From 12934520d7ec3218ce1505787b6066334a24a562 Mon Sep 17 00:00:00 2001 From: jranke Date: Tue, 30 Mar 2010 19:49:44 +0000 Subject: 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 --- man/DFOP.Rd | 37 +++++++++++++++++++ man/FOCUS_2006_A.Rd | 29 +++++++++++++++ man/FOCUS_2006_B.Rd | 29 +++++++++++++++ man/FOCUS_2006_C.Rd | 30 +++++++++++++++ man/FOCUS_2006_D.Rd | 33 +++++++++++++++++ man/FOCUS_2006_DFOP_ref_A_to_B.Rd | 43 ++++++++++++++++++++++ man/FOCUS_2006_E.Rd | 32 ++++++++++++++++ man/FOCUS_2006_F.Rd | 32 ++++++++++++++++ man/FOCUS_2006_FOMC_ref_A_to_F.Rd | 42 +++++++++++++++++++++ man/FOCUS_2006_HS_ref_A_to_F.Rd | 43 ++++++++++++++++++++++ man/FOCUS_2006_SFO_ref_A_to_F.Rd | 41 +++++++++++++++++++++ man/FOMC.Rd | 49 +++++++++++++++++++++++++ man/HS.Rd | 35 ++++++++++++++++++ man/SFO.Rd | 30 +++++++++++++++ man/kinerrmin.Rd | 43 ++++++++++++++++++++++ man/kinfit.Rd | 77 +++++++++++++++++++++++++++++++++++++++ man/kinobject.Rd | 29 +++++++++++++++ man/kinobjects.Rd | 29 +++++++++++++++ man/kinplot.Rd | 50 +++++++++++++++++++++++++ man/kinreport.Rd | 48 ++++++++++++++++++++++++ man/kinresplot.Rd | 49 +++++++++++++++++++++++++ man/kinresults.Rd | 45 +++++++++++++++++++++++ man/kinwrite.KinGUI.Rd | 47 ++++++++++++++++++++++++ 23 files changed, 922 insertions(+) create mode 100644 man/DFOP.Rd create mode 100644 man/FOCUS_2006_A.Rd create mode 100644 man/FOCUS_2006_B.Rd create mode 100644 man/FOCUS_2006_C.Rd create mode 100644 man/FOCUS_2006_D.Rd create mode 100644 man/FOCUS_2006_DFOP_ref_A_to_B.Rd create mode 100644 man/FOCUS_2006_E.Rd create mode 100644 man/FOCUS_2006_F.Rd create mode 100644 man/FOCUS_2006_FOMC_ref_A_to_F.Rd create mode 100644 man/FOCUS_2006_HS_ref_A_to_F.Rd create mode 100644 man/FOCUS_2006_SFO_ref_A_to_F.Rd create mode 100644 man/FOMC.Rd create mode 100644 man/HS.Rd create mode 100644 man/SFO.Rd create mode 100644 man/kinerrmin.Rd create mode 100644 man/kinfit.Rd create mode 100644 man/kinobject.Rd create mode 100644 man/kinobjects.Rd create mode 100644 man/kinplot.Rd create mode 100644 man/kinreport.Rd create mode 100644 man/kinresplot.Rd create mode 100644 man/kinresults.Rd create mode 100644 man/kinwrite.KinGUI.Rd (limited to 'man') 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 . +} +\author{ +Johannes Ranke +} + +\keyword{ IO } -- cgit v1.2.1