Merge branch 'master' into mxkin

Merge DESCRIPTION manually to combine dependencies and rerun check to
update check.log

4 files changed, 44 insertions, 20 deletions

diff --git a/man/endpoints.Rd b/man/endpoints.Rd
index 13182369..be180737 100644
--- a/man/endpoints.Rd
+++ b/man/endpoints.Rd
@@ -26,7 +26,7 @@ The function is used internally by \code{\link{summary.mkinfit}}.
 \examples{
 
   fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-  endpoints(fit)  
+  endpoints(fit)
 
 }
 \author{
diff --git a/man/mkinds.Rd b/man/mkinds.Rd
index 79eb0167..3bbb1c4b 100644
--- a/man/mkinds.Rd
+++ b/man/mkinds.Rd
@@ -1,38 +1,43 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mkinds.R
-\docType{class}
 \name{mkinds}
 \alias{mkinds}
 \title{A dataset class for mkin}
-\format{An \code{\link{R6Class}} generator object.}
 \description{
-A dataset class for mkin
+At the moment this dataset class is hardly used in mkin. For example,
+mkinfit does not take mkinds datasets as argument, but works with dataframes
+such as the on contained in the data field of mkinds objects. Some datasets
+provided by this package come as mkinds objects nevertheless.
 }
-\section{Fields}{
+\examples{
 
+mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
+print(mds)
 
-\describe{ \item{list("title")}{A full title for the dataset}
+}
+\seealso{
+The S3 printing method \code{\link{print.mkinds}}
+}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{title}}{A full title for the dataset}
 
-\item{list("sampling")}{times The sampling times}
+\item{\code{sampling_times}}{The sampling times}
 
-\item{list("time_unit")}{The time unit}
+\item{\code{time_unit}}{The time unit}
 
-\item{list("observed")}{Names of the observed compounds}
+\item{\code{observed}}{Names of the observed variables}
 
-\item{list("unit")}{The unit of the observations}
+\item{\code{unit}}{The unit of the observations}
 
-\item{list("replicates")}{The number of replicates}
+\item{\code{replicates}}{The maximum number of replicates per sampling time}
 
-\item{list("data")}{A dataframe with at least the columns name, time and
-value in order to be compatible with mkinfit} }
+\item{\code{data}}{A data frame with at least the columns name, time
+and value in order to be compatible with mkinfit}
 }
-
-\examples{
-
-mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
-
+\if{html}{\out{</div>}}
 }
-\keyword{datasets}
 \section{Methods}{
 \subsection{Public methods}{
 \itemize{
@@ -43,10 +48,24 @@ mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-new"></a>}}
 \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>}}
 }
 
+\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-clone"></a>}}
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index f14e0362..982e8db6 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -10,6 +10,7 @@ of an mmkin object}
   main = "auto",
   legends = 1,
   resplot = c("time", "errmod"),
+  standardized = FALSE,
   show_errmin = TRUE,
   errmin_var = "All data",
   errmin_digits = 3,
@@ -31,6 +32,10 @@ column.}
 \code{\link{mkinresplot}}, or as squared residuals against predicted
 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"`.}
+
 \item{show_errmin}{Should the chi2 error level be shown on top of the plots
 to the left?}
 
diff --git a/man/print.mkinds.Rd b/man/print.mkinds.Rd
index 54dc5a12..51ef3b76 100644
--- a/man/print.mkinds.Rd
+++ b/man/print.mkinds.Rd
@@ -12,5 +12,5 @@
 \item{\dots}{Not used.}
 }
 \description{
-Print mkinds objects.
+Print mkinds objects
 }