresults.Rd new file mode 100644 index 0000000..6ab93a7 --- /dev/null +++ b/man/kinresults.Rd @@ -0,0 +1,45 @@ +\name{kinresults}
+\Rdversion{1.1}
+\alias{kinresults}
+\title{
+Function to collect useful results for a set of fitted kinetic models
+}
+\description{
+This function collects the parameters and some statistics for the fitted kinetic
+models. It also generates DT50 and DT90 estimates.
+}
+\usage{
+kinresults(kinfits, alpha = 0.05, SFORB = TRUE)
+}
+\arguments{
+ \item{kinfits}{
+The list of kinetic model(s) for which to collect results. Usually this will
+have been generated by \code{\link{kinfit}}.
+}
+ \item{alpha}{
+The confidence level chosen for the chi-squared test used in the call to
+\code{\link{kinerrmin}}.
+}
+ \item{SFORB}{
+Should the results of the \code{\link{DFOP}} model be presented as parameters
+to the Single First-Order Reversible Binding (SFORB) model? }
+}
+\value{
+A list containing a list of the parameters fitted by the models, a dataframe
+containing some statistics for each of the fitted models, and a dataframe with
+the resulting DT50 and DT90 values.
+}
+\references{
+ 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}
+}
+\author{ Johannes Ranke }
+\examples{
+data(FOCUS_2006_A)
+kinfits <- kinfit(FOCUS_2006_A)
+kinresults(kinfits)
+}
+\keyword{ manip }
diff --git a/man/kinwrite.KinGUI.Rd b/man/kinwrite.KinGUI.Rd new file mode 100644 index 0000000..f5a5ddc --- /dev/null +++ b/man/kinwrite.KinGUI.Rd @@ -0,0 +1,47 @@ +\name{kinwrite.KinGUI}
+\Rdversion{1.1}
+\alias{kinwrite.KinGUI}
+\encoding{latin1}
+\title{
+Function to write KinGUI input files from kinetic data
+}
+\description{
+This function takes an R object as used by the \code{kinfit} package
+and tries to write a text file which is compatible with the KinGUI
+software tool.
+}
+\usage{
+kinwrite.KinGUI(kinobject, file, comment=NA)
+}
+\arguments{
+ \item{kinobject}{
+ A list containing the following elements:
+ The name of the parent compound to be output (\code{parent}),
+ the type of the test system (\code{type}),
+ the name of the specific test system used for generating this dataset
+ (\code{system}),
+ a data frame containing the raw data (\code{data}),
+ which should be in the same form as required by
+ by \code{\link{kinfit}}.
+}
+ \item{file}{
+The filename, potentially including the full path, specifying where the output whould be written.
+}
+ \item{comment}{
+An optional comment that will be integrated in the header of the KinGUI input file.
+}
+}
+\value{
+The function is called for its side effect, namely the generation of a text file.
+}
+\references{
+Schäfer D, Kikolasch 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.
+}
+\note{
+The KinGUI software tool was announced to be freely available on CD from the main author of the paper cited above, Dieter Schäfer <dieter.schaefer@bayercropscience.com>.
+}
+\author{
+Johannes Ranke
+}
+
+\keyword{ IO }
|