Documentation improvements, rebuild static docs

30 files changed, 236 insertions, 225 deletions

diff --git a/man/AIC.mmkin.Rd b/man/AIC.mmkin.Rd
index a10d0aeb..13081561 100644
--- a/man/AIC.mmkin.Rd
+++ b/man/AIC.mmkin.Rd
@@ -19,7 +19,7 @@ column.}
 }
 \value{
 As in the generic method (a numeric value for single fits, or a
-  dataframe if there are several fits in the column).
+dataframe if there are several fits in the column).
 }
 \description{
 Provides a convenient way to compare different kinetic models fitted to the
diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd
index 8ada60c5..d8c4553e 100644
--- a/man/DFOP.solution.Rd
+++ b/man/DFOP.solution.Rd
@@ -32,15 +32,15 @@ two exponential decline functions.
 }
 \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}
+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}
 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}
+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}
 }
 \seealso{
 Other parent solutions: 
diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd
index e5e46c87..eeee85f9 100644
--- a/man/FOMC.solution.Rd
+++ b/man/FOMC.solution.Rd
@@ -30,8 +30,8 @@ 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}.
+\code{\link{SFO.solution}} for large values of \code{alpha} and
+\code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}.
 }
 \examples{
 
@@ -40,20 +40,20 @@ The solution of the FOMC kinetic model reduces to the
 }
 \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}
+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}
 
 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}
+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}
 
-  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
+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
 }
 \seealso{
 Other parent solutions: 
diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
index f72df23b..2940e949 100644
--- a/man/HS.solution.Rd
+++ b/man/HS.solution.Rd
@@ -33,15 +33,15 @@ between them.
 }
 \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}
+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}
 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}
+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}
 }
 \seealso{
 Other parent solutions: 
diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd
index e1f1be1a..1150f023 100644
--- a/man/IORE.solution.Rd
+++ b/man/IORE.solution.Rd
@@ -25,9 +25,9 @@ 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.
+\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{
 
@@ -46,7 +46,7 @@ The solution of the IORE kinetic model reduces to the
 }
 \references{
 NAFTA Technical Working Group on Pesticides (not dated) Guidance
-  for Evaluating and Calculating Degradation Kinetics in Environmental Media
+for Evaluating and Calculating Degradation Kinetics in Environmental Media
 }
 \seealso{
 Other parent solutions: 
diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd
index 6892cccc..c0aac237 100644
--- a/man/SFO.solution.Rd
+++ b/man/SFO.solution.Rd
@@ -26,15 +26,15 @@ Function describing exponential decline from a defined starting value.
 }
 \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}
+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}
 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}
+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}
 }
 \seealso{
 Other parent solutions: 
diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd
index 98a8c684..dc78d1f1 100644
--- a/man/SFORB.solution.Rd
+++ b/man/SFORB.solution.Rd
@@ -20,7 +20,7 @@ fraction.}
 }
 \value{
 The value of the response variable, which is the sum of free and
-  bound fractions at time \code{t}.
+bound fractions at time \code{t}.
 }
 \description{
 Function describing the solution of the differential equations describing
@@ -36,15 +36,15 @@ and no substance in the bound fraction.
 }
 \references{
 FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
-  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
-  EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+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}
 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}
+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}
 }
 \seealso{
 Other parent solutions: 
diff --git a/man/add_err.Rd b/man/add_err.Rd
index 3452923e..1171e0fd 100644
--- a/man/add_err.Rd
+++ b/man/add_err.Rd
@@ -40,7 +40,7 @@ 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}}.
+components of the list are datasets compatible with \code{\link{mkinfit}}.
 }
 \description{
 Normally distributed errors are added to data predicted for a specific
diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd
index 81d7a6e8..f295afc4 100644
--- a/man/confint.mkinfit.Rd
+++ b/man/confint.mkinfit.Rd
@@ -45,7 +45,7 @@ applied to the likelihood based on the transformed parameters?}
 transformed parameters, should we backtransform the parameters with
 their confidence intervals?}
 
-\item{cores}{The number of cores to be used for multicore processing. 
+\item{cores}{The number of cores to be used for multicore processing.
 On Windows machines, cores > 1 is currently not supported.}
 
 \item{quiet}{Should we suppress the message "Profiling the likelihood"}
@@ -54,7 +54,7 @@ On Windows machines, cores > 1 is currently not supported.}
 }
 \value{
 A matrix with columns giving lower and upper confidence limits for
-  each parameter.
+each parameter.
 }
 \description{
 The default method 'quadratic' is based on the quadratic approximation of
@@ -143,10 +143,10 @@ confint(f_tc_2, "parent_0", method = "quadratic")
 \references{
 Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications
 
-  Pawitan Y (2013) In all likelihood - Statistical modelling and
-  inference using likelihood. Clarendon Press, Oxford.
+Pawitan Y (2013) In all likelihood - Statistical modelling and
+inference using likelihood. Clarendon Press, Oxford.
 
-  Venzon DJ and Moolgavkar SH (1988) A Method for Computing
-  Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
-  87–94.
+Venzon DJ and Moolgavkar SH (1988) A Method for Computing
+Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
+87–94.
 }
diff --git a/man/endpoints.Rd b/man/endpoints.Rd
index 26b5ee08..49f44d74 100644
--- a/man/endpoints.Rd
+++ b/man/endpoints.Rd
@@ -13,9 +13,9 @@ endpoints(fit)
 }
 \value{
 A list with a matrix of dissipation times named distimes,
-  and, if applicable, a vector of formation fractions named ff
-  and, if the SFORB model was in use, a vector of eigenvalues
-  of these SFORB models, equivalent to DFOP rate constants
+and, if applicable, a vector of formation fractions named ff
+and, if the SFORB model was in use, a vector of eigenvalues
+of these SFORB models, equivalent to DFOP rate constants
 }
 \description{
 This function calculates DT50 and DT90 values as well as formation fractions
diff --git a/man/get_deg_func.Rd b/man/get_deg_func.Rd
index 1d8a3de9..75743448 100644
--- a/man/get_deg_func.Rd
+++ b/man/get_deg_func.Rd
@@ -8,7 +8,7 @@ get_deg_func()
 }
 \value{
 A function that was likely previously assigned from within
-  nlme.mmkin
+nlme.mmkin
 }
 \description{
 Retrieve a degradation function from the mmkin namespace
diff --git a/man/ilr.Rd b/man/ilr.Rd
index 0cbd7e2c..f691ec23 100644
--- a/man/ilr.Rd
+++ b/man/ilr.Rd
@@ -15,8 +15,8 @@ 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.
+components always sum to 1 for the case of the inverse log-ratio
+transformation.
 }
 \description{
 This implementation is a special case of the class of isometric log-ratio
@@ -48,11 +48,11 @@ ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5)
 }
 \references{
 Peter Filzmoser, Karel Hron (2008) Outlier Detection for
-  Compositional Data Using Robust Methods. Math Geosci 40 233-248
+Compositional Data Using Robust Methods. Math Geosci 40 233-248
 }
 \seealso{
 Another implementation can be found in R package
-  \code{robCompositions}.
+\code{robCompositions}.
 }
 \author{
 René Lehmann and Johannes Ranke
diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd
index 502fb4d7..637570e4 100644
--- a/man/logLik.mkinfit.Rd
+++ b/man/logLik.mkinfit.Rd
@@ -13,8 +13,8 @@
 }
 \value{
 An object of class \code{\link{logLik}} with the number of estimated
-  parameters (degradation model parameters plus variance model parameters)
-  as attribute.
+parameters (degradation model parameters plus variance model parameters)
+as attribute.
 }
 \description{
 This function returns the product of the likelihood densities of each
@@ -45,7 +45,7 @@ and the fitted error model parameters.
 }
 \seealso{
 Compare the AIC of columns of \code{\link{mmkin}} objects using
-  \code{\link{AIC.mmkin}}.
+\code{\link{AIC.mmkin}}.
 }
 \author{
 Johannes Ranke
diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd
index 33b3d44a..efa12e7a 100644
--- a/man/logistic.solution.Rd
+++ b/man/logistic.solution.Rd
@@ -26,7 +26,7 @@ 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}.
+\code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}.
 }
 \examples{
 
@@ -67,15 +67,15 @@ The solution of the logistic model reduces to the
 }
 \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}
+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}
 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}
+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}
 }
 \seealso{
 Other parent solutions: 
diff --git a/man/max_twa_parent.Rd b/man/max_twa_parent.Rd
index 7c9f4861..107eebd0 100644
--- a/man/max_twa_parent.Rd
+++ b/man/max_twa_parent.Rd
@@ -48,8 +48,8 @@ factor (f_twa) is calculated.}
 }
 \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').
+\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
@@ -66,10 +66,10 @@ soil section of the FOCUS guidance.
 }
 \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}
+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/mkinerrplot.Rd b/man/mkinerrplot.Rd
index 9564ec19..82178aa9 100644
--- a/man/mkinerrplot.Rd
+++ b/man/mkinerrplot.Rd
@@ -50,7 +50,7 @@ be passed on to \code{\link{legend}}.}
 }
 \value{
 Nothing is returned by this function, as it is called for its side
-  effect, namely to produce a plot.
+effect, namely to produce a plot.
 }
 \description{
 This function plots the squared residuals for the specified subset of the
@@ -70,7 +70,7 @@ mkinerrplot(fit)
 }
 \seealso{
 \code{\link{mkinplot}}, for a way to plot the data and the fitted
-  lines of the mkinfit object.
+lines of the mkinfit object.
 }
 \author{
 Johannes Ranke
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index db3f5f3e..97dffef7 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -3,10 +3,6 @@
 \name{mkinfit}
 \alias{mkinfit}
 \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,
@@ -53,16 +49,16 @@ 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.
+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.}
+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
@@ -141,48 +137,50 @@ is 1e-8, lower than in \code{\link{lsoda}}.}
 is 1e-10, much lower than in \code{\link{lsoda}}.}
 
 \item{error_model}{If the error model is "const", a constant standard
-  deviation is assumed.
+deviation is assumed.
 
-  If the error model is "obs", each observed variable is assumed to have its
-  own variance.
+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.}
+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 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
+\itemize{
+\item 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 "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 "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 "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 "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.}
+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.}
@@ -196,7 +194,7 @@ the error model parameters in IRLS fits.}
 }
 \value{
 A list with "mkinfit" in the class attribute.  A summary can be
-  obtained by \code{\link{summary.mkinfit}}.
+obtained by \code{\link{summary.mkinfit}}.
 }
 \description{
 This function maximises the likelihood of the observed data using the Port
@@ -214,9 +212,9 @@ estimators.
 }
 \note{
 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.
+"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.
 }
 \examples{
 
@@ -268,7 +266,7 @@ fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.o
 }
 
 \dontrun{
-# Weighted fits, including IRLS
+# Weighted fits, including IRLS (error_model = "obs")
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
 f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
@@ -281,15 +279,23 @@ summary(f.tc)
 
 
 }
+\references{
+Rocke DM and Lorenzato S (1995) A two-component model
+for measurement error in analytical chemistry. \emph{Technometrics} 37(2), 176-184.
+
+Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical
+Degradation Data. \emph{Environments} 6(12) 124
+\href{https://doi.org/10.3390/environments6120124}{doi:10.3390/environments6120124}.
+}
 \seealso{
 Plotting methods \code{\link{plot.mkinfit}} and
-  \code{\link{mkinparplot}}.
+\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}}.
+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}}.
+Fitting of several models to several datasets in a single call to
+\code{\link{mmkin}}.
 }
 \author{
 Johannes Ranke
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index a5736be7..6a6d2027 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -44,25 +44,30 @@ 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{cf}{
-    If generated, the compiled function as returned by cfunction.
-  }
+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{deg_func}{
+If generated, a function containing the solution of the degradation
+model.
+}
+\item{coefmat}{
+The coefficient matrix, if the system of differential equations can be
+represented by one.
+}
+\item{cf}{
+If generated, a compiled function calculating the derivatives as
+returned by cfunction.
+}
 }
 \description{
 The function usually takes several expressions, each assigning a compound
@@ -76,8 +81,8 @@ 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}}.
+model for metabolites, you may want to read the second note in the help
+page to \code{\link{mkinfit}}.
 }
 \examples{
 
@@ -115,13 +120,13 @@ fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
 }
 \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}
+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
+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 975a0203..07b25009 100644
--- a/man/mkinparplot.Rd
+++ b/man/mkinparplot.Rd
@@ -11,7 +11,7 @@ mkinparplot(object)
 }
 \value{
 Nothing is returned by this function, as it is called for its side
-  effect, namely to produce a plot.
+effect, namely to produce a plot.
 }
 \description{
 This function plots the confidence intervals for the parameters fitted using
diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
index 2a8b2d41..498d914d 100644
--- a/man/mkinresplot.Rd
+++ b/man/mkinresplot.Rd
@@ -54,7 +54,7 @@ be passed on to \code{\link{legend}}.}
 }
 \value{
 Nothing is returned by this function, as it is called for its side
-  effect, namely to produce a plot.
+effect, namely to produce a plot.
 }
 \description{
 This function plots the residuals for the specified subset of the observed
@@ -71,8 +71,8 @@ mkinresplot(fit, "m1")
 }
 \seealso{
 \code{\link{mkinplot}}, for a way to plot the data and the fitted
-  lines of the mkinfit object, and \code{\link{plot_res}} for a function
-  combining the plot of the fit and the residual plot.
+lines of the mkinfit object, and \code{\link{plot_res}} for a function
+combining the plot of the fit and the residual plot.
 }
 \author{
 Johannes Ranke
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index 99895400..eda0d837 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -33,8 +33,8 @@ for parallel execution.}
 }
 \value{
 A two-dimensional \code{\link{array}} of \code{\link{mkinfit}}
-  objects that can be indexed using the model names for the first index (row index) 
-  and the dataset names for the second index (column index).
+objects that can be indexed using the model names for the first index (row index)
+and the dataset names for the second index (column index).
 }
 \description{
 This function calls \code{\link{mkinfit}} on all combinations of models and
@@ -79,7 +79,7 @@ plot(fits.0[1, 1])
 }
 \seealso{
 \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for
-  plotting.
+plotting.
 }
 \author{
 Johannes Ranke
diff --git a/man/nafta.Rd b/man/nafta.Rd
index 49c13afc..4f05324b 100644
--- a/man/nafta.Rd
+++ b/man/nafta.Rd
@@ -6,15 +6,15 @@
 \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
+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}
+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, ...)
@@ -41,9 +41,9 @@ 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.
+\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.
 }
 \description{
 The function fits the SFO, IORE and DFOP models using \code{\link{mmkin}}
diff --git a/man/nlme.Rd b/man/nlme.Rd
index a9e368dd..bf527320 100644
--- a/man/nlme.Rd
+++ b/man/nlme.Rd
@@ -21,9 +21,9 @@ nlme_data(object)
 A function that can be used with nlme
 
 If random is FALSE (default), a named vector containing mean values
-  of the fitted degradation model parameters. If random is TRUE, a list with
-  fixed and random effects, in the format required by the start argument of
-  nlme for the case of a single grouping variable ds?
+of the fitted degradation model parameters. If random is TRUE, a list with
+fixed and random effects, in the format required by the start argument of
+nlme for the case of a single grouping variable ds?
 
 A \code{\link{groupedData}} object
 }
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index 430dbda1..ae2b2d22 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -67,7 +67,7 @@ parameters taken from the mmkin object are used}
 }
 \value{
 Upon success, a fitted nlme.mmkin object, which is an nlme object
-  with additional elements
+with additional elements
 }
 \description{
 This functions sets up a nonlinear mixed effects model for an mmkin row
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 4235557e..bf38c5a5 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -85,7 +85,7 @@ 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. If this is set to
 'standardized', a plot of the residuals divided by the standard deviation
- given by the fitted error model will be shown.}
+given by the fitted error model will be shown.}
 
 \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
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index 600881ea..998e25e1 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -34,7 +34,7 @@ values, with the error model, using \code{\link{mkinerrplot}}.}
 
 \item{standardized}{Should the residuals be standardized? This option
 is passed to \code{\link{mkinresplot}}, it only takes effect if
-`resplot = "time"`.}
+\code{resplot = "time"}.}
 
 \item{show_errmin}{Should the chi2 error level be shown on top of the plots
 to the left?}
diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd
index 9bea7013..91130402 100644
--- a/man/plot.nlme.mmkin.Rd
+++ b/man/plot.nlme.mmkin.Rd
@@ -36,7 +36,7 @@ values, with the error model, using \code{\link{mkinerrplot}}.}
 
 \item{standardized}{Should the residuals be standardized? This option
 is passed to \code{\link{mkinresplot}}, it only takes effect if
-`resplot = "time"`.}
+\code{resplot = "time"}.}
 
 \item{show_errmin}{Should the chi2 error level be shown on top of the plots
 to the left?}
diff --git a/man/sigma_twocomp.Rd b/man/sigma_twocomp.Rd
index 0004144f..4e1f7c38 100644
--- a/man/sigma_twocomp.Rd
+++ b/man/sigma_twocomp.Rd
@@ -33,9 +33,9 @@ y.
 }
 \references{
 Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978)
-  Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry
-  24(11), 1895-1898.
+Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry
+24(11), 1895-1898.
 
-  Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for
-  measurement error in analytical chemistry. Technometrics 37(2), 176-184.
+Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for
+measurement error in analytical chemistry. Technometrics 37(2), 176-184.
 }
diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
index fabe31d0..24991d71 100644
--- a/man/summary.mkinfit.Rd
+++ b/man/summary.mkinfit.Rd
@@ -29,27 +29,27 @@ distribution}
 }
 \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.
+\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
@@ -65,10 +65,10 @@ values.
 }
 \references{
 FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
-  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
-  EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+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 5257fe12..e250483a 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -48,7 +48,7 @@ fitting procedure.}
 }
 \value{
 A vector of transformed or backtransformed parameters with the same
-  names as the original parameters.
+names as the original parameters.
 }
 \description{
 The transformations are intended to map parameters that should only take on