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authorJohannes Ranke <jranke@uni-bremen.de>2019-10-25 00:37:42 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-10-25 02:03:54 +0200
commit0a3eb0893cb4bd1b12f07a79069d1c7f5e991495 (patch)
tree1bf0ffeb710b3438fee224d0a657606b4c36b495 /man
parent053bf27d3f265c7a7378e2df3e00cf891e0d1bb2 (diff)
Use roxygen for functions and methods
Diffstat (limited to 'man')
-rw-r--r--man/AIC.mmkin.Rd39
-rw-r--r--man/CAKE_export.Rd104
-rw-r--r--man/DFOP.solution.Rd74
-rw-r--r--man/Extract.mmkin.Rd22
-rw-r--r--man/FOMC.solution.Rd99
-rw-r--r--man/HS.solution.Rd73
-rw-r--r--man/IORE.solution.Rd95
-rw-r--r--man/SFO.solution.Rd61
-rw-r--r--man/SFORB.solution.Rd78
-rw-r--r--man/add_err.Rd92
-rw-r--r--man/endpoints.Rd38
-rw-r--r--man/ilr.Rd52
-rw-r--r--man/logLik.mkinfit.Rd54
-rw-r--r--man/logistic.solution.Rd52
-rw-r--r--man/max_twa_parent.Rd112
-rw-r--r--man/mkin_long_to_wide.Rd44
-rw-r--r--man/mkin_wide_to_long.Rd37
-rw-r--r--man/mkinds.Rd26
-rw-r--r--man/mkinerrmin.Rd106
-rw-r--r--man/mkinerrplot.Rd118
-rw-r--r--man/mkinfit.Rd438
-rw-r--r--man/mkinmod.Rd238
-rw-r--r--man/mkinparplot.Rd67
-rw-r--r--man/mkinplot.Rd28
-rw-r--r--man/mkinpredict.Rd133
-rw-r--r--man/mkinresplot.Rd141
-rw-r--r--man/mkinsub.Rd54
-rw-r--r--man/mmkin.Rd76
-rw-r--r--man/nafta.Rd79
-rw-r--r--man/plot.mkinfit.Rd213
-rw-r--r--man/plot.mmkin.Rd96
-rw-r--r--man/plot.nafta.Rd43
-rw-r--r--man/print.mkinds.Rd21
-rw-r--r--man/print.mkinmod.Rd28
-rw-r--r--man/print.nafta.Rd27
-rw-r--r--man/sigma_twocomp.Rd41
-rw-r--r--man/summary.mkinfit.Rd152
-rw-r--r--man/transform_odeparms.Rd110
38 files changed, 1656 insertions, 1705 deletions
diff --git a/man/AIC.mmkin.Rd b/man/AIC.mmkin.Rd
index ca3fcf20..42c9a73b 100644
--- a/man/AIC.mmkin.Rd
+++ b/man/AIC.mmkin.Rd
@@ -1,31 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AIC.mmkin.R
\name{AIC.mmkin}
\alias{AIC.mmkin}
-\title{
- Calculated the AIC for a column of an mmkin object
-}
-\description{
- Provides a convenient way to compare different kineti models fitted to the
- same dataset.
-}
+\title{Calculated the AIC for a column of an mmkin object}
\usage{
- \method{AIC}{mmkin}(object, ..., k = 2)
+\method{AIC}{mmkin}(object, ..., k = 2)
}
\arguments{
- \item{object}{
- An object of class \code{\link{mmkin}}, containing only one column.
- }
- \item{\dots}{
- For compatibility with the generic method
- }
- \item{k}{
- As in the generic method
- }
+\item{object}{An object of class \code{\link{mmkin}}, containing only one
+column.}
+
+\item{\dots}{For compatibility with the generic method}
+
+\item{k}{As in the generic method}
}
\value{
- As in the generic method (a numeric value for single fits, or a dataframe if
- there are several fits in the column).
+As in the generic method (a numeric value for single fits, or a
+ dataframe if there are several fits in the column).
+}
+\description{
+Provides a convenient way to compare different kinetic models fitted to the
+same dataset.
}
\examples{
+
\dontrun{ # skip, as it takes > 10 s on winbuilder
f <- mmkin(c("SFO", "FOMC", "DFOP"),
list("FOCUS A" = FOCUS_2006_A,
@@ -40,7 +38,8 @@
# For FOCUS C, the more complex models fit better
AIC(f[, "FOCUS C"])
}
+
}
\author{
- Johannes Ranke
+Johannes Ranke
}
diff --git a/man/CAKE_export.Rd b/man/CAKE_export.Rd
index c7111bc8..142b4a75 100644
--- a/man/CAKE_export.Rd
+++ b/man/CAKE_export.Rd
@@ -1,73 +1,55 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CAKE_export.R
\name{CAKE_export}
\alias{CAKE_export}
-\title{
- Export a list of datasets format to a CAKE study file
-}
-\description{
- In addition to the datasets, the pathways in the degradation
- model can be specified as well.
-}
+\title{Export a list of datasets format to a CAKE study file}
\usage{
-CAKE_export(ds, map = c(parent = "Parent"),
- links = NA,
+CAKE_export(ds, map = c(parent = "Parent"), links = NA,
filename = "CAKE_export.csf", path = ".", overwrite = FALSE,
- study = "Codlemone aerobic soil degradation",
- description = "",
- time_unit = "days",
- res_unit = "\% AR",
- comment = "Created using mkin::CAKE_export",
- date = Sys.Date(),
+ study = "Codlemone aerobic soil degradation", description = "",
+ time_unit = "days", res_unit = "\% AR",
+ comment = "Created using mkin::CAKE_export", date = Sys.Date(),
optimiser = "IRLS")
}
\arguments{
- \item{ds}{
- A named list of datasets in long format as compatible with
- \code{\link{mkinfit}}.
- }
- \item{map}{
- A character vector with CAKE compartment names (Parent, A1, ...),
- named with the names used in the list of datasets.
- }
- \item{links}{
- An optional character vector of target compartments, named with
- the names of the source compartments. In order to make this
- easier, the names are used as in the datasets supplied.
- }
- \item{filename}{
- Where to write the result. Should end in .csf in order to be compatible
- with CAKE.
- }
- \item{path}{
- An optional path to the output file.
- }
- \item{overwrite}{
- If TRUE, existing files are overwritten.
- }
- \item{study}{
- The name of the study.
- }
- \item{description}{
- An optional description.
- }
- \item{time_unit}{
- The time unit for the residue data.
- }
- \item{res_unit}{
- The unit used for the residues.
- }
- \item{comment}{
- An optional comment.
- }
- \item{date}{
- The date of file creation.
- }
- \item{optimiser}{
- Can be OLS or IRLS.
- }
+\item{ds}{A named list of datasets in long format as compatible with
+\code{\link{mkinfit}}.}
+
+\item{map}{A character vector with CAKE compartment names (Parent, A1, ...),
+named with the names used in the list of datasets.}
+
+\item{links}{An optional character vector of target compartments, named with
+the names of the source compartments. In order to make this easier, the
+names are used as in the datasets supplied.}
+
+\item{filename}{Where to write the result. Should end in .csf in order to be
+compatible with CAKE.}
+
+\item{path}{An optional path to the output file.}
+
+\item{overwrite}{If TRUE, existing files are overwritten.}
+
+\item{study}{The name of the study.}
+
+\item{description}{An optional description.}
+
+\item{time_unit}{The time unit for the residue data.}
+
+\item{res_unit}{The unit used for the residues.}
+
+\item{comment}{An optional comment.}
+
+\item{date}{The date of file creation.}
+
+\item{optimiser}{Can be OLS or IRLS.}
}
\value{
- The function is called for its side effect.
+The function is called for its side effect.
+}
+\description{
+In addition to the datasets, the pathways in the degradation model can be
+specified as well.
}
\author{
- Johannes Ranke
+Johannes Ranke
}
diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd
index 50c4dce1..b145984a 100644
--- a/man/DFOP.solution.Rd
+++ b/man/DFOP.solution.Rd
@@ -1,35 +1,39 @@
-\name{DFOP.solution}
-\alias{DFOP.solution}
-\title{
-Double 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-}
-\examples{
- plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))
-}
-\keyword{ manip }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/DFOP.solution.R
+\name{DFOP.solution}
+\alias{DFOP.solution}
+\title{Double First-Order in Parallel kinetics}
+\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}.
+}
+\description{
+Function describing decline from a defined starting value using the sum of
+two exponential decline functions.
+}
+\examples{
+
+ plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim = c(0,100))
+
+}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
diff --git a/man/Extract.mmkin.Rd b/man/Extract.mmkin.Rd
index 973dc28f..7677bdba 100644
--- a/man/Extract.mmkin.Rd
+++ b/man/Extract.mmkin.Rd
@@ -1,12 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mmkin.R
\name{[.mmkin}
\alias{[.mmkin}
\title{Subsetting method for mmkin objects}
\usage{
\method{[}{mmkin}(x, i, j, ..., drop = FALSE)
}
-\description{
- Subsetting method for mmkin objects.
-}
\arguments{
\item{x}{An \code{\link{mmkin} object}}
@@ -16,16 +15,17 @@
\item{...}{Not used, only there to satisfy the generic method definition}
-\item{drop}{If FALSE, the method always returns an mmkin object, otherwise either
- a list of mkinfit objects or a single mkinfit object.}
+\item{drop}{If FALSE, the method always returns an mmkin object, otherwise
+either a list of mkinfit objects or a single mkinfit object.}
}
\value{
- An object of class \code{\link{mmkin}}.
+An object of class \code{\link{mmkin}}.
}
-\author{
- Johannes Ranke
+\description{
+Subsetting method for mmkin objects.
}
\examples{
+
# Only use one core, to pass R CMD check --as-cran
fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
cores = 1, quiet = TRUE)
@@ -35,6 +35,10 @@
head(
# This extracts an mkinfit object with lots of components
- fits[["FOMC", "B"]]
+ fits[["FOMC", "B"]]
)
+
+}
+\author{
+Johannes Ranke
}
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
index 55d89709..54430dd1 100644
--- a/man/FOMC.solution.Rd
+++ b/man/FOMC.solution.Rd
@@ -1,48 +1,51 @@
-\name{FOMC.solution}
-\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-
- 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{
- plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))
-}
-\keyword{ manip }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/FOMC.solution.R
+\name{FOMC.solution}
+\alias{FOMC.solution}
+\title{First-Order Multi-Compartment kinetics}
+\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.}
+}
+\value{
+The value of the response variable at time \code{t}.
+}
+\description{
+Function describing exponential decline from a defined starting value, with
+a decreasing rate constant.
+}
+\details{
+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.
+}
+\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}.
+}
+\examples{
+
+ plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))
+
+}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+
+ 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
+}
diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
index 41e36c68..ba96b139 100644
--- a/man/HS.solution.Rd
+++ b/man/HS.solution.Rd
@@ -1,33 +1,40 @@
-\name{HS.solution}
-\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-}
-\examples{
- plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
-}
-\keyword{ manip }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/HS.solution.R
+\name{HS.solution}
+\alias{HS.solution}
+\title{Hockey-Stick kinetics}
+\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}.
+}
+\description{
+Function describing two exponential decline functions with a break point
+between them.
+}
+\examples{
+
+ plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
+
+}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd
index 65760f95..ad2df3df 100644
--- a/man/IORE.solution.Rd
+++ b/man/IORE.solution.Rd
@@ -1,44 +1,51 @@
-\name{IORE.solution}
-\alias{IORE.solution}
-\title{ Indeterminate order rate equation kinetics }
-\description{
- Function describing exponential decline from a defined starting value, with
- a concentration dependent rate constant.
-}
-\usage{
- IORE.solution(t, parent.0, k__iore, N)
-}
-\arguments{
- \item{t}{ Time. }
- \item{parent.0}{ Starting value for the response variable at time zero. }
- \item{k__iore}{ Rate constant. Note that this depends on the concentration units used. }
- \item{N}{ Exponent describing the nonlinearity of the rate equation }
-}
-\note{
- The solution of the IORE kinetic model reduces to the
- \code{\link{SFO.solution}} if N = 1.
- The parameters of the IORE model can be transformed to equivalent parameters
- of the FOMC mode - see the NAFTA guidance for details.
-}
-\value{
- The value of the response variable at time \code{t}.
-}
-\references{
- NAFTA Technical Working Group on Pesticides (not dated) Guidance for
- Evaluating and Calculating Degradation Kinetics in Environmental
- Media
-}
-\examples{
- plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100))
- \dontrun{
- fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
- fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
- fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
-
- print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par,
- row.names = paste("model par", 1:4)))
- print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
- iore.deS = endpoints(fit.iore)$distimes))
- }
-}
-\keyword{ manip }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/IORE.solution.R
+\name{IORE.solution}
+\alias{IORE.solution}
+\title{Indeterminate order rate equation kinetics}
+\usage{
+IORE.solution(t, parent.0, k__iore, N)
+}
+\arguments{
+\item{t}{Time.}
+
+\item{parent.0}{Starting value for the response variable at time zero.}
+
+\item{k__iore}{Rate constant. Note that this depends on the concentration
+units used.}
+
+\item{N}{Exponent describing the nonlinearity of the rate equation}
+}
+\value{
+The value of the response variable at time \code{t}.
+}
+\description{
+Function describing exponential decline from a defined starting value, with
+a concentration dependent rate constant.
+}
+\note{
+The solution of the IORE kinetic model reduces to the
+ \code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can
+ be transformed to equivalent parameters of the FOMC mode - see the NAFTA
+ guidance for details.
+}
+\examples{
+
+ plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100))
+ \dontrun{
+ fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+ fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
+ fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
+
+ print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par,
+ row.names = paste("model par", 1:4)))
+ print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
+ iore.deS = endpoints(fit.iore)$distimes))
+ }
+
+}
+\references{
+NAFTA Technical Working Group on Pesticides (not dated) Guidance
+ for Evaluating and Calculating Degradation Kinetics in Environmental Media
+}
+\keyword{manip}
diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd
index 5853d566..03c0dce8 100644
--- a/man/SFO.solution.Rd
+++ b/man/SFO.solution.Rd
@@ -1,28 +1,33 @@
-\name{SFO.solution}
-\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-}
-\examples{
- \dontrun{plot(function(x) SFO.solution(x, 100, 3), 0, 2)}
-}
-\keyword{ manip }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/SFO.solution.R
+\name{SFO.solution}
+\alias{SFO.solution}
+\title{Single First-Order kinetics}
+\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}.
+}
+\description{
+Function describing exponential decline from a defined starting value.
+}
+\examples{
+
+ \dontrun{plot(function(x) SFO.solution(x, 100, 3), 0, 2)}
+
+}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd
index 67c4c3f2..ce9dce73 100644
--- a/man/SFORB.solution.Rd
+++ b/man/SFORB.solution.Rd
@@ -1,35 +1,43 @@
-\name{SFORB.solution}
-\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-}
-\examples{
- \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)}
-}
-\keyword{ manip }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/SFORB.solution.R
+\name{SFORB.solution}
+\alias{SFORB.solution}
+\title{Single First-Order Reversible Binding kinetics}
+\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}.
+}
+\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.
+}
+\examples{
+
+ \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)}
+
+}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
diff --git a/man/add_err.Rd b/man/add_err.Rd
index 00b50878..36b98be9 100644
--- a/man/add_err.Rd
+++ b/man/add_err.Rd
@@ -1,61 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/add_err.R
\name{add_err}
\alias{add_err}
-\title{
- Add normally distributed errors to simulated kinetic degradation data
-}
-\description{
- Normally distributed errors are added to data predicted for a specific
- degradation model using \code{\link{mkinpredict}}. The variance of the error
- may depend on the predicted value and is specified as a standard deviation.
-}
+\title{Add normally distributed errors to simulated kinetic degradation data}
\usage{
- add_err(prediction, sdfunc, secondary = c("M1", "M2"),
- n = 1000, LOD = 0.1, reps = 2,
- digits = 1, seed = NA)
+add_err(prediction, sdfunc, secondary = c("M1", "M2"), n = 1000,
+ LOD = 0.1, reps = 2, digits = 1, seed = NA)
}
\arguments{
- \item{prediction}{
- A prediction from a kinetic model as produced by \code{\link{mkinpredict}}.
- }
- \item{sdfunc}{
- A function taking the predicted value as its only argument and returning
- a standard deviation that should be used for generating the random error
- terms for this value.
- }
- \item{secondary}{
- The names of state variables that should have an initial value of zero
- }
- \item{n}{
- The number of datasets to be generated.
- }
- \item{LOD}{
- The limit of detection (LOD). Values that are below the LOD after adding
- the random error will be set to NA.
- }
- \item{reps}{
- The number of replicates to be generated within the datasets.
- }
- \item{digits}{
- The number of digits to which the values will be rounded.
- }
- \item{seed}{
- The seed used for the generation of random numbers. If NA, the seed
- is not set.
- }
+\item{prediction}{A prediction from a kinetic model as produced by
+\code{\link{mkinpredict}}.}
+
+\item{sdfunc}{A function taking the predicted value as its only argument and
+returning a standard deviation that should be used for generating the
+random error terms for this value.}
+
+\item{secondary}{The names of state variables that should have an initial
+value of zero}
+
+\item{n}{The number of datasets to be generated.}
+
+\item{LOD}{The limit of detection (LOD). Values that are below the LOD after
+adding the random error will be set to NA.}
+
+\item{reps}{The number of replicates to be generated within the datasets.}
+
+\item{digits}{The number of digits to which the values will be rounded.}
+
+\item{seed}{The seed used for the generation of random numbers. If NA, the
+seed is not set.}
}
\value{
- A list of datasets compatible with \code{\link{mmkin}}, i.e.
- the components of the list are datasets compatible with
- \code{\link{mkinfit}}.
+A list of datasets compatible with \code{\link{mmkin}}, i.e. the
+ components of the list are datasets compatible with \code{\link{mkinfit}}.
}
-\references{
- Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy
- http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf
-}
-\author{
- Johannes Ranke
+\description{
+Normally distributed errors are added to data predicted for a specific
+degradation model using \code{\link{mkinpredict}}. The variance of the error
+may depend on the predicted value and is specified as a standard deviation.
}
\examples{
+
# The kinetic model
m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
M1 = mkinsub("SFO"), use_of_ff = "max")
@@ -97,5 +82,14 @@ plot(f_SFO_SFO[[3]], show_residuals = TRUE)
# and plot.mmkin is used
plot(f_SFO_SFO[1, 3])
}
+
+}
+\references{
+Ranke J and Lehmann R (2015) To t-test or not to t-test, that is
+the question. XV Symposium on Pesticide Chemistry 2-4 September 2015,
+Piacenza, Italy
+http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf
+}
+\author{
+Johannes Ranke
}
-\keyword{ manip }
diff --git a/man/endpoints.Rd b/man/endpoints.Rd
index 55a4cb0a..13182369 100644
--- a/man/endpoints.Rd
+++ b/man/endpoints.Rd
@@ -1,33 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/endpoints.R
\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.
-}
+\title{Function to calculate endpoints for further use from kinetic models fitted
+with mkinfit}
\usage{
endpoints(fit)
}
\arguments{
- \item{fit}{
- An object of class \code{\link{mkinfit}}.
- }
-}
-\note{
- The function is used internally by \code{\link{summary.mkinfit}}.
+\item{fit}{An object of class \code{\link{mkinfit}}.}
}
\value{
- A list with the components mentioned above.
+A list with the components mentioned above.
+}
+\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.
+}
+\note{
+The function is used internally by \code{\link{summary.mkinfit}}.
}
\examples{
+
fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
endpoints(fit)
+
}
\author{
- Johannes Ranke
+Johannes Ranke
}
-\keyword{ manip }
+\keyword{manip}
diff --git a/man/ilr.Rd b/man/ilr.Rd
index 29bf7d87..0cbd7e2c 100644
--- a/man/ilr.Rd
+++ b/man/ilr.Rd
@@ -1,36 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ilr.R
\name{ilr}
\alias{ilr}
\alias{invilr}
-\title{
- Function to perform isometric log-ratio transformation
-}
-\description{
- This implementation is a special case of the class of isometric log-ratio transformations.
-}
+\title{Function to perform isometric log-ratio transformation}
\usage{
- ilr(x)
- invilr(x)
+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.
- }
+\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
+The result of the forward or backward transformation. The returned
+ components always sum to 1 for the case of the inverse log-ratio
+ transformation.
}
-\seealso{
- Another implementation can be found in R package \code{robCompositions}.
+\description{
+This implementation is a special case of the class of isometric log-ratio
+transformations.
}
\examples{
+
# Order matters
ilr(c(0.1, 1, 10))
ilr(c(10, 1, 0.1))
@@ -51,6 +44,17 @@ 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 }
+}
+\references{
+Peter Filzmoser, Karel Hron (2008) Outlier Detection for
+ Compositional Data Using Robust Methods. Math Geosci 40 233-248
+}
+\seealso{
+Another implementation can be found in R package
+ \code{robCompositions}.
+}
+\author{
+René Lehmann and Johannes Ranke
+}
+\keyword{manip}
diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd
index 5e910c2e..bb2c2957 100644
--- a/man/logLik.mkinfit.Rd
+++ b/man/logLik.mkinfit.Rd
@@ -1,39 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/logLik.mkinfit.R
\name{logLik.mkinfit}
\alias{logLik.mkinfit}
-\title{
- Calculated the log-likelihood of a fitted mkinfit object
-}
-\description{
- This function simply calculates the product of the likelihood densities
- calculated using \code{\link{dnorm}}, i.e. assuming normal distribution,
- with of the mean predicted by the degradation model, and the
- standard deviation predicted by the error model.
-
- The total number of estimated parameters returned with the value
- of the likelihood is calculated as the sum of fitted degradation
- model parameters and the fitted error model parameters.
-}
+\title{Calculated the log-likelihood of a fitted mkinfit object}
\usage{
- \method{logLik}{mkinfit}(object, ...)
+\method{logLik}{mkinfit}(object, ...)
}
\arguments{
- \item{object}{
- An object of class \code{\link{mkinfit}}.
- }
- \item{\dots}{
- For compatibility with the generic method
- }
+\item{object}{An object of class \code{\link{mkinfit}}.}
+
+\item{\dots}{For compatibility with the generic method}
}
\value{
- An object of class \code{\link{logLik}} with the number of
- estimated parameters (degradation model parameters plus variance
- model parameters) as attribute.
+An object of class \code{\link{logLik}} with the number of estimated
+ parameters (degradation model parameters plus variance model parameters)
+ as attribute.
}
-\seealso{
- Compare the AIC of columns of \code{\link{mmkin}} objects using
- \code{\link{AIC.mmkin}}.
+\description{
+This function simply calculates the product of the likelihood densities
+calculated using \code{\link{dnorm}}, i.e. assuming normal distribution,
+with of the mean predicted by the degradation model, and the standard
+deviation predicted by the error model.
+}
+\details{
+The total number of estimated parameters returned with the value of the
+likelihood is calculated as the sum of fitted degradation model parameters
+and the fitted error model parameters.
}
\examples{
+
\dontrun{
sfo_sfo <- mkinmod(
parent = mkinsub("SFO", to = "m1"),
@@ -45,7 +40,12 @@
f_tc <- mkinfit(sfo_sfo, d_t, error_model = "tc", quiet = TRUE)
AIC(f_nw, f_obs, f_tc)
}
+
+}
+\seealso{
+Compare the AIC of columns of \code{\link{mmkin}} objects using
+ \code{\link{AIC.mmkin}}.
}
\author{
- Johannes Ranke
+Johannes Ranke
}
diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd
index 05b6c0aa..def776aa 100644
--- a/man/logistic.solution.Rd
+++ b/man/logistic.solution.Rd
@@ -1,36 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/logistic.solution.R
\name{logistic.solution}
\alias{logistic.solution}
-\title{ Logistic kinetics }
-\description{
- Function describing exponential decline from a defined starting value, with
- an increasing rate constant, supposedly caused by microbial growth
-}
+\title{Logistic kinetics}
\usage{
logistic.solution(t, parent.0, kmax, k0, r)
}
\arguments{
- \item{t}{ Time. }
- \item{parent.0}{ Starting value for the response variable at time zero. }
- \item{kmax}{ Maximum rate constant. }
- \item{k0}{ Minumum rate constant effective at time zero. }
- \item{r}{ Growth rate of the increase in the rate constant. }
-}
-\note{
- The solution of the logistic model reduces to the
- \code{\link{SFO.solution}} if \code{k0} is equal to
- \code{kmax}.
+\item{t}{Time.}
+
+\item{parent.0}{Starting value for the response variable at time zero.}
+
+\item{kmax}{Maximum rate constant.}
+
+\item{k0}{Minumum rate constant effective at time zero.}
+
+\item{r}{Growth rate of the increase in the rate constant.}
}
\value{
- The value of the response variable at time \code{t}.
+The value of the response variable at time \code{t}.
}
-\references{
- FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence and
- Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
- Registration} Report of the FOCUS Work Group on Degradation Kinetics,
- Version 1.1, 18 December 2014
- \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+\description{
+Function describing exponential decline from a defined starting value, with
+an increasing rate constant, supposedly caused by microbial growth
+}
+\note{
+The solution of the logistic model reduces to the
+ \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}.
}
\examples{
+
# Reproduce the plot on page 57 of FOCUS (2014)
plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
from = 0, to = 100, ylim = c(0, 100),
@@ -64,5 +63,12 @@ logistic.solution(t, parent.0, kmax, k0, r)
plot_sep(m)
summary(m)$bpar
endpoints(m)$distimes
+
+}
+\references{
+FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+ Version 1.1, 18 December 2014
+ \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
}
-\keyword{ manip }
diff --git a/man/max_twa_parent.Rd b/man/max_twa_parent.Rd
index c601b768..7c9f4861 100644
--- a/man/max_twa_parent.Rd
+++ b/man/max_twa_parent.Rd
@@ -1,80 +1,76 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/max_twa_parent.R
\name{max_twa_parent}
\alias{max_twa_parent}
\alias{max_twa_sfo}
\alias{max_twa_fomc}
\alias{max_twa_dfop}
\alias{max_twa_hs}
-\title{
- Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
-}
-\description{
-This function calculates maximum moving window time weighted average concentrations
-(TWAs) for kinetic models fitted with \code{\link{mkinfit}}. Currently, only
-calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models,
-using the analytical formulas given in the PEC soil section of the FOCUS
-guidance.}
+\title{Function to calculate maximum time weighted average concentrations from
+kinetic models fitted with mkinfit}
\usage{
- max_twa_parent(fit, windows)
- max_twa_sfo(M0 = 1, k, t)
- max_twa_fomc(M0 = 1, alpha, beta, t)
- max_twa_dfop(M0 = 1, k1, k2, g, t)
- max_twa_hs(M0 = 1, k1, k2, tb, t)
+max_twa_parent(fit, windows)
+
+max_twa_sfo(M0 = 1, k, t)
+
+max_twa_fomc(M0 = 1, alpha, beta, t)
+
+max_twa_dfop(M0 = 1, k1, k2, g, t)
+
+max_twa_hs(M0 = 1, k1, k2, tb, t)
}
\arguments{
- \item{fit}{
- An object of class \code{\link{mkinfit}}.
- }
- \item{windows}{
- The width of the time windows for which the TWAs should be calculated.
- }
- \item{M0}{
- The initial concentration for which the maximum time weighted
- average over the decline curve should be calculated. The default
- is to use a value of 1, which means that a relative maximum time
- weighted average factor (f_twa) is calculated.
- }
- \item{k}{
- The rate constant in the case of SFO kinetics.
- }
- \item{t}{
- The width of the time window.
- }
- \item{alpha}{
- Parameter of the FOMC model.
- }
- \item{beta}{
- Parameter of the FOMC model.
- }
- \item{k1}{
- The first rate constant of the DFOP or the HS kinetics.
- }
- \item{k2}{
- The second rate constant of the DFOP or the HS kinetics.
- }
- \item{g}{
- Parameter of the DFOP model.
- }
- \item{tb}{
- Parameter of the HS model.
- }
+\item{fit}{An object of class \code{\link{mkinfit}}.}
+
+\item{windows}{The width of the time windows for which the TWAs should be
+calculated.}
+
+\item{M0}{The initial concentration for which the maximum time weighted
+average over the decline curve should be calculated. The default is to use
+a value of 1, which means that a relative maximum time weighted average
+factor (f_twa) is calculated.}
+
+\item{k}{The rate constant in the case of SFO kinetics.}
+
+\item{t}{The width of the time window.}
+
+\item{alpha}{Parameter of the FOMC model.}
+
+\item{beta}{Parameter of the FOMC model.}
+
+\item{k1}{The first rate constant of the DFOP or the HS kinetics.}
+
+\item{k2}{The second rate constant of the DFOP or the HS kinetics.}
+
+\item{g}{Parameter of the DFOP model.}
+
+\item{tb}{Parameter of the HS model.}
}
\value{
- For \code{max_twa_parent}, a numeric vector, named using the \code{windows} argument.
- For the other functions, a numeric vector of length one (also known as 'a
- number').
+For \code{max_twa_parent}, a numeric vector, named using the
+ \code{windows} argument. For the other functions, a numeric vector of
+ length one (also known as 'a number').
+}
+\description{
+This function calculates maximum moving window time weighted average
+concentrations (TWAs) for kinetic models fitted with \code{\link{mkinfit}}.
+Currently, only calculations for the parent are implemented for the SFO,
+FOMC, DFOP and HS models, using the analytical formulas given in the PEC
+soil section of the FOCUS guidance.
}
\examples{
+
fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
max_twa_parent(fit, c(7, 21))
+
}
\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,
+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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
}
\author{
- Johannes Ranke
+Johannes Ranke
}
-\keyword{ manip }
diff --git a/man/mkin_long_to_wide.Rd b/man/mkin_long_to_wide.Rd
index c83f7c78..e76709b9 100644
--- a/man/mkin_long_to_wide.Rd
+++ b/man/mkin_long_to_wide.Rd
@@ -1,36 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkin_long_to_wide.R
\name{mkin_long_to_wide}
\alias{mkin_long_to_wide}
-\title{
- Convert a dataframe from long to wide format
-}
+\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, i.e. with a row
- for each observed value, 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.
-}
+\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.
+Dataframe in wide format.
}
-\author{
- Johannes Ranke
+\description{
+This function takes a dataframe in the long form, i.e. with a row for each
+observed value, and converts it into a dataframe with one independent
+variable and several dependent variables as columns.
}
\examples{
+
mkin_long_to_wide(FOCUS_2006_D)
+
+}
+\author{
+Johannes Ranke
}
-\keyword{ manip }
diff --git a/man/mkin_wide_to_long.Rd b/man/mkin_wide_to_long.Rd
index dc523755..402911d7 100644
--- a/man/mkin_wide_to_long.Rd
+++ b/man/mkin_wide_to_long.Rd
@@ -1,32 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkin_wide_to_long.R
\name{mkin_wide_to_long}
\alias{mkin_wide_to_long}
-\title{
- Convert a dataframe with observations over time into long format
-}
+\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{mkinfit}}.
-}
\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.
-}
+\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{mkinfit}}.
+Dataframe in long format as needed for \code{\link{mkinfit}}.
}
-\author{
- Johannes Ranke
+\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{mkinfit}}.
}
\examples{
+
wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5))
mkin_wide_to_long(wide)
+
+}
+\author{
+Johannes Ranke
}
-\keyword{ manip }
+\keyword{manip}
diff --git a/man/mkinds.Rd b/man/mkinds.Rd
index 239ab328..0ea562ed 100644
--- a/man/mkinds.Rd
+++ b/man/mkinds.Rd
@@ -1,3 +1,5 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinds.R
\docType{class}
\name{mkinds}
\alias{mkinds}
@@ -11,24 +13,26 @@ A dataset class for mkin
}
\section{Fields}{
-\describe{
-\item{\code{title}}{A full title for the dataset}
-\item{\code{sampling}}{times The sampling times}
+\describe{ \item{list("title")}{A full title for the dataset}
-\item{\code{time_unit}}{The time unit}
+\item{list("sampling")}{times The sampling times}
-\item{\code{observed}}{Names of the observed compounds}
+\item{list("time_unit")}{The time unit}
-\item{\code{unit}}{The unit of the observations}
+\item{list("observed")}{Names of the observed compounds}
-\item{\code{replicates}}{The number of replicates}
+\item{list("unit")}{The unit of the observations}
+
+\item{list("replicates")}{The number of replicates}
+
+\item{list("data")}{A dataframe with at least the columns name, time and
+value in order to be compatible with mkinfit} }
+}
-\item{\code{data}}{A dataframe with at least the columns name, time and value
-in order to be compatible with mkinfit}
-}}
\examples{
+
mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
+
}
\keyword{datasets}
-
diff --git a/man/mkinerrmin.Rd b/man/mkinerrmin.Rd
index 25aba7c0..be929130 100644
--- a/man/mkinerrmin.Rd
+++ b/man/mkinerrmin.Rd
@@ -1,54 +1,52 @@
-\name{mkinerrmin}
-\alias{mkinerrmin}
-\title{
-Calculate the minimum error to assume in order to pass the variance test
-}
-\description{
-This function finds 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}}.
-}
-\examples{
-SFO_SFO = mkinmod(parent = mkinsub("SFO", to = "m1"),
- m1 = mkinsub("SFO"),
- use_of_ff = "max")
-
-fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-round(mkinerrmin(fit_FOCUS_D), 4)
-\dontrun{
- fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
- round(mkinerrmin(fit_FOCUS_E), 4)
-}
-}
-\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-}
-\keyword{ manip }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinerrmin.R
+\name{mkinerrmin}
+\alias{mkinerrmin}
+\title{Calculate the minimum error to assume in order to pass the variance test}
+\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.
+}
+\description{
+This function finds the smallest relative error still resulting in passing
+the chi-squared test as defined in the FOCUS kinetics report from 2006.
+}
+\details{
+This function is used internally by \code{\link{summary.mkinfit}}.
+}
+\examples{
+
+SFO_SFO = mkinmod(parent = mkinsub("SFO", to = "m1"),
+ m1 = mkinsub("SFO"),
+ use_of_ff = "max")
+
+fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+round(mkinerrmin(fit_FOCUS_D), 4)
+\dontrun{
+ fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
+ round(mkinerrmin(fit_FOCUS_E), 4)
+}
+
+}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
+\keyword{manip}
diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd
index 37338d01..3c53e7f8 100644
--- a/man/mkinerrplot.Rd
+++ b/man/mkinerrplot.Rd
@@ -1,81 +1,69 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinerrplot.R
\name{mkinerrplot}
\alias{mkinerrplot}
-\title{
- Function to plot squared residuals and the error model for an mkin object
-}
-\description{
- This function plots the squared residuals for the specified subset of the
- observed variables from an mkinfit object. In addition, one or more
- dashed line(s) show the fitted error model.
- A combined plot of the fitted model and this error model plot can be
- obtained with \code{\link{plot.mkinfit}}
- using the argument \code{show_errplot = TRUE}.
-}
+\title{Function to plot squared residuals and the error model for an mkin object}
\usage{
- mkinerrplot(object,
- obs_vars = names(object$mkinmod$map),
- xlim = c(0, 1.1 * max(object$data$predicted)),
- xlab = "Predicted", ylab = "Squared residual",
- maxy = "auto", legend= TRUE, lpos = "topright",
- col_obs = "auto", pch_obs = "auto",
- frame = TRUE,
- ...)
+mkinerrplot(object, obs_vars = names(object$mkinmod$map), xlim = c(0,
+ 1.1 * max(object$data$predicted)), xlab = "Predicted",
+ ylab = "Squared residual", maxy = "auto", legend = TRUE,
+ lpos = "topright", col_obs = "auto", pch_obs = "auto",
+ frame = TRUE, ...)
}
\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{xlim}{
- plot range in x direction.
- }
- \item{xlab}{
- Label for the x axis.
- }
- \item{ylab}{
- Label for the y axis.
- }
- \item{maxy}{
- Maximum 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?
- }
- \item{lpos}{
- Where should the legend be placed? Default is "topright". Will be passed on to
- \code{\link{legend}}.
- }
- \item{col_obs}{
- Colors for the observed variables.
- }
- \item{pch_obs}{
- Symbols to be used for the observed variables.
- }
- \item{frame}{
- Should a frame be drawn around the plots?
- }
- \item{\dots}{
- further arguments passed to \code{\link{plot}}.
- }
+\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{xlim}{plot range in x direction.}
+
+\item{xlab}{Label for the x axis.}
+
+\item{ylab}{Label for the y axis.}
+
+\item{maxy}{Maximum 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?}
+
+\item{lpos}{Where should the legend be placed? Default is "topright". Will
+be passed on to \code{\link{legend}}.}
+
+\item{col_obs}{Colors for the observed variables.}
+
+\item{pch_obs}{Symbols to be used for the observed variables.}
+
+\item{frame}{Should a frame be drawn around the plots?}
+
+\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.
+Nothing is returned by this function, as it is called for its side
+ effect, namely to produce a plot.
}
-\author{
- Johannes Ranke
+\description{
+This function plots the squared residuals for the specified subset of the
+observed variables from an mkinfit object. In addition, one or more dashed
+line(s) show the fitted error model. A combined plot of the fitted model
+and this error model plot can be obtained with \code{\link{plot.mkinfit}}
+using the argument \code{show_errplot = TRUE}.
}
-\seealso{
- \code{\link{mkinplot}}, for a way to plot the data and the fitted lines of the
- mkinfit object. }
\examples{
+
\dontrun{
model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
fit <- mkinfit(model, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
mkinerrplot(fit)
}
+
+}
+\seealso{
+\code{\link{mkinplot}}, for a way to plot the data and the fitted
+ lines of the mkinfit object.
+}
+\author{
+Johannes Ranke
}
-\keyword{ hplot }
+\keyword{hplot}
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 09af4918..d9afb753 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -1,253 +1,214 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinfit.R
\name{mkinfit}
\alias{mkinfit}
-\title{
- Fit a kinetic model to data with one or more state variables
-}
-\description{
- This function maximises the likelihood of the observed data using
- the Port algorithm \code{\link{nlminb}}, and 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 parameters
- of the selected error model are fitted simultaneously with the degradation
- model parameters, as both of them are arguments of the likelihood function.
-
- Per default, parameters in the kinetic models are internally transformed in
- order to better satisfy the assumption of a normal distribution of their
- estimators.
+\title{Fit a kinetic model to data with one or more state variables}
+\source{
+Rocke, David M. und Lorenzato, Stefan (1995) A two-component model
+ for measurement error in analytical chemistry. Technometrics 37(2), 176-184.
}
\usage{
-mkinfit(mkinmod, observed,
- parms.ini = "auto",
- state.ini = "auto",
- err.ini = "auto",
- fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1],
- from_max_mean = FALSE,
+mkinfit(mkinmod, observed, parms.ini = "auto", state.ini = "auto",
+ err.ini = "auto", fixed_parms = NULL,
+ fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE,
solution_type = c("auto", "analytical", "eigen", "deSolve"),
- method.ode = "lsoda",
- use_compiled = "auto",
+ method.ode = "lsoda", use_compiled = "auto",
control = list(eval.max = 300, iter.max = 200),
- transform_rates = TRUE,
- transform_fractions = TRUE,
- quiet = FALSE,
- atol = 1e-8, rtol = 1e-10, n.outtimes = 100,
+ transform_rates = TRUE, transform_fractions = TRUE, quiet = FALSE,
+ atol = 1e-08, rtol = 1e-10, n.outtimes = 100,
error_model = c("const", "obs", "tc"),
- error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep",
- "fourstep", "IRLS", "OLS"),
- reweight.tol = 1e-8, reweight.max.iter = 10,
- trace_parms = FALSE, ...)
+ error_model_algorithm = c("auto", "d_3", "direct", "twostep",
+ "threestep", "fourstep", "IRLS", "OLS"), reweight.tol = 1e-08,
+ 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, or one of the shorthand names ("SFO", "FOMC", "DFOP",
- "HS", "SFORB", "IORE"). If a shorthand name is given, a parent only degradation
- model is generated for the variable with the highest value in
- \code{observed}.
- }
- \item{observed}{
- A dataframe with the observed data. 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. Zero values
- in the "value" column will be removed, with a warning, in order to
- avoid problems with fitting the two-component error model. This is not
- expected to be a problem, because in general, values of zero are not
- observed in degradation data, because there is a lower limit of detection.
- }
- \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 the mean of the time zero
- values for the variable with the maximum observed value, and all others to 0.
- If this variable has no time zero observations, its initial value is set to 100.
- }
- \item{err.ini}{
- A named vector of initial values for the error model parameters to be
- optimised. If set to "auto", initial values are set to default values.
- Otherwise, inital values for all error model parameters must be
- given.
- }
- \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{from_max_mean}{
- If this is set to TRUE, and the model has only one observed variable, then
- data before the time of the maximum observed value (after averaging for each
- sampling time) are discarded, and this time is subtracted from all
- remaining time values, so the time of the maximum observed mean value is
- the new time zero.
- }
- \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 "deSolve" if a compiler is present, and "eigen" if no
- compiler is present and the model can be expressed using eigenvalues and
- eigenvectors. 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{use_compiled}{
- If set to \code{FALSE}, no compiled version of the \code{\link{mkinmod}}
- model is used in the calls to \code{\link{mkinpredict}} even if a compiled
- version is present.
- }
- \item{control}{
- A list of control arguments passed to \code{\link{nlminb}}.
- }
- \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. If FALSE, 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. If TRUE, 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{quiet}{
- Suppress printing out the current value of the negative log-likelihood
- after each improvement?
- }
- \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{error_model}{
- If the error model is "const", a constant standard deviation
- is assumed.
-
- If the error model is "obs", each observed variable is assumed to have its
- own variance.
-
- If the error model is "tc" (two-component error model), a two component
- error model similar to the one described by Rocke and Lorenzato (1995) is
- used for setting up the likelihood function. Note that this model deviates
- from the model by Rocke and Lorenzato, as their model implies that the
- errors follow a lognormal distribution for large values, not a normal
- distribution as assumed by this method.
- }
- \item{error_model_algorithm}{
- If "auto", the selected algorithm depends on the error model.
- If the error model is "const", unweighted nonlinear least squares fitting
- ("OLS") is selected. If the error model is "obs", or "tc", the "d_3"
- algorithm is selected.
-
- The algorithm "d_3" will directly minimize the negative
- log-likelihood and - independently - also use the three step algorithm
- described below. The fit with the higher likelihood is returned.
-
- The algorithm "direct" will directly minimize the negative
- log-likelihood.
-
- The algorithm "twostep" will minimize the negative log-likelihood
- after an initial unweighted least squares optimisation step.
-
- The algorithm "threestep" starts with unweighted least squares,
- then optimizes only the error model using the degradation model
- parameters found, and then minimizes the negative log-likelihood
- with free degradation and error model parameters.
-
- The algorithm "fourstep" starts with unweighted least squares,
- then optimizes only the error model using the degradation model
- parameters found, then optimizes the degradation model again
- with fixed error model parameters, and finally minimizes the negative
- log-likelihood with free degradation and error model parameters.
-
- The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with
- unweighted least squares, and then iterates optimization of the error model
- parameters and subsequent
- optimization of the degradation model using those error model parameters,
- until the error model parameters converge.
- }
- \item{reweight.tol}{
- Tolerance for the convergence criterion calculated from the error model
- parameters in IRLS fits.
- }
- \item{reweight.max.iter}{
- Maximum number of iterations in IRLS fits.
- }
- \item{trace_parms}{
- Should a trace of the parameter values be listed?
- }
- \item{\dots}{
- Further arguments that will be passed on to \code{\link{deSolve}}.
- }
+\item{mkinmod}{A list of class \code{\link{mkinmod}}, containing the kinetic
+model to be fitted to the data, or one of the shorthand names ("SFO",
+"FOMC", "DFOP", "HS", "SFORB", "IORE"). If a shorthand name is given, a
+parent only degradation model is generated for the variable with the
+highest value in \code{observed}.}
+
+\item{observed}{A dataframe with the observed data. 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.
+Zero values in the "value" column will be removed, with a warning, in
+order to avoid problems with fitting the two-component error model. This
+is not expected to be a problem, because in general, values of zero are
+not observed in degradation data, because there is a lower limit of
+detection.}
+
+\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 the mean of the
+time zero values for the variable with the maximum observed value, and all
+others to 0. If this variable has no time zero observations, its initial
+value is set to 100.}
+
+\item{err.ini}{A named vector of initial values for the error model
+parameters to be optimised. If set to "auto", initial values are set to
+default values. Otherwise, inital values for all error model parameters
+must be given.}
+
+\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{from_max_mean}{If this is set to TRUE, and the model has only one
+observed variable, then data before the time of the maximum observed value
+(after averaging for each sampling time) are discarded, and this time is
+subtracted from all remaining time values, so the time of the maximum
+observed mean value is the new time zero.}
+
+\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 "deSolve" if a compiler is present,
+and "eigen" if no compiler is present and the model can be expressed using
+eigenvalues and eigenvectors. 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{use_compiled}{If set to \code{FALSE}, no compiled version of the
+\code{\link{mkinmod}} model is used in the calls to
+\code{\link{mkinpredict}} even if a compiled version is present.}
+
+\item{control}{A list of control arguments passed to \code{\link{nlminb}}.}
+
+\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. If FALSE, 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. If TRUE,
+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{quiet}{Suppress printing out the current value of the negative
+log-likelihood after each improvement?}
+
+\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{error_model}{If the error model is "const", a constant standard
+ deviation is assumed.
+
+ If the error model is "obs", each observed variable is assumed to have its
+ own variance.
+
+ If the error model is "tc" (two-component error model), a two component
+ error model similar to the one described by Rocke and Lorenzato (1995) is
+ used for setting up the likelihood function. Note that this model
+ deviates from the model by Rocke and Lorenzato, as their model implies
+ that the errors follow a lognormal distribution for large values, not a
+ normal distribution as assumed by this method.}
+
+\item{error_model_algorithm}{If "auto", the selected algorithm depends on
+ the error model. If the error model is "const", unweighted nonlinear
+ least squares fitting ("OLS") is selected. If the error model is "obs", or
+ "tc", the "d_3" algorithm is selected.
+
+ The algorithm "d_3" will directly minimize the negative log-likelihood and
+ - independently - also use the three step algorithm described below. The
+ fit with the higher likelihood is returned.
+
+ The algorithm "direct" will directly minimize the negative log-likelihood.
+
+ The algorithm "twostep" will minimize the negative log-likelihood after an
+ initial unweighted least squares optimisation step.
+
+ The algorithm "threestep" starts with unweighted least squares, then
+ optimizes only the error model using the degradation model parameters
+ found, and then minimizes the negative log-likelihood with free
+ degradation and error model parameters.
+
+ The algorithm "fourstep" starts with unweighted least squares, then
+ optimizes only the error model using the degradation model parameters
+ found, then optimizes the degradation model again with fixed error model
+ parameters, and finally minimizes the negative log-likelihood with free
+ degradation and error model parameters.
+
+ The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with
+ unweighted least squares, and then iterates optimization of the error
+ model parameters and subsequent optimization of the degradation model
+ using those error model parameters, until the error model parameters
+ converge.}
+
+\item{reweight.tol}{Tolerance for the convergence criterion calculated from
+the error model parameters in IRLS fits.}
+
+\item{reweight.max.iter}{Maximum number of iterations in IRLS fits.}
+
+\item{trace_parms}{Should a trace of the parameter values be listed?}
+
+\item{\dots}{Further arguments that will be passed on to
+\code{\link{deSolve}}.}
}
\value{
- A list with "mkinfit" in the class attribute. A summary can be obtained by
- \code{\link{summary.mkinfit}}.
+A list with "mkinfit" in the class attribute. A summary can be
+ obtained by \code{\link{summary.mkinfit}}.
}
-\seealso{
- Plotting methods \code{\link{plot.mkinfit}} and \code{\link{mkinparplot}}.
-
- Comparisons of models fitted to the same data can be made using \code{\link{AIC}}
- by virtue of the method \code{\link{logLik.mkinfit}}.
-
- Fitting of several models to several datasets in a single call to
- \code{\link{mmkin}}.
+\description{
+This function maximises the likelihood of the observed data using the Port
+algorithm \code{\link{nlminb}}, and 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
+parameters of the selected error model are fitted simultaneously with the
+degradation model parameters, as both of them are arguments of the
+likelihood function.
+}
+\details{
+Per default, parameters in the kinetic models are internally transformed in
+order to better satisfy the assumption of a normal distribution of their
+estimators.
}
\note{
- When using the "IORE" submodel for metabolites, fitting with
+When using the "IORE" submodel for metabolites, fitting with
"transform_rates = TRUE" (the default) often leads to failures of the
numerical ODE solver. In this situation it may help to switch off the
internal rate transformation.
}
-\source{
- Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
- measurement error in analytical chemistry. Technometrics 37(2), 176-184.
-}
-\author{
- Johannes Ranke
-}
\examples{
+
# Use shorthand notation for parent only degradation
fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
summary(fit)
@@ -307,5 +268,18 @@ f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
summary(f.tc)
}
+
+}
+\seealso{
+Plotting methods \code{\link{plot.mkinfit}} and
+ \code{\link{mkinparplot}}.
+
+ Comparisons of models fitted to the same data can be made using
+ \code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}.
+
+ Fitting of several models to several datasets in a single call to
+ \code{\link{mmkin}}.
+}
+\author{
+Johannes Ranke
}
-\keyword{ optimize }
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 62b02775..91f285e2 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -1,115 +1,123 @@
-\name{mkinmod}
-\alias{mkinmod}
-\title{
- Function to set up a kinetic model with one or more state variables
-}
-\description{
- The function usually takes several expressions, each assigning a compound name to
- a list, specifying the kinetic model type and reaction or transfer to other
- observed compartments. Instead of specifying several expressions, a list
- of lists can be given in the speclist argument.
-
- For the definition of model types and their parameters, the equations given
- in the FOCUS and NAFTA guidance documents are used.
-}
-\usage{
-mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)
-}
-\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",
- indeterminate order rate equation kinetics "IORE", 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.
- }
- \item{quiet}{
- Should messages be suppressed?
- }
- \item{verbose}{
- If \code{TRUE}, passed to \code{\link{cfunction}} if applicable to give
- detailed information about the C function being built.
- }
-}
-\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. }
-}
-\note{
- The IORE submodel is not well tested (yet). When using this model for metabolites,
- you may want to read the second note in the help page to
- \code{\link{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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-
- NAFTA Technical Working Group on Pesticides (not dated) Guidance for
- Evaluating and Calculating Degradation Kinetics in Environmental
- Media
-}
-\author{
- Johannes Ranke
-}
-\examples{
-# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
-SFO <- mkinmod(parent = list(type = "SFO"))
-
-# One parent compound, one metabolite, both single first order
-SFO_SFO <- mkinmod(
- parent = mkinsub("SFO", "m1"),
- m1 = mkinsub("SFO"))
-
-\dontrun{
-# The above model used to be specified like this, before the advent of mkinsub()
-SFO_SFO <- mkinmod(
- parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO"))
-
-# Show details of creating the C function
-SFO_SFO <- mkinmod(
- parent = mkinsub("SFO", "m1"),
- m1 = mkinsub("SFO"), verbose = TRUE)
-
-# If we have several parallel metabolites
-# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
- M1 = mkinsub("SFO"),
- M2 = mkinsub("SFO"),
- use_of_ff = "max", quiet = TRUE)
-
-fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
- synthetic_data_for_UBA_2014[[12]]$data,
- quiet = TRUE)
-}
-}
-\keyword{ models }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinmod.R
+\name{mkinmod}
+\alias{mkinmod}
+\title{Function to set up a kinetic model with one or more state variables}
+\usage{
+mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE,
+ verbose = FALSE)
+}
+\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", indeterminate order rate equation kinetics "IORE", 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.}
+
+\item{quiet}{Should messages be suppressed?}
+
+\item{verbose}{If \code{TRUE}, passed to \code{\link{cfunction}} if
+applicable to give detailed information about the C function being built.}
+}
+\value{
+A list of class \code{mkinmod} for use with \code{\link{mkinfit}},
+ containing, among others,
+ \item{diffs}{
+ A vector of string representations of differential equations, one for
+ each modelling variable.
+ }
+ \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.
+ }
+ \item{ll}{
+ The likelihood function, taking the parameter vector as the first argument.
+ }
+}
+\description{
+The function usually takes several expressions, each assigning a compound
+name to a list, specifying the kinetic model type and reaction or transfer
+to other observed compartments. Instead of specifying several expressions, a
+list of lists can be given in the speclist argument.
+}
+\details{
+For the definition of model types and their parameters, the equations given
+in the FOCUS and NAFTA guidance documents are used.
+}
+\note{
+The IORE submodel is not well tested for metabolites. When using this
+ model for metabolites, you may want to read the second note in the help
+ page to \code{\link{mkinfit}}.
+}
+\examples{
+
+# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
+SFO <- mkinmod(parent = list(type = "SFO"))
+
+# One parent compound, one metabolite, both single first order
+SFO_SFO <- mkinmod(
+ parent = mkinsub("SFO", "m1"),
+ m1 = mkinsub("SFO"))
+
+\dontrun{
+# The above model used to be specified like this, before the advent of mkinsub()
+SFO_SFO <- mkinmod(
+ parent = list(type = "SFO", to = "m1"),
+ m1 = list(type = "SFO"))
+
+# Show details of creating the C function
+SFO_SFO <- mkinmod(
+ parent = mkinsub("SFO", "m1"),
+ m1 = mkinsub("SFO"), verbose = TRUE)
+
+# If we have several parallel metabolites
+# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+ M1 = mkinsub("SFO"),
+ M2 = mkinsub("SFO"),
+ use_of_ff = "max", quiet = TRUE)
+
+fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
+ synthetic_data_for_UBA_2014[[12]]$data,
+ quiet = TRUE)
+}
+
+}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+
+ NAFTA Technical Working Group on Pesticides (not dated) Guidance for
+ Evaluating and Calculating Degradation Kinetics in Environmental Media
+}
+\author{
+Johannes Ranke
+}
diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd
index a880151d..975a0203 100644
--- a/man/mkinparplot.Rd
+++ b/man/mkinparplot.Rd
@@ -1,34 +1,33 @@
-\name{mkinparplot}
-\alias{mkinparplot}
-\title{
- Function to plot the confidence intervals obtained using 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{
-\dontrun{
-model <- mkinmod(
- T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE),
- phenol = mkinsub("SFO", to = c("anisole")),
- anisole = mkinsub("SFO"), use_of_ff = "max")
-fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
-mkinparplot(fit)
-}}
-\keyword{ hplot }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinparplot.R
+\name{mkinparplot}
+\alias{mkinparplot}
+\title{Function to plot the confidence intervals obtained using 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.
+}
+\description{
+This function plots the confidence intervals for the parameters fitted using
+\code{\link{mkinfit}}.
+}
+\examples{
+
+\dontrun{
+model <- mkinmod(
+ T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE),
+ phenol = mkinsub("SFO", to = c("anisole")),
+ anisole = mkinsub("SFO"), use_of_ff = "max")
+fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
+mkinparplot(fit)
+}
+}
+\author{
+Johannes Ranke
+}
diff --git a/man/mkinplot.Rd b/man/mkinplot.Rd
index 50654004..3eade395 100644
--- a/man/mkinplot.Rd
+++ b/man/mkinplot.Rd
@@ -1,25 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.mkinfit.R
\name{mkinplot}
\alias{mkinplot}
-\title{
- Plot the observed data and the fitted model of an mkinfit object
-}
-\description{
- Deprecated function. It now only calls the plot method \code{\link{plot.mkinfit}}.
-}
+\title{Plot the observed data and the fitted model of an mkinfit object}
\usage{
- mkinplot(fit, ...)
+mkinplot(fit, ...)
}
\arguments{
- \item{fit}{
- an object of class \code{\link{mkinfit}}.
- }
- \item{\dots}{
- further arguments passed to \code{\link{plot.mkinfit}}.
-}
+\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.
+The function is called for its side effect.
+}
+\description{
+Deprecated function. It now only calls the plot method
+\code{\link{plot.mkinfit}}.
}
\author{
- Johannes Ranke
+Johannes Ranke
}
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 24b918dc..53f02dea 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -1,78 +1,80 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinpredict.R
\name{mkinpredict}
\alias{mkinpredict}
\alias{mkinpredict.mkinmod}
\alias{mkinpredict.mkinfit}
-\title{
- Produce predictions from a kinetic model using specific 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.
-}
+\title{Produce predictions from a kinetic model using specific parameters}
\usage{
- mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
- solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda",
- atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)
+mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve", use_compiled = "auto",
+ method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
+ map_output = TRUE, ...)
+
+\method{mkinpredict}{mkinmod}(x, odeparms = c(k_parent_sink = 0.1),
+ odeini = c(parent = 100), outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve", use_compiled = "auto",
+ method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
+ map_output = TRUE, ...)
+
+\method{mkinpredict}{mkinfit}(x, odeparms = x$bparms.ode,
+ odeini = x$bparms.state, outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve", use_compiled = "auto",
+ method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
+ map_output = TRUE, ...)
}
\arguments{
- \item{x}{
- A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic
- fit as fitted by \code{\link{mkinfit}}. In the latter case, the fitted
- parameters are used for the prediction.
- }
- \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{use_compiled}{
- If set to \code{FALSE}, no compiled version of the \code{\link{mkinmod}}
- model is used, even if is present.
- }
- \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.
- }
+\item{x}{A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic
+fit as fitted by \code{\link{mkinfit}}. In the latter case, the fitted
+parameters are used for the prediction.}
+
+\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{use_compiled}{If set to \code{FALSE}, no compiled version of the
+\code{\link{mkinmod}} model is used, even if is present.}
+
+\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}}.
+A matrix in the same format as the output of \code{\link{ode}}.
}
-\author{
- Johannes Ranke
+\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.
}
\examples{
+
SFO <- mkinmod(degradinol = mkinsub("SFO"))
# Compare solution types
mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
@@ -124,5 +126,8 @@
f <- mkinfit(SFO_SFO, FOCUS_2006_C)
head(mkinpredict(f))
}
+
+}
+\author{
+Johannes Ranke
}
-\keyword{ manip }
diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
index e788d836..27e1322f 100644
--- a/man/mkinresplot.Rd
+++ b/man/mkinresplot.Rd
@@ -1,76 +1,65 @@
-\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$map),
- xlim = c(0, 1.1 * max(object$data$time)),
- xlab = "Time", ylab = "Residual",
- maxabs = "auto", legend = TRUE, lpos = "topright",
- col_obs = "auto", pch_obs = "auto",
- frame = TRUE,
- ...)
-}
-\arguments{
- \item{object}{
- A fit represented in an \code{\link{mkinfit}} object.
- }
- \item{obs_vars}{
- A character vector of names of the observed variables for which residuals
- should be plotted. Defaults to all observed variables in the model
- }
- \item{xlim}{
- plot range in x direction.
- }
- \item{xlab}{
- Label for the x axis. Defaults to "Time [days]".
- }
- \item{ylab}{
- Label for the y axis. Defaults to "Residual [\% of applied radioactivity]".
- }
- \item{maxabs}{
- Maximum absolute value of the residuals. This is used for the scaling of
- the y axis and defaults to "auto".
- }
- \item{legend}{
- Should a legend be plotted? Defaults to "TRUE".
- }
- \item{lpos}{
- Where should the legend be placed? Default is "topright". Will be passed on to
- \code{\link{legend}}. }
- \item{col_obs}{
- Colors for the observed variables.
- }
- \item{pch_obs}{
- Symbols to be used for the observed variables.
- }
- \item{frame}{
- Should a frame be drawn around the plots?
- }
- \item{\dots}{
- further arguments passed to \code{\link{plot}}.
- }
-}
-\value{
- Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.
-}
-\author{
- Johannes Ranke
-}
-\seealso{
- \code{\link{mkinplot}}, for a way to plot the data and the fitted lines of the
- mkinfit object. }
-\examples{
-model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
-mkinresplot(fit, "m1")
-}
-\keyword{ hplot }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinresplot.R
+\name{mkinresplot}
+\alias{mkinresplot}
+\title{Function to plot residuals stored in an mkin object}
+\usage{
+mkinresplot(object, obs_vars = names(object$mkinmod$map), xlim = c(0,
+ 1.1 * max(object$data$time)), xlab = "Time", ylab = "Residual",
+ maxabs = "auto", legend = TRUE, lpos = "topright",
+ col_obs = "auto", pch_obs = "auto", frame = TRUE, ...)
+}
+\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{xlim}{plot range in x direction.}
+
+\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{col_obs}{Colors for the observed variables.}
+
+\item{pch_obs}{Symbols to be used for the observed variables.}
+
+\item{frame}{Should a frame be drawn around the plots?}
+
+\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.
+}
+\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}.
+}
+\examples{
+
+model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
+fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
+mkinresplot(fit, "m1")
+
+}
+\seealso{
+\code{\link{mkinplot}}, for a way to plot the data and the fitted
+ lines of the mkinfit object.
+}
+\author{
+Johannes Ranke
+}
diff --git a/man/mkinsub.Rd b/man/mkinsub.Rd
index 84e38e21..6522a37e 100644
--- a/man/mkinsub.Rd
+++ b/man/mkinsub.Rd
@@ -1,42 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinsub.R
\name{mkinsub}
\alias{mkinsub}
-\title{
- Function to set up a kinetic submodel for one state variable
-}
-\description{
- This is a convenience function to set up the lists used as arguments for
- \code{\link{mkinmod}}.
-}
+\title{Function to set up a kinetic submodel for one state variable}
\usage{
mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)
}
\arguments{
- \item{submodel}{
- Character vector of length one to specify the submodel type. See
- \code{\link{mkinmod}} for the list of allowed submodel names.
- }
- \item{to}{
- Vector of the names of the state variable to which a transformation
- shall be included in the model.
- }
- \item{sink}{
- Should a pathway to sink be included in the model in addition to the
- pathways to other state variables?
- }
- \item{full_name}{
- An optional name to be used e.g. for plotting fits performed with the model.
- You can use non-ASCII characters here, but then your R code will not be
- portable, \emph{i.e.} may produce unintended plot results on other
- operating systems or system configurations.
- }
+\item{submodel}{Character vector of length one to specify the submodel type.
+See \code{\link{mkinmod}} for the list of allowed submodel names.}
+
+\item{to}{Vector of the names of the state variable to which a
+transformation shall be included in the model.}
+
+\item{sink}{Should a pathway to sink be included in the model in addition to
+the pathways to other state variables?}
+
+\item{full_name}{An optional name to be used e.g. for plotting fits
+performed with the model. You can use non-ASCII characters here, but then
+your R code will not be portable, \emph{i.e.} may produce unintended plot
+results on other operating systems or system configurations.}
}
\value{
- A list for use with \code{\link{mkinmod}}.
+A list for use with \code{\link{mkinmod}}.
}
-\author{
- Johannes Ranke
+\description{
+This is a convenience function to set up the lists used as arguments for
+\code{\link{mkinmod}}.
}
\examples{
+
# One parent compound, one metabolite, both single first order.
SFO_SFO <- mkinmod(
parent = list(type = "SFO", to = "m1"),
@@ -51,5 +44,8 @@ SFO_SFO.2 <- mkinmod(
SFO_SFO.2 <- mkinmod(
parent = mkinsub("SFO", "m1", full_name = "Test compound"),
m1 = mkinsub("SFO", full_name = "Metabolite M1"))
-}
+}
+\author{
+Johannes Ranke
+}
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index e871d78b..a763fcdf 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -1,51 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mmkin.R
\name{mmkin}
\alias{mmkin}
-\title{
- Fit one or more kinetic models with one or more state variables to one or more datasets
-}
-\description{
- This function calls \code{\link{mkinfit}} on all combinations of models and datasets
- specified in its first two arguments.
-}
+\title{Fit one or more kinetic models with one or more state variables to one or
+more datasets}
\usage{
-mmkin(models, datasets,
- cores = round(detectCores()/2), cluster = NULL, ...)
+mmkin(models = c("SFO", "FOMC", "DFOP"), datasets,
+ cores = round(detectCores()/2), cluster = NULL, ...)
}
\arguments{
- \item{models}{
- Either a character vector of shorthand names ("SFO", "FOMC", "DFOP",
- "HS", "SFORB"), or an optionally named list of \code{\link{mkinmod}}
- objects.
- }
- \item{datasets}{
- An optionally named list of datasets suitable as observed data for
- \code{\link{mkinfit}}.
- }
- \item{cores}{
- The number of cores to be used for multicore processing. This is only
- used when the \code{cluster} argument is \code{NULL}. On Windows machines,
- cores > 1 is not supported, you need to use the \code{cluster} argument
- to use multiple logical processors.
- }
- \item{cluster}{
- A cluster as returned by \code{\link{makeCluster}} to be used for parallel
- execution.
- }
- \item{\dots}{
- Further arguments that will be passed to \code{\link{mkinfit}}.
- }
+\item{models}{Either a character vector of shorthand names like
+\code{c("SFO", "FOMC", "DFOP", "HS", "SFORB")}, or an optionally named
+list of \code{\link{mkinmod}} objects.}
+
+\item{datasets}{An optionally named list of datasets suitable as observed
+data for \code{\link{mkinfit}}.}
+
+\item{cores}{The number of cores to be used for multicore processing. This
+is only used when the \code{cluster} argument is \code{NULL}. On Windows
+machines, cores > 1 is not supported, you need to use the \code{cluster}
+argument to use multiple logical processors.}
+
+\item{cluster}{A cluster as returned by \code{\link{makeCluster}} to be used
+for parallel execution.}
+
+\item{\dots}{Further arguments that will be passed to \code{\link{mkinfit}}.}
}
\value{
- A matrix of \code{\link{mkinfit}} objects that can be indexed using the model
- and dataset names as row and column indices.
-}
-\seealso{
- \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for plotting.
+A matrix of \code{\link{mkinfit}} objects that can be indexed using
+ the model and dataset names as row and column indices.
}
-\author{
- Johannes Ranke
+\description{
+This function calls \code{\link{mkinfit}} on all combinations of models and
+datasets specified in its first two arguments.
}
\examples{
+
\dontrun{
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
M1 = mkinsub("SFO", "M2"),
@@ -79,5 +69,13 @@ plot_sep(fits.0[[1, 1]])
# allow to plot the observed variables separately
plot(fits.0[1, 1])
}
+
+}
+\seealso{
+\code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for
+ plotting.
+}
+\author{
+Johannes Ranke
}
-\keyword{ optimize }
+\keyword{optimize}
diff --git a/man/nafta.Rd b/man/nafta.Rd
index 6917d0e9..49c13afc 100644
--- a/man/nafta.Rd
+++ b/man/nafta.Rd
@@ -1,52 +1,65 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/nafta.R
\name{nafta}
\alias{nafta}
-\title{
-Evaluate parent kinetics using the NAFTA guidance
+\alias{print.nafta}
+\title{Evaluate parent kinetics using the NAFTA guidance}
+\source{
+NAFTA (2011) Guidance for evaluating and calculating degradation
+ kinetics in environmental media. NAFTA Technical Working Group on
+ Pesticides
+ \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation}
+ accessed 2019-02-22
+
+ US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
+ Calculate Representative Half-life Values and Characterizing Pesticide
+ Degradation
+ \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance}
}
\usage{
-nafta(ds, title = NA, quiet = FALSE, \dots)
-}
-\description{
- The function fits the SFO, IORE and DFOP models using
- \code{\link{mmkin}} and returns an object of class
- \code{nafta} that has methods for printing and plotting.
+nafta(ds, title = NA, quiet = FALSE, ...)
+
+\method{print}{nafta}(x, quiet = TRUE, digits = 3, ...)
}
\arguments{
- \item{ds}{
- A dataframe that 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{title}{ Optional title of the dataset }
- \item{quiet}{ Should the evaluation text be shown? }
- \item{\dots}{
- Further arguments passed to \code{\link{mmkin}}.
- }
+\item{ds}{A dataframe that 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{title}{Optional title of the dataset}
+
+\item{quiet}{Should the evaluation text be shown?}
+\item{\dots}{Further arguments passed to \code{\link{mmkin}} (not for the
+printing method).}
+
+\item{x}{An \code{\link{nafta}} object.}
+
+\item{digits}{Number of digits to be used for printing parameters and
+dissipation times.}
}
\value{
- An list of class \code{nafta}. The list element named "mmkin" is the
- \code{\link{mmkin}} object containing the fits of the three models.
- The list element named "title" contains the title of the dataset used.
- The list element "data" contains the dataset used in the fits.
+An list of class \code{nafta}. The list element named "mmkin" is the
+ \code{\link{mmkin}} object containing the fits of the three models. The
+ list element named "title" contains the title of the dataset used. The
+ list element "data" contains the dataset used in the fits.
}
-\source{
- NAFTA (2011) Guidance for evaluating and calculating degradation kinetics
- in environmental media. NAFTA Technical Working Group on Pesticides
- \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation}
- accessed 2019-02-22
+\description{
+The function fits the SFO, IORE and DFOP models using \code{\link{mmkin}}
+and returns an object of class \code{nafta} that has methods for printing
+and plotting.
- US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
- Calculate Representative Half-life Values and Characterizing Pesticide
- Degradation
- \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance}
+Print nafta objects. The results for the three models are printed in the
+order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.
}
\examples{
+
nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
print(nafta_evaluation)
plot(nafta_evaluation)
+
}
\author{
- Johannes Ranke
+Johannes Ranke
}
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index fac5663a..3834eaf5 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -1,130 +1,110 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.mkinfit.R
\name{plot.mkinfit}
\alias{plot.mkinfit}
\alias{plot_sep}
\alias{plot_res}
\alias{plot_err}
-\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.
-
- If the current plot device is a \code{\link[tikzDevice]{tikz}} device,
- then latex is being used for the formatting of the chi2 error level,
- if \code{show_errmin = TRUE}.
-}
+\title{Plot the observed data and the fitted model of an mkinfit object}
\usage{
-\method{plot}{mkinfit}(x, fit = x,
- obs_vars = names(fit$mkinmod$map),
- xlab = "Time", ylab = "Observed",
- xlim = range(fit$data$time),
- ylim = "default",
- col_obs = 1:length(obs_vars), pch_obs = col_obs,
- lty_obs = rep(1, length(obs_vars)),
- add = FALSE, legend = !add,
- show_residuals = FALSE,
- show_errplot = FALSE,
- maxabs = "auto",
- sep_obs = FALSE, rel.height.middle = 0.9,
- row_layout = FALSE,
- lpos = "topright", inset = c(0.05, 0.05),
- show_errmin = FALSE, errmin_digits = 3, frame = TRUE, \dots)
-plot_sep(fit, show_errmin = TRUE, \dots)
-plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, \dots)
-plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, \dots)
+\method{plot}{mkinfit}(x, fit = x, obs_vars = names(fit$mkinmod$map),
+ xlab = "Time", ylab = "Observed", xlim = range(fit$data$time),
+ ylim = "default", col_obs = 1:length(obs_vars), pch_obs = col_obs,
+ lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add,
+ show_residuals = FALSE, show_errplot = FALSE, maxabs = "auto",
+ sep_obs = FALSE, rel.height.middle = 0.9, row_layout = FALSE,
+ lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE,
+ errmin_digits = 3, frame = TRUE, ...)
+
+plot_sep(fit, show_errmin = TRUE, ...)
+
+plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
+
+plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
}
\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? If only one plot of the fits is shown, the
- residual plot is in the lower third of the plot. Otherwise, i.e. if
- "sep_obs" is given, the residual plots will be located to the right of
- the plots of the fitted curves.
- }
- \item{show_errplot}{
- Should squared residuals and the error model be shown? If only one plot of
- the fits is shown, this plot is in the lower third of the plot.
- Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
- to the right of the plots of the fitted curves.
- }
- \item{maxabs}{
- Maximum absolute value of the residuals. This is used for the scaling of
- the y axis and defaults to "auto".
- }
- \item{sep_obs}{
- Should the observed variables be shown in separate subplots? If yes, residual plots
- requested by "show_residuals" will be shown next to, not below the plot of the fits.
- }
- \item{rel.height.middle}{
- The relative height of the middle plot, if more than two rows of plots are shown.
- }
- \item{row_layout}{
- Should we use a row layout where the residual plot or the error model plot is shown
- to the right?
- }
- \item{lpos}{
- Position(s) of the legend(s). Passed to \code{\link{legend}} as the first argument.
- If not length one, this should be of the same length as the obs_var argument.
- }
- \item{inset}{
- Passed to \code{\link{legend}} if applicable.
- }
- \item{show_errmin}{
- Should the FOCUS chi2 error value be shown in the upper margin of the plot?
- }
- \item{errmin_digits}{
- The number of significant digits for rounding the FOCUS chi2 error percentage.
- }
- \item{frame}{
- Should a frame be drawn around the plots?
- }
- \item{\dots}{
- Further arguments passed to \code{\link{plot}}.
- }
+\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? If only one plot of the
+fits is shown, the residual plot is in the lower third of the plot.
+Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
+to the right of the plots of the fitted curves.}
+
+\item{show_errplot}{Should squared residuals and the error model be shown?
+If only one plot of the fits is shown, this plot is in the lower third of
+the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will
+be located to the right of the plots of the fitted curves.}
+
+\item{maxabs}{Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".}
+
+\item{sep_obs}{Should the observed variables be shown in separate subplots?
+If yes, residual plots requested by "show_residuals" will be shown next
+to, not below the plot of the fits.}
+
+\item{rel.height.middle}{The relative height of the middle plot, if more
+than two rows of plots are shown.}
+
+\item{row_layout}{Should we use a row layout where the residual plot or the
+error model plot is shown to the right?}
+
+\item{lpos}{Position(s) of the legend(s). Passed to \code{\link{legend}} as
+the first argument. If not length one, this should be of the same length
+as the obs_var argument.}
+
+\item{inset}{Passed to \code{\link{legend}} if applicable.}
+
+\item{show_errmin}{Should the FOCUS chi2 error value be shown in the upper
+margin of the plot?}
+
+\item{errmin_digits}{The number of significant digits for rounding the FOCUS
+chi2 error percentage.}
+
+\item{frame}{Should a frame be drawn around the plots?}
+
+\item{\dots}{Further arguments passed to \code{\link{plot}}.}
}
\value{
- The function is called for its side effect.
+The function is called for its side effect.
+}
+\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.
+}
+\details{
+If the current plot device is a \code{\link[tikzDevice]{tikz}} device, then
+latex is being used for the formatting of the chi2 error level, if
+\code{show_errmin = TRUE}.
}
\examples{
+
# One parent compound, one metabolite, both single first order, path from
# parent to sink included
\dontrun{
@@ -146,7 +126,8 @@ plot_sep(fit, lpos = c("topright", "bottomright"))
plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
show_errmin = TRUE)
}
+
}
\author{
- Johannes Ranke
+Johannes Ranke
}
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index 90b92d27..333998da 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -1,62 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.mmkin.R
\name{plot.mmkin}
\alias{plot.mmkin}
-\title{
- Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
-}
-\description{
- When x is a row selected from an mmkin object (\code{\link{[.mmkin}}), the same model
- fitted for at least one dataset is shown. When it is a column, the fit of at least one model
- to the same dataset is shown.
-
- If the current plot device is a \code{\link[tikzDevice]{tikz}} device,
- then latex is being used for the formatting of the chi2 error level.
-}
+\title{Plot model fits (observed and fitted) and the residuals for a row or column
+of an mmkin object}
\usage{
\method{plot}{mmkin}(x, main = "auto", legends = 1,
- resplot = c("time", "errmod"), show_errmin = TRUE, errmin_var = "All data",
- errmin_digits = 3, cex = 0.7, rel.height.middle = 0.9, ...)
+ resplot = c("time", "errmod"), show_errmin = TRUE,
+ errmin_var = "All data", errmin_digits = 3, cex = 0.7,
+ rel.height.middle = 0.9, ...)
}
\arguments{
- \item{x}{
- An object of class \code{\link{mmkin}}, with either one row or one column.
-}
- \item{main}{
- The main title placed on the outer margin of the plot.
-}
- \item{legends}{
- An index for the fits for which legends should be shown.
-}
- \item{resplot}{
- Should the residuals plotted against time, using \code{\link{mkinresplot}},
- or as squared residuals against predicted values, with the error model,
- using \code{\link{mkinerrplot}}.
-}
- \item{show_errmin}{
- Should the chi2 error level be shown on top of the plots to the left?
- }
- \item{errmin_var}{
- The variable for which the FOCUS chi2 error value should be shown.
-}
- \item{errmin_digits}{
- The number of significant digits for rounding the FOCUS chi2 error percentage.
-}
- \item{cex}{
- Passed to the plot functions and \code{\link{mtext}}.
-}
- \item{rel.height.middle}{
- The relative height of the middle plot, if more than two rows of plots are shown.
-}
- \item{\dots}{
- Further arguments passed to \code{\link{plot.mkinfit}} and \code{\link{mkinresplot}}.
-}
+\item{x}{An object of class \code{\link{mmkin}}, with either one row or one
+column.}
+
+\item{main}{The main title placed on the outer margin of the plot.}
+
+\item{legends}{An index for the fits for which legends should be shown.}
+
+\item{resplot}{Should the residuals plotted against time, using
+\code{\link{mkinresplot}}, or as squared residuals against predicted
+values, with the error model, using \code{\link{mkinerrplot}}.}
+
+\item{show_errmin}{Should the chi2 error level be shown on top of the plots
+to the left?}
+
+\item{errmin_var}{The variable for which the FOCUS chi2 error value should
+be shown.}
+
+\item{errmin_digits}{The number of significant digits for rounding the FOCUS
+chi2 error percentage.}
+
+\item{cex}{Passed to the plot functions and \code{\link{mtext}}.}
+
+\item{rel.height.middle}{The relative height of the middle plot, if more
+than two rows of plots are shown.}
+
+\item{\dots}{Further arguments passed to \code{\link{plot.mkinfit}} and
+\code{\link{mkinresplot}}.}
}
\value{
- The function is called for its side effect.
+The function is called for its side effect.
}
-\author{
- Johannes Ranke
+\description{
+When x is a row selected from an mmkin object (\code{\link{[.mmkin}}), the
+same model fitted for at least one dataset is shown. When it is a column,
+the fit of at least one model to the same dataset is shown.
+}
+\details{
+If the current plot device is a \code{\link[tikzDevice]{tikz}} device, then
+latex is being used for the formatting of the chi2 error level.
}
\examples{
+
\dontrun{
# Only use one core not to offend CRAN checks
fits <- mmkin(c("FOMC", "HS"),
@@ -73,4 +69,8 @@
# Show the error models
plot(fits["FOMC", ], resplot = "errmod")
}
+
+}
+\author{
+Johannes Ranke
}
diff --git a/man/plot.nafta.Rd b/man/plot.nafta.Rd
index 62bbcddf..e7a57de3 100644
--- a/man/plot.nafta.Rd
+++ b/man/plot.nafta.Rd
@@ -1,33 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/nafta.R
\name{plot.nafta}
\alias{plot.nafta}
-\title{
- Plot the results of the three models used in the NAFTA scheme. The plots
- are ordered with increasing complexity of the model in this function
- (SFO, then IORE, then DFOP).
-}
-\description{
- Calls \code{\link{plot.mmkin}}.
-}
+\title{Plot the results of the three models used in the NAFTA scheme.}
\usage{
-\method{plot}{nafta}(x, legend = FALSE, main = "auto", \dots)
+\method{plot}{nafta}(x, legend = FALSE, main = "auto", ...)
}
\arguments{
- \item{x}{
- An object of class \code{\link{nafta}}.
- }
- \item{legend}{
- Should a legend be added?
- }
- \item{main}{
- Possibility to override the main title of the plot.
- }
- \item{\dots}{
- Further arguments passed to \code{\link{plot.mmkin}}.
- }
+\item{x}{An object of class \code{\link{nafta}}.}
+
+\item{legend}{Should a legend be added?}
+
+\item{main}{Possibility to override the main title of the plot.}
+
+\item{\dots}{Further arguments passed to \code{\link{plot.mmkin}}.}
}
\value{
- The function is called for its side effect.
+The function is called for its side effect.
+}
+\description{
+The plots are ordered with increasing complexity of the model in this
+function (SFO, then IORE, then DFOP).
+}
+\details{
+Calls \code{\link{plot.mmkin}}.
}
\author{
- Johannes Ranke
+Johannes Ranke
}
diff --git a/man/print.mkinds.Rd b/man/print.mkinds.Rd
index e7acf30d..54dc5a12 100644
--- a/man/print.mkinds.Rd
+++ b/man/print.mkinds.Rd
@@ -1,19 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinds.R
\name{print.mkinds}
\alias{print.mkinds}
-\title{
- Print mkinds objects
-}
-\description{
- Print mkinds objects.
-}
+\title{Print mkinds objects}
\usage{
\method{print}{mkinds}(x, ...)
}
\arguments{
- \item{x}{
- An \code{\link{mkinds}} object.
- }
- \item{\dots}{
- Not used.
- }
+\item{x}{An \code{\link{mkinds}} object.}
+
+\item{\dots}{Not used.}
+}
+\description{
+Print mkinds objects.
}
diff --git a/man/print.mkinmod.Rd b/man/print.mkinmod.Rd
index 24555def..4e44cde6 100644
--- a/man/print.mkinmod.Rd
+++ b/man/print.mkinmod.Rd
@@ -1,26 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinmod.R
\name{print.mkinmod}
\alias{print.mkinmod}
-\title{
- Print mkinmod objects
-}
-\description{
- Print mkinmod objects in a way that the user finds his way to get to its components.
-}
+\title{Print mkinmod objects}
\usage{
- \method{print}{mkinmod}(x, ...)
+\method{print}{mkinmod}(x, ...)
}
\arguments{
- \item{x}{
- An \code{\link{mkinmod}} object.
- }
- \item{\dots}{
- Not used.
- }
+\item{x}{An \code{\link{mkinmod}} object.}
+
+\item{\dots}{Not used.}
+}
+\description{
+Print mkinmod objects in a way that the user finds his way to get to its
+components.
}
\examples{
+
m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
M1 = list(type = "SFO", to = "M2"),
M2 = list(type = "SFO"), use_of_ff = "max")
-
+
print(m_synth_SFO_lin)
+
}
diff --git a/man/print.nafta.Rd b/man/print.nafta.Rd
deleted file mode 100644
index e42a619d..00000000
--- a/man/print.nafta.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-\name{print.nafta}
-\alias{print.nafta}
-\title{
- Print nafta objects
-}
-\description{
- Print nafta objects. The results for the three models
- are printed in the order of increasing model complexity,
- i.e. SFO, then IORE, and finally DFOP.
-}
-\usage{
- \method{print}{nafta}(x, quiet = TRUE, digits = 3, ...)
-}
-\arguments{
- \item{x}{
- An \code{\link{nafta}} object.
- }
- \item{quiet}{
- Should the evaluation text be shown?
- }
- \item{digits}{
- Number of digits to be used for printing parameters and dissipation times.
- }
- \item{\dots}{
- Not used.
- }
-}
diff --git a/man/sigma_twocomp.Rd b/man/sigma_twocomp.Rd
index 9e91fe78..3e7854f1 100644
--- a/man/sigma_twocomp.Rd
+++ b/man/sigma_twocomp.Rd
@@ -1,31 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sigma_twocomp.R
\name{sigma_twocomp}
\alias{sigma_twocomp}
\title{Two component error model}
-\description{
- Function describing the standard deviation of the measurement error
- in dependence of the measured value \eqn{y}:
-
- \deqn{\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}}
- {sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2)}
-
- This is the error model used for example by Werner et al. (1978). The model
- proposed by Rocke and Lorenzato (1995) can be written in this form as well,
- but assumes approximate lognormal distribution of errors for high values of y.
-}
\usage{
sigma_twocomp(y, sigma_low, rsd_high)
}
\arguments{
- \item{y}{ The magnitude of the observed value }
- \item{sigma_low}{ The asymptotic minimum of the standard deviation for low observed values }
- \item{rsd_high}{ The coefficient describing the increase of the standard deviation with
- the magnitude of the observed value }
+\item{y}{The magnitude of the observed value}
+
+\item{sigma_low}{The asymptotic minimum of the standard deviation for low
+observed values}
+
+\item{rsd_high}{The coefficient describing the increase of the standard
+deviation with the magnitude of the observed value}
}
\value{
- The standard deviation of the response variable.
+The standard deviation of the response variable.
+}
+\description{
+Function describing the standard deviation of the measurement error in
+dependence of the measured value \eqn{y}:
+}
+\details{
+\deqn{\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}} sigma =
+sqrt(sigma_low^2 + y^2 * rsd_high^2)
+
+This is the error model used for example by Werner et al. (1978). The model
+proposed by Rocke and Lorenzato (1995) can be written in this form as well,
+but assumes approximate lognormal distribution of errors for high values of
+y.
}
\references{
- Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978)
+Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978)
Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry
24(11), 1895-1898.
diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
index cbc9098c..fcc1295f 100644
--- a/man/summary.mkinfit.Rd
+++ b/man/summary.mkinfit.Rd
@@ -1,75 +1,77 @@
-\name{summary.mkinfit}
-\alias{summary.mkinfit}
-\alias{print.summary.mkinfit}
-\title{
- Summary method for class "mkinfit"
-}
-\description{
- Lists model equations, initial parameter values, optimised parameters with some
- uncertainty statistics, the chi2 error levels calculated according to FOCUS
- guidance (2006) as defined therein, formation fractions, DT50 values 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 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{errparms }{Error model parameters. }
- \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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-}
-\author{
- Johannes Ranke
-}
-\examples{
- summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
-}
-\keyword{ utilities }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/summary.mkinfit.R
+\name{summary.mkinfit}
+\alias{summary.mkinfit}
+\alias{print.summary.mkinfit}
+\title{Summary method for class "mkinfit"}
+\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{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{\dots}{optional arguments passed to methods like \code{print}.}
+
+\item{x}{an object of class \code{summary.mkinfit}.}
+
+\item{digits}{Number of digits to use for printing}
+}
+\value{
+The summary function returns a list 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{diffs}{The differential equations used in the model}
+ \item{use_of_ff}{Was maximum or minimum use made of formation fractions}
+ \item{bpar}{Optimised and backtransformed
+ parameters}
+ \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{errparms}{Error model parameters.}
+ \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.
+}
+\description{
+Lists model equations, initial parameter values, optimised parameters with
+some uncertainty statistics, the chi2 error levels calculated according to
+FOCUS guidance (2006) as defined therein, formation fractions, DT50 values
+and optionally the data, consisting of observed, predicted and residual
+values.
+}
+\examples{
+
+ summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
+
+}
+\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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
+\author{
+Johannes Ranke
+}
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index 006897d6..5c8c90ba 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -1,66 +1,67 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/transform_odeparms.R
\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.
-
- The transformation of sets of formation fractions is fragile, as it supposes
- the same ordering of the components in forward and backward transformation.
- This is no problem for the internal use in \code{\link{mkinfit}}.
-}
+\title{Functions to transform and backtransform kinetic parameters for fitting}
\usage{
-transform_odeparms(parms, mkinmod,
- transform_rates = TRUE, transform_fractions = TRUE)
-backtransform_odeparms(transparms, mkinmod,
- transform_rates = TRUE, transform_fractions = TRUE)
+transform_odeparms(parms, mkinmod, transform_rates = TRUE,
+ transform_fractions = TRUE)
+
+backtransform_odeparms(transparms, mkinmod, 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{mkinmod}{
- The kinetic model of class \code{\link{mkinmod}}, containing the names of
- the model variables that are needed for grouping the formation fractions
- before \code{\link{ilr}} transformation, the parameter names and
- the information if the pathway to sink is included in the model.
- }
- \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.
- }
+\item{parms}{Parameters of kinetic models as used in the differential
+equations.}
+
+\item{mkinmod}{The kinetic model of class \code{\link{mkinmod}}, containing
+the names of the model variables that are needed for grouping the
+formation fractions before \code{\link{ilr}} transformation, the parameter
+names and the information if the pathway to sink is included in the model.}
+
+\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.}
+
+\item{transparms}{Transformed parameters of kinetic models as used in the
+fitting procedure.}
}
\value{
- A vector of transformed or backtransformed parameters with the same names
- as the original parameters.
+A vector of transformed or backtransformed parameters with the same
+ names as the original parameters.
}
-\author{
- Johannes Ranke
+\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.
}
+\details{
+The transformation of sets of formation fractions is fragile, as it supposes
+the same ordering of the components in forward and backward transformation.
+This is no problem for the internal use in \code{\link{mkinfit}}.
+}
+\section{Functions}{
+\itemize{
+\item \code{backtransform_odeparms}: Backtransform the set of transformed parameters
+}}
+
\examples{
+
SFO_SFO <- mkinmod(
parent = list(type = "SFO", to = "m1", sink = TRUE),
m1 = list(type = "SFO"))
@@ -113,5 +114,8 @@ fit.ff.2.s <- summary(fit.ff.2)
print(fit.ff.2.s$par, 3)
print(fit.ff.2.s$bpar, 3)
}
+
+}
+\author{
+Johannes Ranke
}
-\keyword{ manip }

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