16 files changed, 182 insertions, 153 deletions
diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd
index d8c4553e..61089081 100644
--- a/man/DFOP.solution.Rd
+++ b/man/DFOP.solution.Rd
@@ -43,12 +43,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/DTx.Rd b/man/DTx.Rd
new file mode 100644
index 00000000..67dba5d6
--- /dev/null
+++ b/man/DTx.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/endpoints.R
+\name{DTx}
+\alias{DTx}
+\title{Calculate DTx from parameters of parent degradation models}
+\usage{
+DTx(type = c("SFO", "FOMC", "DFOP", "HS", "SFORB"), parms, exact = FALSE)
+}
+\arguments{
+\item{type}{Character string specifying the degradation model}
+
+\item{parms}{Named numeric vector giving the kinetic parameters}
+
+\item{exact}{Should we used log(10)/log(2) instead of the widely used value
+of 3.32 for backcalculation of DT50 values from DT90 values?}
+}
+\description{
+Calculate DTx from parameters of parent degradation models
+}
+\examples{
+# Check what type of DT50 is given in the bixafen EFSA conclusion from 2012 on p. 42
+DTx("HS", parms = c(k1 = 0.0081, k2 = 0.00023, tb = 53))
+# We get 1200 days for the time the concentration reaches 50\%, the value of 1235
+# was likely based on more digits for the parameters. The half-life corresponding
+# to the slow phase is around 3000 days
+}
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
index d645113c..456b406f 100644
--- a/man/FOMC.solution.Rd
+++ b/man/FOMC.solution.Rd
@@ -56,12 +56,12 @@ A new model based on spatial variability. \emph{Environmental Science and
 Technology} \bold{24}, 1032-1038
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
index 2940e949..9390a2e9 100644
--- a/man/HS.solution.Rd
+++ b/man/HS.solution.Rd
@@ -44,12 +44,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd
index 5d0126a7..9909e87c 100644
--- a/man/IORE.solution.Rd
+++ b/man/IORE.solution.Rd
@@ -49,12 +49,12 @@ NAFTA Technical Working Group on Pesticides (not dated) Guidance
 for Evaluating and Calculating Degradation Kinetics in Environmental Media
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd
index c0aac237..f76837e8 100644
--- a/man/SFO.solution.Rd
+++ b/man/SFO.solution.Rd
@@ -37,12 +37,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFORB.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd
index dc78d1f1..817e9788 100644
--- a/man/SFORB.solution.Rd
+++ b/man/SFORB.solution.Rd
@@ -47,12 +47,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{logistic.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=logistic.solution]{logistic.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/anova.saem.mmkin.Rd b/man/anova.saem.mmkin.Rd
index 34711c41..59c6754e 100644
--- a/man/anova.saem.mmkin.Rd
+++ b/man/anova.saem.mmkin.Rd
@@ -19,7 +19,7 @@
 
 \item{method}{Method for likelihood calculation: "is" (importance sampling),
 "lin" (linear approximation), or "gq" (Gaussian quadrature). Passed
-to \link[saemix:logLik]{saemix::logLik.SaemixObject}}
+to \link[saemix:logLik.SaemixObject]{saemix::logLik.SaemixObject}}
 
 \item{test}{Should a likelihood ratio test be performed? If TRUE,
 the alternative models are tested against the first model. Should
diff --git a/man/logLik.saem.mmkin.Rd b/man/logLik.saem.mmkin.Rd
index bd0bb72e..e3a29ad2 100644
--- a/man/logLik.saem.mmkin.Rd
+++ b/man/logLik.saem.mmkin.Rd
@@ -9,9 +9,9 @@
 \arguments{
 \item{object}{The fitted \link{saem.mmkin} object}
 
-\item{\dots}{Passed to \link[saemix:logLik]{saemix::logLik.SaemixObject}}
+\item{\dots}{Passed to \link[saemix:logLik.SaemixObject]{saemix::logLik.SaemixObject}}
 
-\item{method}{Passed to \link[saemix:logLik]{saemix::logLik.SaemixObject}}
+\item{method}{Passed to \link[saemix:logLik.SaemixObject]{saemix::logLik.SaemixObject}}
 }
 \description{
 logLik method for saem.mmkin objects
diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd
index 22944098..137043d9 100644
--- a/man/logistic.solution.Rd
+++ b/man/logistic.solution.Rd
@@ -78,12 +78,12 @@ Version 1.1, 18 December 2014
 \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
 }
 \seealso{
-Other parent solutions: 
-\code{\link{DFOP.solution}()},
-\code{\link{FOMC.solution}()},
-\code{\link{HS.solution}()},
-\code{\link{IORE.solution}()},
-\code{\link{SFO.solution}()},
-\code{\link{SFORB.solution}()}
+Other parent solutions:
+\code{\link[=DFOP.solution]{DFOP.solution()}},
+\code{\link[=FOMC.solution]{FOMC.solution()}},
+\code{\link[=HS.solution]{HS.solution()}},
+\code{\link[=IORE.solution]{IORE.solution()}},
+\code{\link[=SFO.solution]{SFO.solution()}},
+\code{\link[=SFORB.solution]{SFORB.solution()}}
 }
 \concept{parent solutions}
diff --git a/man/mkinds.Rd b/man/mkinds.Rd
index a2c58300..ce87fb7f 100644
--- a/man/mkinds.Rd
+++ b/man/mkinds.Rd
@@ -27,70 +27,71 @@ print(mds)
 
 }
 \section{Public fields}{
-\if{html}{\out{<div class="r6-fields">}}
-\describe{
-\item{\code{title}}{A full title for the dataset}
+  \if{html}{\out{<div class="r6-fields">}}
+  \describe{
+    \item{\code{title}}{A full title for the dataset}
 
-\item{\code{sampling_times}}{The sampling times}
+    \item{\code{sampling_times}}{The sampling times}
 
-\item{\code{time_unit}}{The time unit}
+    \item{\code{time_unit}}{The time unit}
 
-\item{\code{observed}}{Names of the observed variables}
+    \item{\code{observed}}{Names of the observed variables}
 
-\item{\code{unit}}{The unit of the observations}
+    \item{\code{unit}}{The unit of the observations}
 
-\item{\code{replicates}}{The maximum number of replicates per sampling time}
+    \item{\code{replicates}}{The maximum number of replicates per sampling time}
 
-\item{\code{data}}{A data frame with at least the columns name, time
+    \item{\code{data}}{A data frame with at least the columns name, time
 and value in order to be compatible with mkinfit}
-}
-\if{html}{\out{</div>}}
+  }
+  \if{html}{\out{</div>}}
 }
 \section{Methods}{
 \subsection{Public methods}{
-\itemize{
-\item \href{#method-mkinds-new}{\code{mkinds$new()}}
-\item \href{#method-mkinds-clone}{\code{mkinds$clone()}}
-}
+  \itemize{
+    \item \href{#method-mkinds-initialize}{\code{mkinds$new()}}
+    \item \href{#method-mkinds-clone}{\code{mkinds$clone()}}
+  }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-mkinds-new"></a>}}
-\if{latex}{\out{\hypertarget{method-mkinds-new}{}}}
-\subsection{Method \code{new()}}{
-Create a new mkinds object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{mkinds$new(title = "", data, time_unit = NA, unit = NA)}\if{html}{\out{</div>}}
+\if{html}{\out{<a id="method-mkinds-initialize"></a>}}
+\if{latex}{\out{\hypertarget{method-mkinds-initialize}{}}}
+\subsection{\code{mkinds$new()}}{
+  Create a new mkinds object
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{mkinds$new(title = "", data, time_unit = NA, unit = NA)}
+    \if{html}{\out{</div>}}
+  }
+  \subsection{Arguments}{
+    \if{html}{\out{<div class="arguments">}}
+    \describe{
+      \item{\code{title}}{The dataset title}
+      \item{\code{data}}{The data}
+      \item{\code{time_unit}}{The time unit}
+      \item{\code{unit}}{The unit of the observations}
+    }
+    \if{html}{\out{</div>}}
+  }
 }
 
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{title}}{The dataset title}
-
-\item{\code{data}}{The data}
-
-\item{\code{time_unit}}{The time unit}
-
-\item{\code{unit}}{The unit of the observations}
-}
-\if{html}{\out{</div>}}
-}
-}
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-mkinds-clone"></a>}}
 \if{latex}{\out{\hypertarget{method-mkinds-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{mkinds$clone(deep = FALSE)}\if{html}{\out{</div>}}
+\subsection{\code{mkinds$clone()}}{
+  The objects of this class are cloneable with this method.
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{mkinds$clone(deep = FALSE)}
+    \if{html}{\out{</div>}}
+  }
+  \subsection{Arguments}{
+    \if{html}{\out{<div class="arguments">}}
+    \describe{
+      \item{\code{deep}}{Whether to make a deep clone.}
+    }
+    \if{html}{\out{</div>}}
+  }
 }
 
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{deep}}{Whether to make a deep clone.}
-}
-\if{html}{\out{</div>}}
-}
-}
 }
diff --git a/man/mkindsg.Rd b/man/mkindsg.Rd
index 3b6a9f61..cb0c9bfd 100644
--- a/man/mkindsg.Rd
+++ b/man/mkindsg.Rd
@@ -37,69 +37,70 @@ print(mdsg, verbose = TRUE, data = TRUE)
 
 }
 \section{Public fields}{
-\if{html}{\out{<div class="r6-fields">}}
-\describe{
-\item{\code{title}}{A title for the dataset group}
+  \if{html}{\out{<div class="r6-fields">}}
+  \describe{
+    \item{\code{title}}{A title for the dataset group}
 
-\item{\code{ds}}{A list of mkinds objects}
+    \item{\code{ds}}{A list of mkinds objects}
 
-\item{\code{observed_n}}{Occurrence counts of compounds in datasets}
+    \item{\code{observed_n}}{Occurrence counts of compounds in datasets}
 
-\item{\code{f_time_norm}}{Time normalisation factors}
+    \item{\code{f_time_norm}}{Time normalisation factors}
 
-\item{\code{meta}}{A data frame with a row for each dataset,
+    \item{\code{meta}}{A data frame with a row for each dataset,
 containing additional information in the form
 of categorical data (factors) or numerical data
 (e.g. temperature, moisture,
 or covariates like soil pH).}
-}
-\if{html}{\out{</div>}}
+  }
+  \if{html}{\out{</div>}}
 }
 \section{Methods}{
 \subsection{Public methods}{
-\itemize{
-\item \href{#method-mkindsg-new}{\code{mkindsg$new()}}
-\item \href{#method-mkindsg-clone}{\code{mkindsg$clone()}}
-}
+  \itemize{
+    \item \href{#method-mkindsg-initialize}{\code{mkindsg$new()}}
+    \item \href{#method-mkindsg-clone}{\code{mkindsg$clone()}}
+  }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-mkindsg-new"></a>}}
-\if{latex}{\out{\hypertarget{method-mkindsg-new}{}}}
-\subsection{Method \code{new()}}{
-Create a new mkindsg object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{mkindsg$new(title = "", ds, f_time_norm = rep(1, length(ds)), meta)}\if{html}{\out{</div>}}
+\if{html}{\out{<a id="method-mkindsg-initialize"></a>}}
+\if{latex}{\out{\hypertarget{method-mkindsg-initialize}{}}}
+\subsection{\code{mkindsg$new()}}{
+  Create a new mkindsg object
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{mkindsg$new(title = "", ds, f_time_norm = rep(1, length(ds)), meta)}
+    \if{html}{\out{</div>}}
+  }
+  \subsection{Arguments}{
+    \if{html}{\out{<div class="arguments">}}
+    \describe{
+      \item{\code{title}}{The title}
+      \item{\code{ds}}{A list of mkinds objects}
+      \item{\code{f_time_norm}}{Time normalisation factors}
+      \item{\code{meta}}{The meta data}
+    }
+    \if{html}{\out{</div>}}
+  }
 }
 
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{title}}{The title}
-
-\item{\code{ds}}{A list of mkinds objects}
-
-\item{\code{f_time_norm}}{Time normalisation factors}
-
-\item{\code{meta}}{The meta data}
-}
-\if{html}{\out{</div>}}
-}
-}
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-mkindsg-clone"></a>}}
 \if{latex}{\out{\hypertarget{method-mkindsg-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{mkindsg$clone(deep = FALSE)}\if{html}{\out{</div>}}
+\subsection{\code{mkindsg$clone()}}{
+  The objects of this class are cloneable with this method.
+  \subsection{Usage}{
+    \if{html}{\out{<div class="r">}}
+    \preformatted{mkindsg$clone(deep = FALSE)}
+    \if{html}{\out{</div>}}
+  }
+  \subsection{Arguments}{
+    \if{html}{\out{<div class="arguments">}}
+    \describe{
+      \item{\code{deep}}{Whether to make a deep clone.}
+    }
+    \if{html}{\out{</div>}}
+  }
 }
 
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{deep}}{Whether to make a deep clone.}
-}
-\if{html}{\out{</div>}}
-}
-}
 }
diff --git a/man/reexports.Rd b/man/reexports.Rd
index 43d27ac1..4608450f 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -1,5 +1,6 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/intervals.R, R/lrtest.mkinfit.R, R/nlme.mmkin.R
+% Please edit documentation in R/intervals.R, R/lrtest.mkinfit.R,
+%   R/nlme.mmkin.R
 \docType{import}
 \name{reexports}
 \alias{reexports}
@@ -13,8 +14,8 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{lmtest}{\code{\link[lmtest]{lrtest}}}
+  \item{lmtest}{\code{\link[lmtest:lrtest]{lrtest()}}}
 
-  \item{nlme}{\code{\link[nlme]{intervals}}, \code{\link[nlme]{nlme}}}
+  \item{nlme}{\code{\link[nlme:intervals]{intervals()}}, \code{\link[nlme:nlme]{nlme()}}}
 }}
 
diff --git a/man/saem.Rd b/man/saem.Rd
index 5a125ab6..73e42535 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -118,7 +118,7 @@ iterations}
 \item{control}{Passed to \link[saemix:saemix]{saemix::saemix}.}
 
 \item{verbose}{Should we print information about created objects of
-type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?}
+type \link[saemix:SaemixModel]{saemix::SaemixModel} and \link[saemix:SaemixData]{saemix::SaemixData}?}
 
 \item{quiet}{Should we suppress the messages saemix prints at the beginning
 and the end of the optimisation process?}
@@ -129,12 +129,12 @@ and the end of the optimisation process?}
 }
 \value{
 An S3 object of class 'saem.mmkin', containing the fitted
-\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The
+\link[saemix:SaemixObject]{saemix::SaemixObject} as a list component named 'so'. The
 object also inherits from 'mixed.mmkin'.
 
-An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object.
+An \link[saemix:SaemixModel]{saemix::SaemixModel} object.
 
-An \link[saemix:SaemixData-class]{saemix::SaemixData} object.
+An \link[saemix:SaemixData]{saemix::SaemixData} object.
 }
 \description{
 This function uses \code{\link[saemix:saemix]{saemix::saemix()}} as a backend for fitting nonlinear mixed
diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd
index 41932547..1c27e941 100644
--- a/man/summary.saem.mmkin.Rd
+++ b/man/summary.saem.mmkin.Rd
@@ -42,7 +42,7 @@ included.}
 \item{digits}{Number of digits to use for printing}
 }
 \value{
-The summary function returns a list based on the \link[saemix:SaemixObject-class]{saemix::SaemixObject}
+The summary function returns a list based on the \link[saemix:SaemixObject]{saemix::SaemixObject}
 obtained in the fit, with at least the following additional components
 \item{saemixversion, mkinversion, Rversion}{The saemix, mkin and R versions used}
 \item{date.fit, date.summary}{The dates where the fit and the summary were
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index 3a97ff8d..09723fb8 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -42,7 +42,7 @@ of the estimator. The default (TRUE) is to do transformations.
 The g parameter of the DFOP model is also seen as a fraction.
 If a single fraction is transformed (g parameter of DFOP or only a single
 target variable e.g. a single metabolite plus a pathway to sink), a
-logistic transformation is used \code{\link[stats:Logistic]{stats::qlogis()}}. In other cases, i.e. if
+logistic transformation is used \code{\link[stats:qlogis]{stats::qlogis()}}. In other cases, i.e. if
 two or more formation fractions need to be transformed whose sum cannot
 exceed one, the \link{ilr} transformation is used.}