From e959fde98f95f3595e01490b67892678bbcd1b27 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 7 May 2014 14:47:28 +0200 Subject: Fork the gmkin GUI from mkin. See ChangeLog for details --- man/DFOP.solution.Rd | 36 ------ man/FOCUS_2006_DFOP_ref_A_to_B.Rd | 39 ------ man/FOCUS_2006_FOMC_ref_A_to_F.Rd | 38 ------ man/FOCUS_2006_HS_ref_A_to_F.Rd | 39 ------ man/FOCUS_2006_SFO_ref_A_to_F.Rd | 37 ------ man/FOCUS_2006_datasets.Rd | 35 ------ man/FOMC.solution.Rd | 49 -------- man/HS.solution.Rd | 34 ----- man/SFO.solution.Rd | 29 ----- man/SFORB.solution.Rd | 36 ------ man/endpoints.Rd | 33 ----- man/ilr.Rd | 56 --------- man/mccall81_245T.Rd | 42 ------- man/mkin_long_to_wide.Rd | 36 ------ man/mkin_wide_to_long.Rd | 32 ----- man/mkinerrmin.Rd | 44 ------- man/mkinfit.Rd | 254 -------------------------------------- man/mkinmod.Rd | 63 ---------- man/mkinparplot.Rd | 35 ------ man/mkinplot.Rd | 26 ---- man/mkinpredict.Rd | 91 -------------- man/mkinresplot.Rd | 67 ---------- man/plot.mkinfit.Rd | 94 -------------- man/schaefer07_complex_case.Rd | 42 ------- man/summary.mkinfit.Rd | 75 ----------- man/transform_odeparms.Rd | 69 ----------- 26 files changed, 1431 deletions(-) delete mode 100644 man/DFOP.solution.Rd delete mode 100644 man/FOCUS_2006_DFOP_ref_A_to_B.Rd delete mode 100644 man/FOCUS_2006_FOMC_ref_A_to_F.Rd delete mode 100644 man/FOCUS_2006_HS_ref_A_to_F.Rd delete mode 100644 man/FOCUS_2006_SFO_ref_A_to_F.Rd delete mode 100644 man/FOCUS_2006_datasets.Rd delete mode 100644 man/FOMC.solution.Rd delete mode 100644 man/HS.solution.Rd delete mode 100644 man/SFO.solution.Rd delete mode 100644 man/SFORB.solution.Rd delete mode 100644 man/endpoints.Rd delete mode 100644 man/ilr.Rd delete mode 100644 man/mccall81_245T.Rd delete mode 100644 man/mkin_long_to_wide.Rd delete mode 100644 man/mkin_wide_to_long.Rd delete mode 100644 man/mkinerrmin.Rd delete mode 100644 man/mkinfit.Rd delete mode 100644 man/mkinmod.Rd delete mode 100644 man/mkinparplot.Rd delete mode 100644 man/mkinplot.Rd delete mode 100644 man/mkinpredict.Rd delete mode 100644 man/mkinresplot.Rd delete mode 100644 man/plot.mkinfit.Rd delete mode 100644 man/schaefer07_complex_case.Rd delete mode 100644 man/summary.mkinfit.Rd delete mode 100644 man/transform_odeparms.Rd (limited to 'man') diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd deleted file mode 100644 index d30cf7f..0000000 --- a/man/DFOP.solution.Rd +++ /dev/null @@ -1,36 +0,0 @@ -\name{DFOP.solution} -\Rdversion{1.1} -\alias{DFOP.solution} -\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.solution(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} -} -\examples{ - \dontrun{plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))} -} -\keyword{ manip } diff --git a/man/FOCUS_2006_DFOP_ref_A_to_B.Rd b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd deleted file mode 100644 index 88bd4ac..0000000 --- a/man/FOCUS_2006_DFOP_ref_A_to_B.Rd +++ /dev/null @@ -1,39 +0,0 @@ -\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 deleted file mode 100644 index 2fcc2db..0000000 --- a/man/FOCUS_2006_FOMC_ref_A_to_F.Rd +++ /dev/null @@ -1,38 +0,0 @@ -\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 deleted file mode 100644 index 6fc9993..0000000 --- a/man/FOCUS_2006_HS_ref_A_to_F.Rd +++ /dev/null @@ -1,39 +0,0 @@ -\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 deleted file mode 100644 index 19650ed..0000000 --- a/man/FOCUS_2006_SFO_ref_A_to_F.Rd +++ /dev/null @@ -1,37 +0,0 @@ -\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/FOCUS_2006_datasets.Rd b/man/FOCUS_2006_datasets.Rd deleted file mode 100644 index 5053b88..0000000 --- a/man/FOCUS_2006_datasets.Rd +++ /dev/null @@ -1,35 +0,0 @@ -\name{FOCUS_2006_datasets} -\Rdversion{1.1} -\alias{FOCUS_2006_A} -\alias{FOCUS_2006_B} -\alias{FOCUS_2006_C} -\alias{FOCUS_2006_D} -\alias{FOCUS_2006_E} -\alias{FOCUS_2006_F} -\docType{data} -\title{ -Datasets A to F from the FOCUS Kinetics report from 2006 -} -\description{ -Data taken from FOCUS (2006), p. 258. -} -\usage{FOCUS_2006_datasets} -\format{ - 6 datasets with observations on the following variables. - \describe{ - \item{\code{name}}{a factor containing the name of the observed variable} - \item{\code{time}}{a numeric vector containing time points} - \item{\code{value}}{a numeric vector containing 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{ -FOCUS_2006_C -} -\keyword{datasets} diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd deleted file mode 100644 index d04d34e..0000000 --- a/man/FOMC.solution.Rd +++ /dev/null @@ -1,49 +0,0 @@ -\name{FOMC.solution} -\Rdversion{1.1} -\alias{FOMC.solution} -\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.solution(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 solution of the FOMC kinetic model reduces to the - \code{\link{SFO.solution}} 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 -} -\examples{ - \dontrun{plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2)} -} -\keyword{ manip } diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd deleted file mode 100644 index 71f68a1..0000000 --- a/man/HS.solution.Rd +++ /dev/null @@ -1,34 +0,0 @@ -\name{HS.solution} -\Rdversion{1.1} -\alias{HS.solution} -\title{ Hockey-Stick kinetics } -\description{ - Function describing two exponential decline functions with a break point - between them. -} -\usage{ -HS.solution(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} -} -\examples{ - \dontrun{plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))} -} -\keyword{ manip } diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd deleted file mode 100644 index 41a9ba9..0000000 --- a/man/SFO.solution.Rd +++ /dev/null @@ -1,29 +0,0 @@ -\name{SFO.solution} -\Rdversion{1.1} -\alias{SFO.solution} -\title{ Single First-Order kinetics } -\description{ - Function describing exponential decline from a defined starting value. -} -\usage{ - SFO.solution(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} -} -\examples{ - \dontrun{plot(function(x) SFO.solution(x, 100, 3), 0, 2)} -} -\keyword{ manip } diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd deleted file mode 100644 index a935f69..0000000 --- a/man/SFORB.solution.Rd +++ /dev/null @@ -1,36 +0,0 @@ -\name{SFORB.solution} -\Rdversion{1.1} -\alias{SFORB.solution} -\title{ Single First-Order Reversible Binding kinetics } -\description{ - Function describing the solution of the differential equations describing - the kinetic model with first-order terms for a two-way transfer from a free - to a bound fraction, and a first-order degradation term for the free - fraction. The initial condition is a defined amount in the free fraction and - no substance in the bound fraction. -} -\usage{ - SFORB.solution(t, parent.0, k_12, k_21, k_1output) -} -\arguments{ - \item{t}{ Time. } - \item{parent.0}{ Starting value for the response variable at time zero. } - \item{k_12}{ Kinetic constant describing transfer from free to bound. } - \item{k_21}{ Kinetic constant describing transfer from bound to free. } - \item{k_1output}{ Kinetic constant describing degradation of the free fraction. } -} -\value{ - The value of the response variable, which is the sum of free and bound - fractions 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} -} -\examples{ - \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)} -} -\keyword{ manip } diff --git a/man/endpoints.Rd b/man/endpoints.Rd deleted file mode 100644 index 21316cf..0000000 --- a/man/endpoints.Rd +++ /dev/null @@ -1,33 +0,0 @@ -\name{endpoints} -\alias{endpoints} -\title{ -Function to calculate endpoints for further use from kinetic models fitted with mkinfit -} -\description{ -This function calculates DT50 and DT90 values as well as formation fractions from kinetic models -fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, -the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but -with the advantage that the SFORB model can also be used for metabolites. -} -\usage{ -endpoints(fit, pseudoDT50 = FALSE) -} -\arguments{ - \item{fit}{ - An object of class \code{\link{mkinfit}}. -} - \item{pseudoDT50}{ - Should pseudoDT50 values for FOMC, DFOP and SFORB models be reported, as - recommended by the FOCUS group? Currently not implemented. -} -} -\note{ - The function is used internally by \code{\link{summary.mkinfit}}. -} -\value{ - A list with the components mentioned above. -} -\author{ - Johannes Ranke -} -\keyword{ manip } diff --git a/man/ilr.Rd b/man/ilr.Rd deleted file mode 100644 index cedb49c..0000000 --- a/man/ilr.Rd +++ /dev/null @@ -1,56 +0,0 @@ -\name{ilr} -\alias{ilr} -\alias{invilr} -\title{ - Function to perform isotropic log-ratio transformation -} -\description{ - This implementation is a special case of the class of isotropic log-ratio transformations. -} -\usage{ - ilr(x) - invilr(x) -} -\arguments{ - \item{x}{ - A numeric vector. Naturally, the forward transformation is only sensible for - vectors with all elements being greater than zero. - } -} -\value{ - The result of the forward or backward transformation. The returned components always - sum to 1 for the case of the inverse log-ratio transformation. -} -\references{ - Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248 -} -\author{ - René Lehmann and Johannes Ranke -} -\seealso{ - Other implementations are in R packages \code{compositions} and \code{robCompositions}. -} -\examples{ -# Order matters -ilr(c(0.1, 1, 10)) -ilr(c(10, 1, 0.1)) -# Equal entries give ilr transformations with zeros as elements -ilr(c(3, 3, 3)) -# Almost equal entries give small numbers -ilr(c(0.3, 0.4, 0.3)) -# Only the ratio between the numbers counts, not their sum -invilr(ilr(c(0.7, 0.29, 0.01))) -invilr(ilr(2.1 * c(0.7, 0.29, 0.01))) -# Inverse transformation of larger numbers gives unequal elements -invilr(-10) -invilr(c(-10, 0)) -# The sum of the elements of the inverse ilr is 1 -sum(invilr(c(-10, 0))) -# This is why we do not need all elements of the inverse transformation to go back: -a <- c(0.1, 0.3, 0.5) -b <- invilr(a) -length(b) # Four elements -ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5) -} - -\keyword{ manip } diff --git a/man/mccall81_245T.Rd b/man/mccall81_245T.Rd deleted file mode 100644 index 6c1a137..0000000 --- a/man/mccall81_245T.Rd +++ /dev/null @@ -1,42 +0,0 @@ -\name{mccall81_245T} -\alias{mccall81_245T} -\docType{data} -\title{ - Datasets on aerobic soil metabolism of 2,4,5-T in six soils -} -\description{ - Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding - 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether - extracts. -} -\usage{mccall81_245T} -\format{ - A dataframe containing the following variables. - \describe{ - \item{\code{name}}{the name of the compound observed. Note that T245 is used as - an acronym for 2,4,5-T. T245 is a legitimate object name - in R, which is necessary for specifying models using - \code{\link{mkinmod}}.} - \item{\code{time}}{a numeric vector containing sampling times in days after - treatment} - \item{\code{value}}{a numeric vector containing concentrations in percent of applied radioactivity} - \item{\code{soil}}{a factor containing the name of the soil} - } -} -\source{ - McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 - \url{http://dx.doi.org/10.1021/jf00103a026} -} -\examples{ - SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"), - phenol = list(type = "SFO", to = "anisole"), - anisole = list(type = "SFO")) - \dontrun{fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce")) - summary(fit.1, data = FALSE)} - # No covariance matrix and k_phenol_sink is really small, therefore fix it to zero - fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), - parms.ini = c(k_phenol_sink = 0), - fixed_parms = "k_phenol_sink") - summary(fit.2, data = FALSE) -} -\keyword{datasets} diff --git a/man/mkin_long_to_wide.Rd b/man/mkin_long_to_wide.Rd deleted file mode 100644 index e583664..0000000 --- a/man/mkin_long_to_wide.Rd +++ /dev/null @@ -1,36 +0,0 @@ -\name{mkin_long_to_wide} -\alias{mkin_long_to_wide} -\title{ - Convert a dataframe from long to wide format. -} -\usage{ -mkin_long_to_wide(long_data, time = "time", outtime = "time") -} -\description{ - This function takes a dataframe in the long form as required by \code{\link{modCost}} - and converts it into a dataframe with one independent variable and several - dependent variables as columns. -} -\arguments{ - \item{long_data}{ - The dataframe must contain one variable called "time" with the time values specified by the - \code{time} argument, one column called "name" with the grouping of the observed values, and - finally one column of observed values called "value". -} - \item{time}{ - The name of the time variable in the long input data. -} - \item{outtime}{ - The name of the time variable in the wide output data. -} -} -\value{ - Dataframe in wide format. -} -\author{ - Johannes Ranke -} -\examples{ -mkin_long_to_wide(FOCUS_2006_D) -} -\keyword{ manip } diff --git a/man/mkin_wide_to_long.Rd b/man/mkin_wide_to_long.Rd deleted file mode 100644 index d3dd200..0000000 --- a/man/mkin_wide_to_long.Rd +++ /dev/null @@ -1,32 +0,0 @@ -\name{mkin_wide_to_long} -\alias{mkin_wide_to_long} -\title{ - Convert a dataframe with observations over time into long format. -} -\usage{ -mkin_wide_to_long(wide_data, time = "t") -} -\description{ - This function simply takes a dataframe with one independent variable and several - dependent variable and converts it into the long form as required by \code{\link{modCost}}. -} -\arguments{ - \item{wide_data}{ - The dataframe must contain one variable with the time values specified by the - \code{time} argument and usually more than one column of observed values. -} - \item{time}{ - The name of the time variable. -} -} -\value{ - Dataframe in long format as needed for \code{\link{modCost}}. -} -\author{ - Johannes Ranke -} -\examples{ -wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5)) -mkin_wide_to_long(wide) -} -\keyword{ manip } diff --git a/man/mkinerrmin.Rd b/man/mkinerrmin.Rd deleted file mode 100644 index c43d87a..0000000 --- a/man/mkinerrmin.Rd +++ /dev/null @@ -1,44 +0,0 @@ -\name{mkinerrmin} -\Rdversion{1.1} -\alias{mkinerrmin} -\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{ -mkinerrmin(fit, alpha = 0.05) -} -\arguments{ - \item{fit}{ - an object of class \code{\link{mkinfit}}. - } - \item{alpha}{ - The confidence level chosen for the chi-squared test. -} -} -\value{ - A dataframe with the following components: - \item{err.min}{The relative error, expressed as a fraction.} - \item{n.optim}{The number of optimised parameters attributed to the data series.} - \item{df}{The number of remaining degrees of freedom for the chi2 error level - calculations. Note that mean values are used for the chi2 statistic and - therefore every time point with observed values in the series only counts - one time.} - The dataframe has one row for the total dataset and one further row for - each observed state variable in the model. -} -\details{ - This function is used internally by \code{\link{summary.mkinfit}}. -} -\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} -} -\keyword{ manip } diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd deleted file mode 100644 index 823ceee..0000000 --- a/man/mkinfit.Rd +++ /dev/null @@ -1,254 +0,0 @@ -\name{mkinfit} -\alias{mkinfit} -\title{ - Fit a kinetic model to data with one or more state variables. -} -\description{ - This function uses the Flexible Modelling Environment package - \code{\link{FME}} to create a function calculating the model cost, i.e. the - deviation between the kinetic model and the observed data. This model cost is - then minimised using the Levenberg-Marquardt algorithm \code{\link{nls.lm}}, - using the specified initial or fixed parameters and starting values. - In each step of the optimsation, the kinetic model is solved using the - function \code{\link{mkinpredict}}. The variance of the residuals for each - observed variable can optionally be iteratively reweighted until convergence - using the argument \code{reweight.method = "obs"}. -} -\usage{ -mkinfit(mkinmod, observed, - parms.ini = "auto", - state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), - fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], - solution_type = "auto", - method.ode = "lsoda", - method.modFit = "Marq", - control.modFit = list(), - transform_rates = TRUE, - transform_fractions = TRUE, - plot = FALSE, quiet = FALSE, err = NULL, weight = "none", - scaleVar = FALSE, - atol = 1e-8, rtol = 1e-10, n.outtimes = 100, - reweight.method = NULL, - reweight.tol = 1e-8, reweight.max.iter = 10, - trace_parms = FALSE, ...) -} -\arguments{ - \item{mkinmod}{ - A list of class \code{\link{mkinmod}}, containing the kinetic model to be fitted to the data. - } - \item{observed}{ - The observed data. It has to be in the long format as described in - \code{\link{modFit}}, i.e. the first column called "name" must contain the - name of the observed variable for each data point. The second column must - contain the times of observation, named "time". The third column must be - named "value" and contain the observed values. Optionally, a further column - can contain weights for each data point. If it is not named "err", its name - must be passed as a further argument named \code{err} which is then passed - on to \code{\link{modFit}}. - } - \item{parms.ini}{ - A named vector of initial values for the parameters, including parameters - to be optimised and potentially also fixed parameters as indicated by - \code{fixed_parms}. If set to "auto", initial values for rate constants - are set to default values. Using parameter names that are not in the model - gives an error. - - It is possible to only specify a subset of the parameters that the model - needs. You can use the parameter lists "bparms.ode" from a previously - fitted model, which contains the differential equation parameters from this - model. This works nicely if the models are nested. An example is given - below. - } - \item{state.ini}{ - A named vector of initial values for the state variables of the model. In - case the observed variables are represented by more than one model - variable, the names will differ from the names of the observed variables - (see \code{map} component of \code{\link{mkinmod}}). The default is to set - the initial value of the first model variable to 100 and all others to 0. - } - \item{fixed_parms}{ - The names of parameters that should not be optimised but rather kept at the - values specified in \code{parms.ini}. - } - \item{fixed_initials}{ - The names of model variables for which the initial state at time 0 should - be excluded from the optimisation. Defaults to all state variables except - for the first one. - } - \item{solution_type}{ - If set to "eigen", the solution of the system of differential equations is - based on the spectral decomposition of the coefficient matrix in cases that - this is possible. If set to "deSolve", a numerical ode solver from package - \code{\link{deSolve}} is used. If set to "analytical", an analytical - solution of the model is used. This is only implemented for simple - degradation experiments with only one state variable, i.e. with no - metabolites. The default is "auto", which uses "analytical" if possible, - otherwise "eigen" if the model can be expressed using eigenvalues and - eigenvectors, and finally "deSolve" for the remaining models (time - dependence of degradation rates and metabolites). This argument is passed - on to the helper function \code{\link{mkinpredict}}. - } - \item{method.ode}{ - The solution method passed via \code{\link{mkinpredict}} to - \code{\link{ode}} in case the solution type is "deSolve". The default - "lsoda" is performant, but sometimes fails to converge. - } - \item{method.modFit}{ - The optimisation method passed to \code{\link{modFit}}. The default "Marq" - is the Levenberg Marquardt algorithm \code{\link{nls.lm}} from the package - \code{minpack.lm}. Often other methods need more iterations to find the - same result. When using "Pseudo", "upper" and "lower" need to be - specified for the transformed parameters. - } - \item{control.modFit}{ - Additional arguments passed to the optimisation method used by - \code{\link{modFit}}. - } - \item{transform_rates}{ - Boolean specifying if kinetic rate constants should be transformed in the - model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. If TRUE, also - alpha and beta parameters of the FOMC model are log-transformed, as well - as k1 and k2 rate constants for the DFOP and HS models. - If TRUE, zero is used as a lower bound for the rates in the optimisation. - } - \item{transform_fractions}{ - Boolean specifying if formation fractions constants should be transformed in the - model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. The default (TRUE) is - to do transformations. The g parameter of the DFOP and HS models are also - transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the \code{\link{ilr}} - transformation. - } - \item{plot}{ - Should the observed values and the numerical solutions be plotted at each - stage of the optimisation? - } - \item{quiet}{ - Suppress printing out the current model cost after each improvement? - } - \item{err }{either \code{NULL}, or the name of the column with the - \emph{error} estimates, used to weigh the residuals (see details of - \code{\link{modCost}}); if \code{NULL}, then the residuals are not weighed. - } - \item{weight}{ - only if \code{err}=\code{NULL}: how to weight the residuals, one of "none", - "std", "mean", see details of \code{\link{modCost}}. - } - \item{scaleVar}{ - Will be passed to \code{\link{modCost}}. Default is not to scale Variables - according to the number of observations. - } - \item{atol}{ - Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8, - lower than in \code{\link{lsoda}}. - } - \item{rtol}{ - Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10, - much lower than in \code{\link{lsoda}}. - } - \item{n.outtimes}{ - The length of the dataseries that is produced by the model prediction - function \code{\link{mkinpredict}}. This impacts the accuracy of - the numerical solver if that is used (see \code{solution_type} argument. - The default value is 100. - } - \item{reweight.method}{ - The method used for iteratively reweighting residuals, also known - as iteratively reweighted least squares (IRLS). Default is NULL, - the other method implemented is called "obs", meaning that each - observed variable is assumed to have its own variance, this is - estimated from the fit and used for weighting the residuals - in each iteration until convergence of this estimate up to - \code{reweight.tol} or up to the maximum number of iterations - specified by \code{reweight.max.iter}. - } - \item{reweight.tol}{ - Tolerance for convergence criterion for the variance components - in IRLS fits. - } - \item{reweight.max.iter}{ - Maximum iterations in IRLS fits. - } - \item{trace_parms}{ - Should a trace of the parameter values be listed? - } - \item{\dots}{ - Further arguments that will be passed to \code{\link{modFit}}. - } -} -\value{ - A list with "mkinfit" and "modFit" in the class attribute. - A summary can be obtained by \code{\link{summary.mkinfit}}. -} -\note{ - The implementation of iteratively reweighted least squares is inspired by the - work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei - Gao). A similar implemention can also be found in CAKE 2.0, which is the - other GUI derivative of mkin, sponsored by Syngenta. -} -\author{ - Johannes Ranke -} -\examples{ -# One parent compound, one metabolite, both single first order. -SFO_SFO <- mkinmod( - parent = list(type = "SFO", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) -# Fit the model to the FOCUS example dataset D using defaults -fit <- mkinfit(SFO_SFO, FOCUS_2006_D) -summary(fit) - -# Use stepwise fitting, using optimised parameters from parent only fit, FOMC -\dontrun{ -FOMC <- mkinmod(parent = list(type = "FOMC")) -FOMC_SFO <- mkinmod( - parent = list(type = "FOMC", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) -# Fit the model to the FOCUS example dataset D using defaults -fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D) -# Use starting parameters from parent only FOMC fit -fit.FOMC = mkinfit(FOMC, FOCUS_2006_D, plot=TRUE) -fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, - parms.ini = fit.FOMC$bparms.ode, plot=TRUE) - -# Use stepwise fitting, using optimised parameters from parent only fit, SFORB -SFORB <- mkinmod(parent = list(type = "SFORB")) -SFORB_SFO <- mkinmod( - parent = list(type = "SFORB", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) -# Fit the model to the FOCUS example dataset D using defaults -fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D) -# Use starting parameters from parent only SFORB fit (not really needed in this case) -fit.SFORB = mkinfit(SFORB, FOCUS_2006_D) -fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode) -} - -# Weighted fits, including IRLS -SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), use_of_ff = "max") -f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D) -summary(f.noweight) -f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs") -summary(f.irls) -f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean") -summary(f.w.mean) -f.w.mean.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", - reweight.method = "obs") -summary(f.w.mean.irls) - -\dontrun{ -# Manual weighting -dw <- FOCUS_2006_D -errors <- c(parent = 2, m1 = 1) -dw$err.man <- errors[FOCUS_2006_D$name] -f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man") -summary(f.w.man) -f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", - reweight.method = "obs") -summary(f.w.man.irls) -} -} -\keyword{ models } -\keyword{ optimize } diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd deleted file mode 100644 index 76127c5..0000000 --- a/man/mkinmod.Rd +++ /dev/null @@ -1,63 +0,0 @@ -\name{mkinmod} -\alias{mkinmod} -\title{ - Function to set up a kinetic model with one or more state variables. -} -\description{ - The function takes a specification, consisting of a list of the observed variables - in the data. Each observed variable is again represented by a list, specifying the - kinetic model type and reaction or transfer to other observed compartments. -} -\usage{ -mkinmod(..., use_of_ff = "min", speclist = NULL) -} -\arguments{ - \item{...}{ - For each observed variable, a list has to be specified as an argument, containing - at least a component \code{type}, specifying the type of kinetics to use - for the variable. Currently, single first order kinetics "SFO" or - single first order with reversible binding "SFORB" are implemented for all - variables, while - "FOMC", "DFOP" and "HS" can additionally be chosen for the first - variable which is assumed to be the source compartment. - Additionally, each component of the list can include a character vector \code{to}, - specifying names of variables to which a transfer is to be assumed in the - model. - If the argument \code{use_of_ff} is set to "min" (default) and the model for - the compartment is "SFO" or "SFORB", an additional component of the list - can be "sink=FALSE" effectively fixing the flux to sink to zero. - } - \item{use_of_ff}{ - Specification of the use of formation fractions in the model equations and, if - applicable, the coefficient matrix. If "min", a minimum use of formation - fractions is made in order to avoid fitting the product of formation fractions - and rate constants. If "max", formation fractions are always used. - } - \item{speclist}{ - The specification of the observed variables and their submodel types and - pathways can be given as a single list using this argument. Default is NULL. - } -} -\value{ - A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, containing - \item{diffs}{ A vector of string representations of differential equations, - one for each modelling variable. } - \item{parms}{ A vector of parameter names occurring in the differential equations. } - \item{map}{ A list containing named character vectors for each observed variable, specifying - the modelling variables by which it is represented. } - \item{use_of_ff}{ The content of \code{use_of_ff} is passed on in this list component. } - \item{coefmat}{ The coefficient matrix, if the system of differential equations can be represented by one. } -} -\author{ - Johannes Ranke -} -\examples{ -# Specify the SFO model -SFO <- mkinmod(parent = list(type = "SFO")) - -# One parent compound, one metabolite, both single first order. -SFO_SFO <- mkinmod( - parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO")) -} -\keyword{ models } diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd deleted file mode 100644 index 60103b8..0000000 --- a/man/mkinparplot.Rd +++ /dev/null @@ -1,35 +0,0 @@ -\name{mkinparplot} -\alias{mkinparplot} -\title{ - Function to plot the confidence intervals obtained using - \code{\link{mkinfit}} -} -\description{ - This function plots the confidence intervals for the parameters - fitted using \code{\link{mkinfit}}. -} -\usage{ - mkinparplot(object) -} -\arguments{ - \item{object}{ - A fit represented in an \code{\link{mkinfit}} object. - } -} -\value{ - Nothing is returned by this function, as it is called for its side effect, namely to produce a plot. -} -\author{ - Johannes Ranke -} - -\examples{ -model <- mkinmod( - T245 = list(type = "SFO", to = c("phenol")), - phenol = list(type = "SFO", to = c("anisole")), - anisole = list(type = "SFO"), use_of_ff = "max") -fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), - parms.ini = c(f_phenol_to_anisole = 1), fixed_parms = "f_phenol_to_anisole") -\dontrun{mkinparplot(fit)} -} -\keyword{ hplot } diff --git a/man/mkinplot.Rd b/man/mkinplot.Rd deleted file mode 100644 index 4b0fef4..0000000 --- a/man/mkinplot.Rd +++ /dev/null @@ -1,26 +0,0 @@ -\name{mkinplot} -\alias{mkinplot} -\title{ - Plot the observed data and the fitted model of an mkinfit. -} -\description{ - Deprecated function. It now only calls the plot method \code{\link{plot.mkinfit}}. -} -\usage{ - mkinplot(fit, ...) -} -\arguments{ - \item{fit}{ - an object of class \code{\link{mkinfit}}. - } - \item{\dots}{ - further arguments passed to \code{\link{plot.mkinfit}}. -} -} -\value{ - The function is called for its side effect. -} -\author{ - Johannes Ranke -} -\keyword{ hplot } diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd deleted file mode 100644 index 97db90e..0000000 --- a/man/mkinpredict.Rd +++ /dev/null @@ -1,91 +0,0 @@ -\name{mkinpredict} -\alias{mkinpredict} -\title{ - Produce predictions from a kinetic model using specifc parameters -} -\description{ - This function produces a time series for all the observed variables in a - kinetic model as specified by \code{\link{mkinmod}}, using a specific set of - kinetic parameters and initial values for the state variables. -} -\usage{ - mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", - method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...) -} -\arguments{ - \item{mkinmod}{ - A kinetic model as produced by \code{\link{mkinmod}}. - } - \item{odeparms}{ - A numeric vector specifying the parameters used in the kinetic model, which - is generally defined as a set of ordinary differential equations. - } - \item{odeini}{ - A numeric vectory containing the initial values of the state variables of - the model. Note that the state variables can differ from the observed - variables, for example in the case of the SFORB model. - } - \item{outtimes}{ - A numeric vector specifying the time points for which model predictions - should be generated. - } - \item{solution_type}{ - The method that should be used for producing the predictions. This should - generally be "analytical" if there is only one observed variable, and - usually "deSolve" in the case of several observed variables. The third - possibility "eigen" is faster but not applicable to some models e.g. - using FOMC for the parent compound. - } - \item{method.ode}{ - The solution method passed via \code{\link{mkinpredict}} to - \code{\link{ode}} in case the solution type is "deSolve". The default - "lsoda" is performant, but sometimes fails to converge. - } - \item{atol}{ - Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8, - lower than in \code{\link{lsoda}}. - } - \item{rtol}{ - Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10, - much lower than in \code{\link{lsoda}}. - } - \item{map_output}{ - Boolean to specify if the output should list values for the observed - variables (default) or for all state variables (if set to FALSE). - } - \item{\dots}{ - Further arguments passed to the ode solver in case such a solver is used. - } -} -\value{ - A matrix in the same format as the output of \code{\link{ode}}. -} -\author{ - Johannes Ranke -} -\examples{ - SFO <- mkinmod(degradinol = list(type = "SFO")) - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - solution_type = "analytical") - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - solution_type = "eigen") - - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20, - solution_type = "analytical")[20,] - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - atol = 1e-20)[20,] - - # The integration method does not make a lot of difference - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - atol = 1e-20, method = "ode45")[20,] - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, - atol = 1e-20, method = "rk4")[20,] - - # The number of output times used to make a lot of difference until the - # default for atol was adjusted - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), - seq(0, 20, by = 0.1))[201,] - mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), - seq(0, 20, by = 0.01))[2001,] -} -\keyword{ manip } diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd deleted file mode 100644 index 3f53dd1..0000000 --- a/man/mkinresplot.Rd +++ /dev/null @@ -1,67 +0,0 @@ -\name{mkinresplot} -\alias{mkinresplot} -\title{ - Function to plot residuals stored in an mkin object -} -\description{ - This function plots the residuals for the specified subset of the - observed variables from an mkinfit object. A combined plot of the fitted - model and the residuals can be obtained using \code{\link{plot.mkinfit}} - using the argument \code{show_residuals = TRUE}. -} -\usage{ - mkinresplot(object, - obs_vars = names(object$mkinmod$map), - xlab = "Time", ylab = "Residual", - maxabs = "auto", legend = TRUE, lpos = "topright", ...) -} -\arguments{ - \item{object}{ - A fit represented in an \code{\link{mkinfit}} object. -} - \item{obs_vars}{ - A character vector of names of the observed variables for which residuals - should be plotted. Defaults to all observed variables in the model -} - \item{xlab}{ - Label for the x axis. Defaults to "Time [days]". -} - \item{ylab}{ - Label for the y axis. Defaults to "Residual [\% of applied radioactivity]". -} - \item{maxabs}{ - Maximum absolute value of the residuals. This is used for the scaling of - the y axis and defaults to "auto". -} - \item{legend}{ - Should a legend be plotted? Defaults to "TRUE". -} - \item{lpos}{ - Where should the legend be placed? Default is "topright". Will be passed on to - \code{\link{legend}}. } - \item{\dots}{ - further arguments passed to \code{\link{plot}}. -} -} -\value{ - Nothing is returned by this function, as it is called for its side effect, namely to produce a plot. -} -\author{ - Johannes Ranke -} - -\seealso{ - \code{\link{mkinplot}}, for a way to plot the data and the fitted lines of the - mkinfit object. } -\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{fit <- mkinfit(model, data, plot=TRUE)} -\dontrun{mkinresplot(fit, "A1")} -} -\keyword{ hplot } diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd deleted file mode 100644 index 7009e7d..0000000 --- a/man/plot.mkinfit.Rd +++ /dev/null @@ -1,94 +0,0 @@ -\name{plot.mkinfit} -\alias{plot.mkinfit} -\title{ - Plot the observed data and the fitted model of an mkinfit object. -} -\description{ - Solves the differential equations with the optimised and fixed parameters - from a previous successful call to \code{\link{mkinfit}} and plots - the observed data together with the solution of the fitted model. -} -\usage{ -\method{plot}{mkinfit}(x, fit = x, - obs_vars = names(fit$mkinmod$map), - xlab = "Time", ylab = "Observed", - xlim = range(fit$data$time), - ylim = "default", - col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, - lty_obs = rep(1, length(fit$mkinmod$map)), - add = FALSE, legend = !add, - show_residuals = FALSE, maxabs = "auto", - lpos = "topright", inset = c(0.05, 0.05), \dots) -} -\arguments{ - \item{x}{ - Alias for fit introduced for compatibility with the generic S3 method. - } - \item{fit}{ - an object of class \code{\link{mkinfit}}. - } - \item{obs_vars}{ - A character vector of names of the observed variables for which the - data and the model should be plotted. Defauls to all observed variables - in the model. - } - \item{xlab}{ - label for the x axis. - } - \item{ylab}{ - label for the y axis. - } - \item{xlim}{ - plot range in x direction. - } - \item{ylim}{ - plot range in y direction. - } - \item{col_obs}{ - colors used for plotting the observed data and the corresponding model prediction lines. - } - \item{pch_obs}{ - symbols to be used for plotting the data. - } - \item{lty_obs}{ - line types to be used for the model predictions. - } - \item{add}{ - should the plot be added to an existing plot? - } - \item{legend}{ - should a legend be added to the plot? - } - \item{show_residuals}{ - should residuals be shown in the lower third of the plot? - } - \item{maxabs}{ - Maximum absolute value of the residuals. This is used for the scaling of - the y axis and defaults to "auto". - } - \item{lpos}{ - position of the legend. Passed to \code{\link{legend}} as the first argument. - } - \item{inset}{ - Passed to \code{\link{legend}} if applicable. - } - \item{\dots}{ - further arguments passed to \code{\link{plot}}. - } -} -\value{ - The function is called for its side effect. -} -\examples{ -# One parent compound, one metabolite, both single first order. -SFO_SFO <- mkinmod( - parent = list(type = "SFO", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) -# Fit the model to the FOCUS example dataset D using defaults -fit <- mkinfit(SFO_SFO, FOCUS_2006_D) -\dontrun{plot(fit)} -} -\author{ - Johannes Ranke -} -\keyword{ hplot } diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd deleted file mode 100644 index ed4f694..0000000 --- a/man/schaefer07_complex_case.Rd +++ /dev/null @@ -1,42 +0,0 @@ -\name{schaefer07_complex_case} -\alias{schaefer07_complex_case} -\alias{schaefer07_complex_results} -\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). - The results from the fitting are also included. -} -\usage{data(schaefer07_complex_case)} -\format{ - The data set is 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} - } - The results are a data frame with 14 results for different parameter values -} -\references{ - 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} diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd deleted file mode 100644 index 472b5de..0000000 --- a/man/summary.mkinfit.Rd +++ /dev/null @@ -1,75 +0,0 @@ -\name{summary.mkinfit} -\alias{summary.mkinfit} -\alias{print.summary.mkinfit} -\title{ - Summary method for class "mkinfit". -} -\description{ - Lists model equations, the summary as returned by \code{\link{summary.modFit}}, - the chi2 error levels calculated according to FOCUS guidance (2006) as far - as defined therein, and optionally the data, consisting of observed, predicted - and residual values. -} -\usage{ -\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...) -\method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") - 3), ...) -} - -\arguments{ - \item{object}{ - an object of class \code{\link{mkinfit}}. -} - \item{x}{ - an object of class \code{summary.mkinfit}. -} - \item{data}{ - logical, indicating whether the data should be included in the summary. -} - \item{distimes}{ - logical, indicating whether DT50 and DT90 values should be included. -} - \item{alpha}{ - error level for confidence interval estimation from t distribution -} - \item{digits}{ - Number of digits to use for printing -} - \item{\dots}{ - optional arguments passed to methods like \code{print}. -} -} -\value{ - The summary function returns a list derived from - \code{\link{summary.modFit}}, with components, among others - \item{version, Rversion}{The mkin and R versions used} - \item{date.fit, date.summary}{The dates where the fit and the summary were produced} - \item{use_of_ff}{Was maximum or minimum use made of formation fractions} - \item{residuals, residualVariance, sigma, modVariance, df}{As in summary.modFit} - \item{cov.unscaled, cov.scaled, info, niter, stopmess, par}{As in summary.modFit} - \item{bpar}{Optimised and backtransformed parameters} - \item{diffs }{The differential equations used in the model} - \item{data }{The data (see Description above).} - \item{start }{The starting values and bounds, if applicable, for optimised parameters.} - \item{fixed }{The values of fixed parameters.} - \item{errmin }{The chi2 error levels for each observed variable.} - \item{bparms.ode }{All backtransformed ODE parameters, for use as starting parameters for - related models.} - \item{ff }{The estimated formation fractions derived from the fitted model.} - \item{distimes }{The DT50 and DT90 values for each observed variable.} - \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} - The print method is called for its side effect, i.e. printing the summary. -} -\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{ - summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A)) -} -\keyword{ utilities } diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd deleted file mode 100644 index c52fb4f..0000000 --- a/man/transform_odeparms.Rd +++ /dev/null @@ -1,69 +0,0 @@ -\name{transform_odeparms} -\alias{transform_odeparms} -\alias{backtransform_odeparms} -\title{ - Functions to transform and backtransform kinetic parameters for fitting -} -\description{ - The transformations are intended to map parameters that should only take - on restricted values to the full scale of real numbers. For kinetic rate - constants and other paramters that can only take on positive values, a - simple log transformation is used. For compositional parameters, such as - the formations fractions that should always sum up to 1 and can not be - negative, the \code{\link{ilr}} transformation is used. -} -\usage{ -transform_odeparms(parms, mod_vars, transform_rates = TRUE, transform_fractions = TRUE) -backtransform_odeparms(transparms, mod_vars, - transform_rates = TRUE, transform_fractions = TRUE) -} -\arguments{ - \item{parms}{ - Parameters of kinetic models as used in the differential equations. - } - \item{transparms}{ - Transformed parameters of kinetic models as used in the fitting procedure. - } - \item{mod_vars}{ - Names of the state variables in the kinetic model. These are used for - grouping the formation fractions before \code{\link{ilr}} transformation. - } - \item{transform_rates}{ - Boolean specifying if kinetic rate constants should be transformed in the - model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. If TRUE, also - alpha and beta parameters of the FOMC model are log-transformed, as well - as k1 and k2 rate constants for the DFOP and HS models and the break point tb - of the HS model - } - \item{transform_fractions}{ - Boolean specifying if formation fractions constants should be transformed in the - model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. The default (TRUE) is - to do transformations. The g parameter of the DFOP and HS models are also - transformed, as they can also be seen as compositional data. The - transformation used for these transformations is the \code{\link{ilr}} - transformation. - } -} -\value{ - A vector of transformed or backtransformed parameters with the same names - as the original parameters. -} -\author{ - Johannes Ranke -} -\examples{ -SFO_SFO <- mkinmod( - parent = list(type = "SFO", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) -# Fit the model to the FOCUS example dataset D using defaults -fit <- mkinfit(SFO_SFO, FOCUS_2006_D) -summary(fit, data=FALSE) # See transformed and backtransformed parameters -initials <- fit$start$value -transformed <- fit$start$transformed -names(initials) <- names(transformed) <- rownames(fit$start) -transform_odeparms(initials, c("parent", "m1")) -backtransform_odeparms(transformed, c("parent", "m1")) -} -\keyword{ manip } -- cgit v1.2.1