Fork the gmkin GUI from mkin. See ChangeLog for details

26 files changed, 0 insertions, 1431 deletions

diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd
deleted file mode 100644
index d30cf7f..0000000
--- a/man/DFOP.solution.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-\name{DFOP.solution}

-\Rdversion{1.1}

-\alias{DFOP.solution}

-\title{

-Dual First-Order in Parallel kinetics

-}

-\description{

-  Function describing decline from a defined starting value using the sum

-  of two exponential decline functions.

-}

-\usage{

-DFOP.solution(t, parent.0, k1, k2, g)

-}

-\arguments{

-  \item{t}{ Time. }

-  \item{parent.0}{ Starting value for the response variable at time zero. }

-  \item{k1}{ First kinetic constant. }

-  \item{k2}{ Second kinetic constant. }

-  \item{g}{ Fraction of the starting value declining according to the

-    first kinetic constant.

-  }

-}

-\value{

-  The value of the response variable at time \code{t}.

-}

-\references{ 

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-  \dontrun{plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))}

-}

-\keyword{ manip }

diff --git a/man/FOCUS_2006_DFOP_ref_A_to_B.Rd b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd
deleted file mode 100644
index 88bd4ac..0000000
--- a/man/FOCUS_2006_DFOP_ref_A_to_B.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-\name{FOCUS_2006_DFOP_ref_A_to_B}

-\Rdversion{1.1}

-\alias{FOCUS_2006_DFOP_ref_A_to_B}

-\docType{data}

-\title{

-Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

-}

-\description{

-A table with the fitted parameters and the resulting DT50 and DT90 values

-generated with different software packages. Taken directly from FOCUS (2006).

-The results from fitting the data with the Topfit software was removed, as

-the initial concentration of the parent compound was fixed to a value of 100

-in this fit.

-}

-\usage{data(FOCUS_2006_DFOP_ref_A_to_B)}

-\format{

-  A data frame containing the following variables.

-  \describe{

-    \item{\code{package}}{a factor giving the name of the software package}

-    \item{\code{M0}}{The fitted initial concentration of the parent compound}

-    \item{\code{f}}{The fitted f parameter}

-    \item{\code{k1}}{The fitted k1 parameter}

-    \item{\code{k2}}{The fitted k2 parameter}

-    \item{\code{DT50}}{The resulting half-life of the parent compound}

-    \item{\code{DT90}}{The resulting DT90 of the parent compound}

-    \item{\code{dataset}}{The FOCUS dataset that was used}

-  }

-}

-\source{

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-data(FOCUS_2006_DFOP_ref_A_to_B)

-}

-\keyword{datasets}

diff --git a/man/FOCUS_2006_FOMC_ref_A_to_F.Rd b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd
deleted file mode 100644
index 2fcc2db..0000000
--- a/man/FOCUS_2006_FOMC_ref_A_to_F.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-\name{FOCUS_2006_FOMC_ref_A_to_F}

-\Rdversion{1.1}

-\alias{FOCUS_2006_FOMC_ref_A_to_F}

-\docType{data}

-\title{

-Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)

-}

-\description{

-A table with the fitted parameters and the resulting DT50 and DT90 values

-generated with different software packages. Taken directly from FOCUS (2006).

-The results from fitting the data with the Topfit software was removed, as

-the initial concentration of the parent compound was fixed to a value of 100

-in this fit.

-}

-\usage{data(FOCUS_2006_FOMC_ref_A_to_F)}

-\format{

-  A data frame containing the following variables.

-  \describe{

-    \item{\code{package}}{a factor giving the name of the software package}

-    \item{\code{M0}}{The fitted initial concentration of the parent compound}

-    \item{\code{alpha}}{The fitted alpha parameter}

-    \item{\code{beta}}{The fitted beta parameter}

-    \item{\code{DT50}}{The resulting half-life of the parent compound}

-    \item{\code{DT90}}{The resulting DT90 of the parent compound}

-    \item{\code{dataset}}{The FOCUS dataset that was used}

-  }

-}

-\source{

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-data(FOCUS_2006_FOMC_ref_A_to_F)

-}

-\keyword{datasets}

diff --git a/man/FOCUS_2006_HS_ref_A_to_F.Rd b/man/FOCUS_2006_HS_ref_A_to_F.Rd
deleted file mode 100644
index 6fc9993..0000000
--- a/man/FOCUS_2006_HS_ref_A_to_F.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-\name{FOCUS_2006_HS_ref_A_to_F}

-\Rdversion{1.1}

-\alias{FOCUS_2006_HS_ref_A_to_F}

-\docType{data}

-\title{

-Results of fitting the HS model to Datasets A to F of FOCUS (2006)

-}

-\description{

-A table with the fitted parameters and the resulting DT50 and DT90 values

-generated with different software packages. Taken directly from FOCUS (2006).

-The results from fitting the data with the Topfit software was removed, as

-the initial concentration of the parent compound was fixed to a value of 100

-in this fit.

-}

-\usage{data(FOCUS_2006_HS_ref_A_to_F)}

-\format{

-  A data frame containing the following variables.

-  \describe{

-    \item{\code{package}}{a factor giving the name of the software package}

-    \item{\code{M0}}{The fitted initial concentration of the parent compound}

-    \item{\code{tb}}{The fitted tb parameter}

-    \item{\code{k1}}{The fitted k1 parameter}

-    \item{\code{k2}}{The fitted k2 parameter}

-    \item{\code{DT50}}{The resulting half-life of the parent compound}

-    \item{\code{DT90}}{The resulting DT90 of the parent compound}

-    \item{\code{dataset}}{The FOCUS dataset that was used}

-  }

-}

-\source{

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-data(FOCUS_2006_HS_ref_A_to_F)

-}

-\keyword{datasets}

diff --git a/man/FOCUS_2006_SFO_ref_A_to_F.Rd b/man/FOCUS_2006_SFO_ref_A_to_F.Rd
deleted file mode 100644
index 19650ed..0000000
--- a/man/FOCUS_2006_SFO_ref_A_to_F.Rd
+++ /dev/null
@@ -1,37 +0,0 @@
-\name{FOCUS_2006_SFO_ref_A_to_F}

-\Rdversion{1.1}

-\alias{FOCUS_2006_SFO_ref_A_to_F}

-\docType{data}

-\title{

-Results of fitting the SFO model to Datasets A to F of FOCUS (2006)

-}

-\description{

-A table with the fitted parameters and the resulting DT50 and DT90 values

-generated with different software packages. Taken directly from FOCUS (2006).

-The results from fitting the data with the Topfit software was removed, as

-the initial concentration of the parent compound was fixed to a value of 100

-in this fit.

-}

-\usage{data(FOCUS_2006_SFO_ref_A_to_F)}

-\format{

-  A data frame containing the following variables.

-  \describe{

-    \item{\code{package}}{a factor giving the name of the software package}

-    \item{\code{M0}}{The fitted initial concentration of the parent compound}

-    \item{\code{k}}{The fitted first-order degradation rate constant}

-    \item{\code{DT50}}{The resulting half-life of the parent compound}

-    \item{\code{DT90}}{The resulting DT90 of the parent compound}

-    \item{\code{dataset}}{The FOCUS dataset that was used}

-  }

-}

-\source{

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-data(FOCUS_2006_SFO_ref_A_to_F)

-}

-\keyword{datasets}

diff --git a/man/FOCUS_2006_datasets.Rd b/man/FOCUS_2006_datasets.Rd
deleted file mode 100644
index 5053b88..0000000
--- a/man/FOCUS_2006_datasets.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-\name{FOCUS_2006_datasets}

-\Rdversion{1.1}

-\alias{FOCUS_2006_A}

-\alias{FOCUS_2006_B}

-\alias{FOCUS_2006_C}

-\alias{FOCUS_2006_D}

-\alias{FOCUS_2006_E}

-\alias{FOCUS_2006_F}

-\docType{data}

-\title{

-Datasets A to F from the FOCUS Kinetics report from 2006

-}

-\description{

-Data taken from FOCUS (2006), p. 258.

-}

-\usage{FOCUS_2006_datasets}

-\format{

-  6 datasets with observations on the following variables.

-  \describe{

-    \item{\code{name}}{a factor containing the name of the observed variable}

-    \item{\code{time}}{a numeric vector containing time points}

-    \item{\code{value}}{a numeric vector containing concentrations in percent of applied radioactivity}

-  }

-}

-\source{

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-FOCUS_2006_C

-}

-\keyword{datasets}

diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
deleted file mode 100644
index d04d34e..0000000
--- a/man/FOMC.solution.Rd
+++ /dev/null
@@ -1,49 +0,0 @@
-\name{FOMC.solution}

-\Rdversion{1.1}

-\alias{FOMC.solution}

-\title{ First-Order Multi-Compartment kinetics }

-\description{

-  Function describing exponential decline from a defined starting value, with 

-  a decreasing rate constant. 

-

-  The form given here differs slightly from the original reference by Gustafson

-  and Holden (1990). The parameter \code{beta} corresponds to 1/beta in the

-  original equation.

-}

-\usage{

-FOMC.solution(t, parent.0, alpha, beta)

-}

-\arguments{

-  \item{t}{ Time. }

-  \item{parent.0}{ Starting value for the response variable at time zero. }

-  \item{alpha}{ 

-    Shape parameter determined by coefficient of variation of rate constant

-    values. }

-  \item{beta}{

-    Location parameter.

-}

-}

-\note{

-  The solution of the FOMC kinetic model reduces to the

-  \code{\link{SFO.solution}} for large values of \code{alpha} and

-  \code{beta} with 

-  \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}.

-}

-\value{

-  The value of the response variable at time \code{t}.

-}

-\references{

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-

-  Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A

-  new model based on spatial variability. \emph{Environmental Science and 

-  Technology} \bold{24}, 1032-1038

-}

-\examples{

-  \dontrun{plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2)}

-}

-\keyword{ manip }

diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
deleted file mode 100644
index 71f68a1..0000000
--- a/man/HS.solution.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-\name{HS.solution}

-\Rdversion{1.1}

-\alias{HS.solution}

-\title{ Hockey-Stick kinetics }

-\description{

-  Function describing two exponential decline functions with a break point

-  between them.

-}

-\usage{

-HS.solution(t, parent.0, k1, k2, tb)

-}

-\arguments{

-  \item{t}{ Time. }

-  \item{parent.0}{ Starting value for the response variable at time zero. }

-  \item{k1}{ First kinetic constant. }

-  \item{k2}{ Second kinetic constant. }

-  \item{tb}{ Break point. Before this time, exponential decline according

-    to \code{k1} is calculated, after this time, exponential decline proceeds

-    according to \code{k2}. }

-}

-\value{

-  The value of the response variable at time \code{t}.

-}

-\references{ 

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-  \dontrun{plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))}

-}

-\keyword{ manip }

diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd
deleted file mode 100644
index 41a9ba9..0000000
--- a/man/SFO.solution.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-\name{SFO.solution}

-\Rdversion{1.1}

-\alias{SFO.solution}

-\title{ Single First-Order kinetics }

-\description{

-  Function describing exponential decline from a defined starting value.

-}

-\usage{

-  SFO.solution(t, parent.0, k)

-}

-\arguments{

-  \item{t}{ Time. }

-  \item{parent.0}{ Starting value for the response variable at time zero. }

-  \item{k}{ Kinetic constant. }

-}

-\value{

-  The value of the response variable at time \code{t}.

-}

-\references{ 

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-  \dontrun{plot(function(x) SFO.solution(x, 100, 3), 0, 2)}

-}

-\keyword{ manip }

diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd
deleted file mode 100644
index a935f69..0000000
--- a/man/SFORB.solution.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-\name{SFORB.solution}

-\Rdversion{1.1}

-\alias{SFORB.solution}

-\title{ Single First-Order Reversible Binding kinetics }

-\description{

-  Function describing the solution of the differential equations describing

-  the kinetic model with first-order terms for a two-way transfer from a free

-  to a bound fraction, and a first-order degradation term for the free

-  fraction.  The initial condition is a defined amount in the free fraction and

-  no substance in the bound fraction.

-}

-\usage{

-  SFORB.solution(t, parent.0, k_12, k_21, k_1output)

-}

-\arguments{

-  \item{t}{ Time. }

-  \item{parent.0}{ Starting value for the response variable at time zero. }

-  \item{k_12}{ Kinetic constant describing transfer from free to bound. }

-  \item{k_21}{ Kinetic constant describing transfer from bound to free. }

-  \item{k_1output}{ Kinetic constant describing degradation of the free fraction. }

-}

-\value{

-  The value of the response variable, which is the sum of free and bound 

-  fractions at time \code{t}.

-}

-\references{ 

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\examples{

-  \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)}

-}

-\keyword{ manip }

diff --git a/man/endpoints.Rd b/man/endpoints.Rd
deleted file mode 100644
index 21316cf..0000000
--- a/man/endpoints.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-\name{endpoints}
-\alias{endpoints}
-\title{
-Function to calculate endpoints for further use from kinetic models fitted with mkinfit
-}
-\description{
-This function calculates DT50 and DT90 values as well as formation fractions from kinetic models
-fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, 
-the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but 
-with the advantage that the SFORB model can also be used for metabolites.
-}
-\usage{
-endpoints(fit, pseudoDT50 = FALSE)
-}
-\arguments{
-  \item{fit}{
-  An object of class \code{\link{mkinfit}}.
-}
-  \item{pseudoDT50}{
-  Should pseudoDT50 values for FOMC, DFOP and SFORB models be reported, as 
-  recommended by the FOCUS group? Currently not implemented.
-}
-}
-\note{
-  The function is used internally by \code{\link{summary.mkinfit}}.
-}
-\value{
-  A list with the components mentioned above.
-}
-\author{
-  Johannes Ranke
-}
-\keyword{ manip }
diff --git a/man/ilr.Rd b/man/ilr.Rd
deleted file mode 100644
index cedb49c..0000000
--- a/man/ilr.Rd
+++ /dev/null
@@ -1,56 +0,0 @@
-\name{ilr}
-\alias{ilr}
-\alias{invilr}
-\title{
-  Function to perform isotropic log-ratio transformation
-}
-\description{
-  This implementation is a special case of the class of isotropic log-ratio transformations.
-}
-\usage{
-  ilr(x)
-  invilr(x)
-}
-\arguments{
-  \item{x}{
-    A numeric vector. Naturally, the forward transformation is only sensible for
-    vectors with all elements being greater than zero.
-  }
-}
-\value{
-  The result of the forward or backward transformation. The returned components always 
-  sum to 1 for the case of the inverse log-ratio transformation.
-}
-\references{
-  Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248
-}
-\author{
-  René Lehmann and Johannes Ranke
-}
-\seealso{
-  Other implementations are in R packages \code{compositions} and \code{robCompositions}.
-}
-\examples{
-# Order matters
-ilr(c(0.1, 1, 10))
-ilr(c(10, 1, 0.1))
-# Equal entries give ilr transformations with zeros as elements
-ilr(c(3, 3, 3))
-# Almost equal entries give small numbers
-ilr(c(0.3, 0.4, 0.3))
-# Only the ratio between the numbers counts, not their sum
-invilr(ilr(c(0.7, 0.29, 0.01)))
-invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))
-# Inverse transformation of larger numbers gives unequal elements
-invilr(-10)
-invilr(c(-10, 0))
-# The sum of the elements of the inverse ilr is 1
-sum(invilr(c(-10, 0)))
-# This is why we do not need all elements of the inverse transformation to go back:
-a <- c(0.1, 0.3, 0.5)
-b <- invilr(a)
-length(b) # Four elements
-ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5)
-}
-
-\keyword{ manip }
diff --git a/man/mccall81_245T.Rd b/man/mccall81_245T.Rd
deleted file mode 100644
index 6c1a137..0000000
--- a/man/mccall81_245T.Rd
+++ /dev/null
@@ -1,42 +0,0 @@
-\name{mccall81_245T}

-\alias{mccall81_245T}

-\docType{data}

-\title{

-  Datasets on aerobic soil metabolism of 2,4,5-T in six soils

-}

-\description{

- Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding

- 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether

- extracts.

-}

-\usage{mccall81_245T}

-\format{

-  A dataframe containing the following variables.

-  \describe{

-    \item{\code{name}}{the name of the compound observed. Note that T245 is used as 

-                       an acronym for 2,4,5-T. T245 is a legitimate object name

-                       in R, which is necessary for specifying models using

-                       \code{\link{mkinmod}}.} 

-    \item{\code{time}}{a numeric vector containing sampling times in days after

-                       treatment}

-    \item{\code{value}}{a numeric vector containing concentrations in percent of applied radioactivity}

-    \item{\code{soil}}{a factor containing the name of the soil}

-  }

-}

-\source{

-  McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107

-  \url{http://dx.doi.org/10.1021/jf00103a026}

-}

-\examples{

-  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),

-                         phenol = list(type = "SFO", to = "anisole"),

-                         anisole = list(type = "SFO"))

-  \dontrun{fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))

-  summary(fit.1, data = FALSE)}

-  # No covariance matrix and k_phenol_sink is really small, therefore fix it to zero

-  fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),

-                 parms.ini = c(k_phenol_sink = 0),

-                 fixed_parms = "k_phenol_sink")

-  summary(fit.2, data = FALSE)

-}

-\keyword{datasets}

diff --git a/man/mkin_long_to_wide.Rd b/man/mkin_long_to_wide.Rd
deleted file mode 100644
index e583664..0000000
--- a/man/mkin_long_to_wide.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-\name{mkin_long_to_wide}
-\alias{mkin_long_to_wide}
-\title{
-  Convert a dataframe from long to wide format.
-}
-\usage{
-mkin_long_to_wide(long_data, time = "time", outtime = "time")
-}
-\description{
-  This function takes a dataframe in the long form as required by \code{\link{modCost}} 
-  and converts it into a dataframe with one independent variable and several 
-  dependent variables as columns.
-}
-\arguments{
-  \item{long_data}{
-  The dataframe must contain one variable called "time" with the time values specified by the 
-  \code{time} argument, one column called "name" with the grouping of the observed values, and 
-  finally one column of observed values called "value".
-}
-  \item{time}{
-  The name of the time variable in the long input data.
-}
-  \item{outtime}{
-  The name of the time variable in the wide output data.
-}
-}
-\value{
-  Dataframe in wide format.
-}
-\author{
-  Johannes Ranke
-}
-\examples{
-mkin_long_to_wide(FOCUS_2006_D)
-}
-\keyword{ manip }
diff --git a/man/mkin_wide_to_long.Rd b/man/mkin_wide_to_long.Rd
deleted file mode 100644
index d3dd200..0000000
--- a/man/mkin_wide_to_long.Rd
+++ /dev/null
@@ -1,32 +0,0 @@
-\name{mkin_wide_to_long}
-\alias{mkin_wide_to_long}
-\title{
-  Convert a dataframe with observations over time into long format.
-}
-\usage{
-mkin_wide_to_long(wide_data, time = "t")
-}
-\description{
-  This function simply takes a dataframe with one independent variable and several 
-  dependent variable and converts it into the long form as required by \code{\link{modCost}}.
-}
-\arguments{
-  \item{wide_data}{
-  The dataframe must contain one variable with the time values specified by the 
-  \code{time} argument and usually more than one column of observed values.
-}
-  \item{time}{
-  The name of the time variable.
-}
-}
-\value{
-  Dataframe in long format as needed for \code{\link{modCost}}.
-}
-\author{
-  Johannes Ranke
-}
-\examples{
-wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5))
-mkin_wide_to_long(wide)
-}
-\keyword{ manip }
diff --git a/man/mkinerrmin.Rd b/man/mkinerrmin.Rd
deleted file mode 100644
index c43d87a..0000000
--- a/man/mkinerrmin.Rd
+++ /dev/null
@@ -1,44 +0,0 @@
-\name{mkinerrmin}

-\Rdversion{1.1}

-\alias{mkinerrmin}

-\title{

-Calculate the minimum error to assume in order to pass the variance test

-}

-\description{

-This function uses \code{\link{optimize}} in order to iteratively find the

-smallest relative error still resulting in passing the chi-squared test

-as defined in the FOCUS kinetics report from 2006.

-}

-\usage{

-mkinerrmin(fit, alpha = 0.05)

-}

-\arguments{

-  \item{fit}{

-    an object of class \code{\link{mkinfit}}.

-  }

-  \item{alpha}{

-    The confidence level chosen for the chi-squared test.

-}

-}

-\value{

-  A dataframe with the following components:

-  \item{err.min}{The relative error, expressed as a fraction.}

-  \item{n.optim}{The number of optimised parameters attributed to the data series.}

-  \item{df}{The number of remaining degrees of freedom for the chi2 error level

-    calculations.  Note that mean values are used for the chi2 statistic and

-    therefore every time point with observed values in the series only counts

-    one time.}

-  The dataframe has one row for the total dataset and one further row for

-  each observed state variable in the model.

-}

-\details{

-    This function is used internally by \code{\link{summary.mkinfit}}.

-}

-\references{ 

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\keyword{ manip }

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
deleted file mode 100644
index 823ceee..0000000
--- a/man/mkinfit.Rd
+++ /dev/null
@@ -1,254 +0,0 @@
-\name{mkinfit}
-\alias{mkinfit}
-\title{
-  Fit a kinetic model to data with one or more state variables.
-}
-\description{
-  This function uses the Flexible Modelling Environment package
-  \code{\link{FME}} to create a function calculating the model cost, i.e. the 
-  deviation between the kinetic model and the observed data. This model cost is
-  then minimised using the Levenberg-Marquardt algorithm \code{\link{nls.lm}}, 
-  using the specified initial or fixed parameters and starting values.
-  In each step of the optimsation, the kinetic model is solved using the
-  function \code{\link{mkinpredict}}. The variance of the residuals for each
-  observed variable can optionally be iteratively reweighted until convergence
-  using the argument \code{reweight.method = "obs"}.
-}
-\usage{
-mkinfit(mkinmod, observed, 
-  parms.ini = "auto",
-  state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), 
-  fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], 
-  solution_type = "auto",
-  method.ode = "lsoda",
-  method.modFit = "Marq",
-  control.modFit = list(),
-  transform_rates = TRUE,
-  transform_fractions = TRUE,
-  plot = FALSE, quiet = FALSE, err = NULL, weight = "none", 
-  scaleVar = FALSE, 
-  atol = 1e-8, rtol = 1e-10, n.outtimes = 100, 
-  reweight.method = NULL,
-  reweight.tol = 1e-8, reweight.max.iter = 10,
-  trace_parms = FALSE, ...)
-}
-\arguments{
-  \item{mkinmod}{
-    A list of class \code{\link{mkinmod}}, containing the kinetic model to be fitted to the data.
-  }
-  \item{observed}{
-    The observed data. It has to be in the long format as described in
-    \code{\link{modFit}}, i.e. the first column called "name" must contain the
-    name of the observed variable for each data point. The second column must
-    contain the times of observation, named "time".  The third column must be
-    named "value" and contain the observed values. Optionally, a further column
-    can contain weights for each data point. If it is not named "err", its name
-    must be passed as a further argument named \code{err} which is then passed
-    on to \code{\link{modFit}}.
-  }
-  \item{parms.ini}{
-    A named vector of initial values for the parameters, including parameters
-    to be optimised and potentially also fixed parameters as indicated by
-    \code{fixed_parms}.  If set to "auto", initial values for rate constants
-    are set to default values.  Using parameter names that are not in the model
-    gives an error.
-
-    It is possible to only specify a subset of the parameters that the model
-    needs. You can use the parameter lists "bparms.ode" from a previously
-    fitted model, which contains the differential equation parameters from this
-    model. This works nicely if the models are nested. An example is given
-    below.
-  }
-  \item{state.ini}{
-    A named vector of initial values for the state variables of the model. In
-    case the observed variables are represented by more than one model
-    variable, the names will differ from the names of the observed variables
-    (see \code{map} component of \code{\link{mkinmod}}). The default is to set
-    the initial value of the first model variable to 100 and all others to 0.
-  }
-  \item{fixed_parms}{
-    The names of parameters that should not be optimised but rather kept at the
-    values specified in \code{parms.ini}.
-  }
-  \item{fixed_initials}{
-    The names of model variables for which the initial state at time 0 should
-    be excluded from the optimisation. Defaults to all state variables except
-    for the first one.
-  }
-  \item{solution_type}{
-    If set to "eigen", the solution of the system of differential equations is
-    based on the spectral decomposition of the coefficient matrix in cases that
-    this is possible. If set to "deSolve", a numerical ode solver from package
-    \code{\link{deSolve}} is used. If set to "analytical", an analytical
-    solution of the model is used. This is only implemented for simple
-    degradation experiments with only one state variable, i.e. with no
-    metabolites. The default is "auto", which uses "analytical" if possible,
-    otherwise "eigen" if the model can be expressed using eigenvalues and
-    eigenvectors, and finally "deSolve" for the remaining models (time
-    dependence of degradation rates and metabolites). This argument is passed
-    on to the helper function \code{\link{mkinpredict}}.
-  }
-  \item{method.ode}{
-    The solution method passed via \code{\link{mkinpredict}} to
-    \code{\link{ode}} in case the solution type is "deSolve". The default
-    "lsoda" is performant, but sometimes fails to converge.
-  }
-  \item{method.modFit}{
-    The optimisation method passed to \code{\link{modFit}}. The default "Marq"
-    is the Levenberg Marquardt algorithm \code{\link{nls.lm}} from the package
-    \code{minpack.lm}. Often other methods need more iterations to find the
-    same result. When using "Pseudo", "upper" and "lower" need to be 
-    specified for the transformed parameters.
-  }
-  \item{control.modFit}{
-    Additional arguments passed to the optimisation method used by
-    \code{\link{modFit}}.
-  }
-  \item{transform_rates}{
-    Boolean specifying if kinetic rate constants should be transformed in the
-    model specification used in the fitting for better compliance with the
-    assumption of normal distribution of the estimator. If TRUE, also 
-    alpha and beta parameters of the FOMC model are log-transformed, as well 
-    as k1 and k2 rate constants for the DFOP and HS models.
-    If TRUE, zero is used as a lower bound for the rates in the optimisation.
-  }
-  \item{transform_fractions}{
-    Boolean specifying if formation fractions constants should be transformed in the
-    model specification used in the fitting for better compliance with the
-    assumption of normal distribution of the estimator. The default (TRUE) is 
-    to do transformations. The g parameter of the DFOP and HS models are also 
-    transformed, as they can also be seen as compositional data. The
-    transformation used for these transformations is the \code{\link{ilr}}
-    transformation.
-  }
-  \item{plot}{
-    Should the observed values and the numerical solutions be plotted at each
-    stage of the optimisation?
-  }
-  \item{quiet}{
-    Suppress printing out the current model cost after each improvement?
-  }
-  \item{err }{either \code{NULL}, or the name of the column with the
-    \emph{error} estimates, used to weigh the residuals (see details of
-    \code{\link{modCost}}); if \code{NULL}, then the residuals are not weighed.
-  }
-  \item{weight}{
-    only if \code{err}=\code{NULL}: how to weight the residuals, one of "none",
-    "std", "mean", see details of \code{\link{modCost}}.
-  }
-  \item{scaleVar}{
-    Will be passed to \code{\link{modCost}}. Default is not to scale Variables
-    according to the number of observations.
-  }
-  \item{atol}{
-    Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
-    lower than in \code{\link{lsoda}}.
-  }
-  \item{rtol}{
-    Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10,
-    much lower than in \code{\link{lsoda}}.
-  }
-  \item{n.outtimes}{
-    The length of the dataseries that is produced by the model prediction
-    function \code{\link{mkinpredict}}. This impacts the accuracy of
-    the numerical solver if that is used (see \code{solution_type} argument. 
-    The default value is 100.
-  }
-  \item{reweight.method}{
-    The method used for iteratively reweighting residuals, also known
-    as iteratively reweighted least squares (IRLS). Default is NULL,
-    the other method implemented is called "obs", meaning that each
-    observed variable is assumed to have its own variance, this is 
-    estimated from the fit and used for weighting the residuals
-    in each iteration until convergence of this estimate up to 
-    \code{reweight.tol} or up to the maximum number of iterations
-    specified by \code{reweight.max.iter}.
-  }
-  \item{reweight.tol}{
-    Tolerance for convergence criterion for the variance components
-    in IRLS fits.
-  }
-  \item{reweight.max.iter}{
-    Maximum iterations in IRLS fits.
-  }
-  \item{trace_parms}{
-    Should a trace of the parameter values be listed?
-  }
-  \item{\dots}{
-    Further arguments that will be passed to \code{\link{modFit}}. 
-  }
-}
-\value{
-  A list with "mkinfit" and "modFit" in the class attribute. 
-  A summary can be obtained by \code{\link{summary.mkinfit}}. 
-}
-\note{
-  The implementation of iteratively reweighted least squares is inspired by the
-  work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei
-  Gao). A similar implemention can also be found in CAKE 2.0, which is the
-  other GUI derivative of mkin, sponsored by Syngenta.
-}
-\author{
-  Johannes Ranke <jranke@uni-bremen.de>
-}
-\examples{
-# One parent compound, one metabolite, both single first order.
-SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
-summary(fit)
-
-# Use stepwise fitting, using optimised parameters from parent only fit, FOMC
-\dontrun{
-FOMC <- mkinmod(parent = list(type = "FOMC"))
-FOMC_SFO <- mkinmod(
-  parent = list(type = "FOMC", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D)
-# Use starting parameters from parent only FOMC fit
-fit.FOMC = mkinfit(FOMC, FOCUS_2006_D, plot=TRUE)
-fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, 
-  parms.ini = fit.FOMC$bparms.ode, plot=TRUE)
-
-# Use stepwise fitting, using optimised parameters from parent only fit, SFORB
-SFORB <- mkinmod(parent = list(type = "SFORB"))
-SFORB_SFO <- mkinmod(
-  parent = list(type = "SFORB", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D)
-# Use starting parameters from parent only SFORB fit (not really needed in this case)
-fit.SFORB = mkinfit(SFORB, FOCUS_2006_D)
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)
-}
-
-# Weighted fits, including IRLS
-SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                      m1 = list(type = "SFO"), use_of_ff = "max")
-f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)
-summary(f.noweight)
-f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs")
-summary(f.irls)
-f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean")
-summary(f.w.mean)
-f.w.mean.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean",
-                         reweight.method = "obs")
-summary(f.w.mean.irls)
-
-\dontrun{
-# Manual weighting
-dw <- FOCUS_2006_D
-errors <- c(parent = 2, m1 = 1)
-dw$err.man <- errors[FOCUS_2006_D$name]
-f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man")
-summary(f.w.man)
-f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man",
-                       reweight.method = "obs")
-summary(f.w.man.irls)
-}
-}
-\keyword{ models }
-\keyword{ optimize }
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
deleted file mode 100644
index 76127c5..0000000
--- a/man/mkinmod.Rd
+++ /dev/null
@@ -1,63 +0,0 @@
-\name{mkinmod}

-\alias{mkinmod}

-\title{

-  Function to set up a kinetic model with one or more state variables.

-}

-\description{

-  The function takes a specification, consisting of a list of the observed variables

-  in the data. Each observed variable is again represented by a list, specifying the 

-  kinetic model type and reaction or transfer to other observed compartments.

-}

-\usage{

-mkinmod(..., use_of_ff = "min", speclist = NULL)

-}

-\arguments{

-  \item{...}{

-    For each observed variable, a list has to be specified as an argument, containing

-    at least a component \code{type}, specifying the type of kinetics to use

-    for the variable. Currently, single first order kinetics "SFO" or

-    single first order with reversible binding "SFORB" are implemented for all

-    variables, while 

-    "FOMC", "DFOP" and "HS" can additionally be chosen for the first

-    variable which is assumed to be the source compartment.

-    Additionally, each component of the list can include a character vector \code{to},

-    specifying names of variables to which a transfer is to be assumed in the

-    model.

-    If the argument \code{use_of_ff} is set to "min" (default) and the model for 

-    the compartment is "SFO" or "SFORB", an additional component of the list

-    can be "sink=FALSE" effectively fixing the flux to sink to zero.

-  }

-  \item{use_of_ff}{

-    Specification of the use of formation fractions in the model equations and, if 

-    applicable, the coefficient matrix. If "min", a minimum use of formation 

-    fractions is made in order to avoid fitting the product of formation fractions 

-    and rate constants. If "max", formation fractions are always used.

-  }

-  \item{speclist}{

-    The specification of the observed variables and their submodel types and 

-    pathways can be given as a single list using this argument. Default is NULL.

-  }

-}

-\value{

-  A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, containing 

-    \item{diffs}{ A vector of string representations of differential equations,

-      one for each modelling variable. }

-    \item{parms}{ A vector of parameter names occurring in the differential equations. }

-    \item{map}{ A list containing named character vectors for each observed variable, specifying

-      the modelling variables by which it is represented. }

-    \item{use_of_ff}{ The content of \code{use_of_ff} is passed on in this list component. }

-    \item{coefmat}{ The coefficient matrix, if the system of differential equations can be represented by one. }

-}

-\author{

-  Johannes Ranke

-}

-\examples{

-# Specify the SFO model

-SFO <- mkinmod(parent = list(type = "SFO"))

-

-# One parent compound, one metabolite, both single first order.

-SFO_SFO <- mkinmod(

-  parent = list(type = "SFO", to = "m1"),

-  m1 = list(type = "SFO"))

-}

-\keyword{ models }

diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd
deleted file mode 100644
index 60103b8..0000000
--- a/man/mkinparplot.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-\name{mkinparplot}

-\alias{mkinparplot}

-\title{

-  Function to plot the confidence intervals obtained using

-  \code{\link{mkinfit}}

-}

-\description{

-  This function plots the confidence intervals for the parameters

-  fitted using \code{\link{mkinfit}}.

-}

-\usage{

-  mkinparplot(object)

-}

-\arguments{

-  \item{object}{

-    A fit represented in an \code{\link{mkinfit}} object.

-  }

-}

-\value{

-  Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.

-}

-\author{

-  Johannes Ranke

-}

-

-\examples{

-model <- mkinmod(

-  T245 = list(type = "SFO", to = c("phenol")),

-  phenol = list(type = "SFO", to = c("anisole")),

-  anisole = list(type = "SFO"), use_of_ff = "max")

-fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), 

-  parms.ini = c(f_phenol_to_anisole = 1), fixed_parms = "f_phenol_to_anisole")

-\dontrun{mkinparplot(fit)}

-}

-\keyword{ hplot }

diff --git a/man/mkinplot.Rd b/man/mkinplot.Rd
deleted file mode 100644
index 4b0fef4..0000000
--- a/man/mkinplot.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-\name{mkinplot}
-\alias{mkinplot}
-\title{
-  Plot the observed data and the fitted model of an mkinfit.
-}
-\description{
-  Deprecated function. It now only calls the plot method \code{\link{plot.mkinfit}}.
-}
-\usage{
-  mkinplot(fit, ...)
-}
-\arguments{
-  \item{fit}{
-    an object of class \code{\link{mkinfit}}.
-  }
-  \item{\dots}{
-   further arguments passed to \code{\link{plot.mkinfit}}.
-}
-}
-\value{
-  The function is called for its side effect.
-}
-\author{
-  Johannes Ranke
-}
-\keyword{ hplot }
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
deleted file mode 100644
index 97db90e..0000000
--- a/man/mkinpredict.Rd
+++ /dev/null
@@ -1,91 +0,0 @@
-\name{mkinpredict}
-\alias{mkinpredict}
-\title{
-  Produce predictions from a kinetic model using specifc parameters
-}
-\description{
-  This function produces a time series for all the observed variables in a
-  kinetic model as specified by \code{\link{mkinmod}}, using a specific set of
-  kinetic parameters and initial values for the state variables.
-}
-\usage{
-  mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
-	      method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)
-}
-\arguments{
-  \item{mkinmod}{
-    A kinetic model as produced by \code{\link{mkinmod}}.
-  }
-  \item{odeparms}{
-    A numeric vector specifying the parameters used in the kinetic model, which
-    is generally defined as a set of ordinary differential equations.
-  }
-  \item{odeini}{
-    A numeric vectory containing the initial values of the state variables of
-    the model. Note that the state variables can differ from the observed
-    variables, for example in the case of the SFORB model.
-  }
-  \item{outtimes}{
-    A numeric vector specifying the time points for which model predictions
-    should be generated.
-  }
-  \item{solution_type}{
-    The method that should be used for producing the predictions. This should
-    generally be "analytical" if there is only one observed variable, and
-    usually "deSolve" in the case of several observed variables. The third
-    possibility "eigen" is faster but not applicable to some models e.g.
-    using FOMC for the parent compound.
-  }
-  \item{method.ode}{
-    The solution method passed via \code{\link{mkinpredict}} to
-    \code{\link{ode}} in case the solution type is "deSolve". The default
-    "lsoda" is performant, but sometimes fails to converge.
-  }
-  \item{atol}{
-    Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
-    lower than in \code{\link{lsoda}}.
-  }
-  \item{rtol}{
-    Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10,
-    much lower than in \code{\link{lsoda}}.
-  }
-  \item{map_output}{
-    Boolean to specify if the output should list values for the observed
-    variables (default) or for all state variables (if set to FALSE). 
-  }
-  \item{\dots}{
-    Further arguments passed to the ode solver in case such a solver is used.
-  }
-}
-\value{
-  A matrix in the same format as the output of \code{\link{ode}}.
-}
-\author{
-  Johannes Ranke
-}
-\examples{
-  SFO <- mkinmod(degradinol = list(type = "SFO"))
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      solution_type = "analytical")
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      solution_type = "eigen")
-
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20, 
-	      solution_type = "analytical")[20,]
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20)[20,]
-
-  # The integration method does not make a lot of difference
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20, method = "ode45")[20,]
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20, method = "rk4")[20,]
-
-  # The number of output times used to make a lot of difference until the
-  # default for atol was adjusted
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 
-	      seq(0, 20, by = 0.1))[201,]
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 
-	      seq(0, 20, by = 0.01))[2001,]
-}
-\keyword{ manip }
diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
deleted file mode 100644
index 3f53dd1..0000000
--- a/man/mkinresplot.Rd
+++ /dev/null
@@ -1,67 +0,0 @@
-\name{mkinresplot}

-\alias{mkinresplot}

-\title{

-  Function to plot residuals stored in an mkin object

-}

-\description{

-  This function plots the residuals for the specified subset of the 

-  observed variables from an mkinfit object. A combined plot of the fitted

-  model and the residuals can be obtained using \code{\link{plot.mkinfit}}

-  using the argument \code{show_residuals = TRUE}.

-}

-\usage{

-  mkinresplot(object, 

-    obs_vars = names(object$mkinmod$map),

-    xlab = "Time", ylab = "Residual", 

-    maxabs = "auto", legend = TRUE, lpos = "topright", ...)

-}

-\arguments{

-  \item{object}{

-    A fit represented in an \code{\link{mkinfit}} object.

-}

-  \item{obs_vars}{

-    A character vector of names of the observed variables for which residuals

-    should be plotted. Defaults to all observed variables in the model

-}

-  \item{xlab}{

-    Label for the x axis. Defaults to "Time [days]".

-}

-  \item{ylab}{

-    Label for the y axis. Defaults to "Residual [\% of applied radioactivity]".

-}

-  \item{maxabs}{

-    Maximum absolute value of the residuals. This is used for the scaling of

-    the y axis and defaults to "auto".

-}

-  \item{legend}{

-    Should a legend be plotted? Defaults to "TRUE".

-}

-  \item{lpos}{ 

-    Where should the legend be placed? Default is "topright". Will be passed on to

-		\code{\link{legend}}. }

-  \item{\dots}{

-   further arguments passed to \code{\link{plot}}.

-}

-}

-\value{

-  Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.

-}

-\author{

-  Johannes Ranke

-}

-

-\seealso{

- \code{\link{mkinplot}}, for a way to plot the data and the fitted lines of the

- mkinfit object.  }

-\examples{

-data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")

-model <- mkinmod(

-  parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),

-  A1 = list(type = "SFO", to = "A2"),

-  B1 = list(type = "SFO"),

-  C1 = list(type = "SFO"),

-  A2 = list(type = "SFO"))

-\dontrun{fit <- mkinfit(model, data, plot=TRUE)}

-\dontrun{mkinresplot(fit, "A1")}

-}

-\keyword{ hplot }

diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
deleted file mode 100644
index 7009e7d..0000000
--- a/man/plot.mkinfit.Rd
+++ /dev/null
@@ -1,94 +0,0 @@
-\name{plot.mkinfit}
-\alias{plot.mkinfit}
-\title{
-  Plot the observed data and the fitted model of an mkinfit object.
-}
-\description{
-  Solves the differential equations with the optimised and fixed parameters
-  from a previous successful call to \code{\link{mkinfit}} and plots 
-  the observed data together with the solution of the fitted model.
-}
-\usage{
-\method{plot}{mkinfit}(x, fit = x,
-  obs_vars = names(fit$mkinmod$map),
-  xlab = "Time", ylab = "Observed", 
-  xlim = range(fit$data$time),
-  ylim = "default",
-  col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, 
-  lty_obs = rep(1, length(fit$mkinmod$map)),
-  add = FALSE, legend = !add,
-  show_residuals = FALSE, maxabs = "auto",
-  lpos = "topright", inset = c(0.05, 0.05), \dots)
-}
-\arguments{
-  \item{x}{
-    Alias for fit introduced for compatibility with the generic S3 method.  
-  }
-  \item{fit}{
-    an object of class \code{\link{mkinfit}}.
-  }
-  \item{obs_vars}{
-    A character vector of names of the observed variables for which the 
-    data and the model should be plotted. Defauls to all observed variables
-    in the model.
-  }
-  \item{xlab}{
-    label for the x axis.
-  }
-  \item{ylab}{
-    label for the y axis.
-  }
-  \item{xlim}{
-    plot range in x direction.
-  }
-  \item{ylim}{
-    plot range in y direction.
-  }
-  \item{col_obs}{
-    colors used for plotting the observed data and the corresponding model prediction lines.
-  }
-  \item{pch_obs}{
-    symbols to be used for plotting the data.
-  }
-  \item{lty_obs}{
-    line types to be used for the model predictions.
-  }
-  \item{add}{
-    should the plot be added to an existing plot?
-  }
-  \item{legend}{
-    should a legend be added to the plot?
-  }
-  \item{show_residuals}{
-    should residuals be shown in the lower third of the plot?
-  }
-  \item{maxabs}{
-    Maximum absolute value of the residuals. This is used for the scaling of
-    the y axis and defaults to "auto".
-  }
-  \item{lpos}{
-    position of the legend. Passed to \code{\link{legend}} as the first argument.
-  }
-  \item{inset}{
-    Passed to \code{\link{legend}} if applicable.
-  }
-  \item{\dots}{
-   further arguments passed to \code{\link{plot}}.
-  }
-}
-\value{
-  The function is called for its side effect.
-}
-\examples{
-# One parent compound, one metabolite, both single first order.
-SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
-\dontrun{plot(fit)}
-}
-\author{
-  Johannes Ranke
-}
-\keyword{ hplot }
diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd
deleted file mode 100644
index ed4f694..0000000
--- a/man/schaefer07_complex_case.Rd
+++ /dev/null
@@ -1,42 +0,0 @@
-\name{schaefer07_complex_case}

-\alias{schaefer07_complex_case}

-\alias{schaefer07_complex_results}

-\encoding{latin1}

-\docType{data}

-\title{

-  Metabolism data set used for checking the software quality of KinGUI

-}

-\description{

-  This dataset was used for a comparison of KinGUI and ModelMaker to check the

-  software quality of KinGUI in the original publication (Schäfer et al., 2007).

-  The results from the fitting are also included.

-}

-\usage{data(schaefer07_complex_case)}

-\format{

-  The data set is a data frame with 8 observations on the following 6 variables.

-  \describe{

-    \item{\code{time}}{a numeric vector}

-    \item{\code{parent}}{a numeric vector}

-    \item{\code{A1}}{a numeric vector}

-    \item{\code{B1}}{a numeric vector}

-    \item{\code{C1}}{a numeric vector}

-    \item{\code{A2}}{a numeric vector}

-  }

-  The results are a data frame with 14 results for different parameter values

-}

-\references{

-  Schäfer D, Mikolasch M, Rainbird P and Harvey B (2007). KinGUI: a new kinetic

-  software tool for evaluations according to FOCUS degradation kinetics. In: Del

-  Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII

-  Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.  }

-\examples{

-data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")

-model <- mkinmod(

-  parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),

-  A1 = list(type = "SFO", to = "A2"),

-  B1 = list(type = "SFO"),

-  C1 = list(type = "SFO"),

-  A2 = list(type = "SFO"))

-\dontrun{mkinfit(model, data, plot=TRUE)}

-}

-\keyword{datasets}

diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
deleted file mode 100644
index 472b5de..0000000
--- a/man/summary.mkinfit.Rd
+++ /dev/null
@@ -1,75 +0,0 @@
-\name{summary.mkinfit}

-\alias{summary.mkinfit}

-\alias{print.summary.mkinfit}

-\title{

-  Summary method for class "mkinfit".

-}

-\description{

-  Lists model equations, the summary as returned by \code{\link{summary.modFit}},

-  the chi2 error levels calculated according to FOCUS guidance (2006) as far

-  as defined therein, and optionally the data, consisting of observed, predicted

-  and residual values.

-}

-\usage{

-\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)

-\method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") - 3), ...)

-}

-

-\arguments{

-  \item{object}{

-  an object of class \code{\link{mkinfit}}.

-}

-  \item{x}{

-  an object of class \code{summary.mkinfit}.

-}

-  \item{data}{

-  logical, indicating whether the data should be included in the summary. 

-}

-  \item{distimes}{

-  logical, indicating whether DT50 and DT90 values should be included.

-}

-  \item{alpha}{

-  error level for confidence interval estimation from t distribution

-}

-  \item{digits}{

-  Number of digits to use for printing

-}

-  \item{\dots}{

-  optional arguments passed to methods like \code{print}.

-}

-}

-\value{

-  The summary function returns a list derived from

-  \code{\link{summary.modFit}}, with components, among others

-  \item{version, Rversion}{The mkin and R versions used}

-  \item{date.fit, date.summary}{The dates where the fit and the summary were produced}

-  \item{use_of_ff}{Was maximum or minimum use made of formation fractions}

-  \item{residuals, residualVariance, sigma, modVariance, df}{As in summary.modFit}

-  \item{cov.unscaled, cov.scaled, info, niter, stopmess, par}{As in summary.modFit}

-  \item{bpar}{Optimised and backtransformed parameters}

-  \item{diffs }{The differential equations used in the model}

-  \item{data }{The data (see Description above).}

-  \item{start }{The starting values and bounds, if applicable, for optimised parameters.}

-  \item{fixed }{The values of fixed parameters.}

-  \item{errmin }{The chi2 error levels for each observed variable.}

-  \item{bparms.ode }{All backtransformed ODE parameters, for use as starting parameters for

-    related models.}

-  \item{ff }{The estimated formation fractions derived from the fitted model.}

-  \item{distimes }{The DT50 and DT90 values for each observed variable.}

-  \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}

-  The print method is called for its side effect, i.e. printing the summary.

-}

-\references{

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://focus.jrc.ec.europa.eu/dk} 

-}

-\author{

-  Johannes Ranke <jranke@{harlan.com,uni-bremen.de}>

-}

-\examples{

-  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A))

-}

-\keyword{ utilities }

diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
deleted file mode 100644
index c52fb4f..0000000
--- a/man/transform_odeparms.Rd
+++ /dev/null
@@ -1,69 +0,0 @@
-\name{transform_odeparms}
-\alias{transform_odeparms}
-\alias{backtransform_odeparms}
-\title{
-  Functions to transform and backtransform kinetic parameters for fitting
-}
-\description{
-  The transformations are intended to map parameters that should only take 
-  on restricted values to the full scale of real numbers. For kinetic rate
-  constants and other paramters that can only take on positive values, a
-  simple log transformation is used. For compositional parameters, such as
-  the formations fractions that should always sum up to 1 and can not be
-  negative, the \code{\link{ilr}} transformation is used.
-}
-\usage{
-transform_odeparms(parms, mod_vars, transform_rates = TRUE, transform_fractions = TRUE)
-backtransform_odeparms(transparms, mod_vars, 
-                       transform_rates = TRUE, transform_fractions = TRUE)
-}
-\arguments{
-  \item{parms}{
-    Parameters of kinetic models as used in the differential equations.
-  }
-  \item{transparms}{
-    Transformed parameters of kinetic models as used in the fitting procedure.
-  }
-  \item{mod_vars}{
-    Names of the state variables in the kinetic model. These are used for 
-    grouping the formation fractions before \code{\link{ilr}} transformation.  
-  }
-  \item{transform_rates}{
-    Boolean specifying if kinetic rate constants should be transformed in the
-    model specification used in the fitting for better compliance with the
-    assumption of normal distribution of the estimator. If TRUE, also 
-    alpha and beta parameters of the FOMC model are log-transformed, as well 
-    as k1 and k2 rate constants for the DFOP and HS models and the break point tb
-    of the HS model
-  }
-  \item{transform_fractions}{
-    Boolean specifying if formation fractions constants should be transformed in the
-    model specification used in the fitting for better compliance with the
-    assumption of normal distribution of the estimator. The default (TRUE) is 
-    to do transformations. The g parameter of the DFOP and HS models are also 
-    transformed, as they can also be seen as compositional data. The
-    transformation used for these transformations is the \code{\link{ilr}}
-    transformation.
-  }
-}
-\value{
-  A vector of transformed or backtransformed parameters with the same names
-  as the original parameters.
-}
-\author{
-  Johannes Ranke
-}
-\examples{
-SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
-summary(fit, data=FALSE) # See transformed and backtransformed parameters
-initials <- fit$start$value
-transformed <- fit$start$transformed
-names(initials) <- names(transformed) <- rownames(fit$start)
-transform_odeparms(initials, c("parent", "m1"))
-backtransform_odeparms(transformed, c("parent", "m1"))
-}
-\keyword{ manip }