Use inline documentation for R6 class mkinds

6 files changed, 126 insertions, 99 deletions

diff --git a/R/mkinds.R b/R/mkinds.R
index a66adb14..d6f296bf 100644
--- a/R/mkinds.R
+++ b/R/mkinds.R
@@ -1,43 +1,50 @@
 #' A dataset class for mkin
 #' 
-#' A dataset class for mkin
-#' 
-#' @name mkinds
-#' @docType class
-#' @format An \code{\link{R6Class}} generator object.
-#' @section Fields:
-#' 
-#' \describe{ \item{list("title")}{A full title for the dataset}
-#' 
-#' \item{list("sampling")}{times The sampling times}
-#' 
-#' \item{list("time_unit")}{The time unit}
-#' 
-#' \item{list("observed")}{Names of the observed compounds}
-#' 
-#' \item{list("unit")}{The unit of the observations}
-#' 
-#' \item{list("replicates")}{The number of replicates}
-#' 
-#' \item{list("data")}{A dataframe with at least the columns name, time and
-#' value in order to be compatible with mkinfit} }
+#' @description
+#' 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.
+#'
 #' @importFrom R6 R6Class
-#' @keywords datasets
+#' @seealso The S3 printing method \code{\link{print.mkinds}}
 #' @examples
 #' 
 #' mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
+#' print(mds)
 #' 
 #' @export
 mkinds <- R6Class("mkinds",
   public = list(
+
+    #' @field title A full title for the dataset
     title = NULL,
+
+    #' @field sampling_times The sampling times
     sampling_times = NULL,
+
+    #' @field time_unit The time unit
     time_unit = NULL,
+
+    #' @field observed Names of the observed variables
     observed = NULL,
+
+    #' @field unit The unit of the observations
     unit = NULL,
+
+    #' @field replicates The maximum number of replicates per sampling time
     replicates = NULL,
+
+    #' @field data A data frame with at least the columns name, time
+    #' and value in order to be compatible with mkinfit
     data = NULL,
 
+    #' @description
+    #' Create a new mkinds object
+    #' @param title The dataset title
+    #' @param data The data
+    #' @param time_unit The time unit
+    #' @param unit The unit of the observations
     initialize = function(title = "", data, time_unit = NA, unit = NA) {
 
       self$title <- title
@@ -56,8 +63,6 @@ mkinds <- R6Class("mkinds",
 
 #' Print mkinds objects
 #' 
-#' Print mkinds objects.
-#' 
 #' @param x An \code{\link{mkinds}} object.
 #' @param \dots Not used.
 #' @export
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index c1cdcf99..ef6fb35c 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -36,7 +36,10 @@
 
 
 <meta property="og:title" content="A dataset class for mkin — mkinds" />
-<meta property="og:description" content="A dataset class for mkin" />
+<meta property="og:description" content="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." />
 <meta name="twitter:card" content="summary" />
 
 
@@ -133,36 +136,36 @@
     </div>
 
     <div class="ref-description">
-    <p>A dataset class for mkin</p>
+    <p>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.</p>
     </div>
 
 
 
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <p>An <code>R6Class</code> generator object.</p>
-    <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
+    <div class='dont-index'><p>The S3 printing method <code><a href='print.mkinds.html'>print.mkinds</a></code></p></div>
+    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
-    
-
-
-<dl class='dl-horizontal'>
-<dt>list("title")</dt><dd><p>A full title for the dataset</p></dd>
+    <p><div class="r6-fields"></p><dl class='dl-horizontal'>
+<dt><code>title</code></dt><dd><p>A full title for the dataset</p></dd>
 
-<dt>list("sampling")</dt><dd><p>times The sampling times</p></dd>
+<dt><code>sampling_times</code></dt><dd><p>The sampling times</p></dd>
 
-<dt>list("time_unit")</dt><dd><p>The time unit</p></dd>
+<dt><code>time_unit</code></dt><dd><p>The time unit</p></dd>
 
-<dt>list("observed")</dt><dd><p>Names of the observed compounds</p></dd>
+<dt><code>observed</code></dt><dd><p>Names of the observed variables</p></dd>
 
-<dt>list("unit")</dt><dd><p>The unit of the observations</p></dd>
+<dt><code>unit</code></dt><dd><p>The unit of the observations</p></dd>
 
-<dt>list("replicates")</dt><dd><p>The number of replicates</p></dd>
+<dt><code>replicates</code></dt><dd><p>The maximum number of replicates per sampling time</p></dd>
 
-<dt>list("data")</dt><dd><p>A dataframe with at least the columns name, time and
-value in order to be compatible with mkinfit</p></dd> 
-</dl>
+<dt><code>data</code></dt><dd><p>A data frame with at least the columns name, time
+and value in order to be compatible with mkinfit</p></dd>
 
+</dl><p></div></p>
     <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
 
     
@@ -174,10 +177,20 @@ value in order to be compatible with mkinfit</p></dd>
 </ul>
 <p><hr>
 <a id="method-new"></a></p><h3>Method <code>new()</code></h3>
-
-<h3>Usage</h3>
+<p>Create a new mkinds object</p><h3>Usage</h3>
 <p><div class="r"></p><pre>mkinds$new(title = "", data, time_unit = NA, unit = NA)</pre><p></div></p>
 
+<h3>Arguments</h3>
+<p><div class="arguments"></p><dl class='dl-horizontal'>
+<dt><code>title</code></dt><dd><p>The dataset title</p></dd>
+
+<dt><code>data</code></dt><dd><p>The data</p></dd>
+
+<dt><code>time_unit</code></dt><dd><p>The time unit</p></dd>
+
+<dt><code>unit</code></dt><dd><p>The unit of the observations</p></dd>
+
+</dl><p></div></p>
 <p><hr>
 <a id="method-clone"></a></p><h3>Method <code>clone()</code></h3>
 <p>The objects of this class are cloneable with this method.</p><h3>Usage</h3>
@@ -193,13 +206,18 @@ value in order to be compatible with mkinfit</p></dd>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='no'>mds</span> <span class='kw'>&lt;-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre>
+<span class='no'>mds</span> <span class='kw'>&lt;-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>mds</span>)</div><div class='output co'>#&gt; &lt;mkinds&gt; with $title:  FOCUS A 
+#&gt; Observed compounds $observed:  parent 
+#&gt; Sampling times $sampling_times:  0, 3, 7, 14, 30, 62, 90, 118 
+#&gt; With a maximum of  1  replicates</div><div class='input'>
+</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
-      <li><a href="#format">Format</a></li>
-      <li><a href="#fields">Fields</a></li>
+      <li><a href="#see-also">See also</a></li>
+      <li><a href="#public-fields">Public fields</a></li>
       <li><a href="#methods">Methods</a></li>
       <li><a href="#examples">Examples</a></li>
     </ul>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index d7ba94e1..de1a2410 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -36,7 +36,7 @@
 
 
 <meta property="og:title" content="Print mkinds objects — print.mkinds" />
-<meta property="og:description" content="Print mkinds objects." />
+<meta property="og:description" content="Print mkinds objects" />
 <meta name="twitter:card" content="summary" />
 
 
@@ -69,7 +69,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span>
       </span>
     </div>
 
@@ -133,7 +133,7 @@
     </div>
 
     <div class="ref-description">
-    <p>Print mkinds objects.</p>
+    <p>Print mkinds objects</p>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mkinds</span>
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/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
 }
diff --git a/test.log b/test.log
index 2db18301..77130814 100644
--- a/test.log
+++ b/test.log
@@ -2,52 +2,37 @@ Loading mkin
 Testing mkin
 ✔ |  OK F W S | Context
 ✔ |   2       | Export dataset for reading into CAKE
-✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.8 s]
+✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [2.3 s]
-✔ |   4       | Fitting the SFORB model [1.7 s]
+✔ |   4       | Fitting the SFORB model [1.8 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [10.2 s]
-✔ |  14       | Error model fitting [40.7 s]
+✔ |  10       | Confidence intervals and p-values [10.7 s]
+✔ |  14       | Error model fitting [42.8 s]
 ✔ |   6       | Test fitting the decline of metabolites from their maximum [0.8 s]
 ✔ |   1       | Fitting the logistic model [1.0 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
-✖ |  11 1     | Special cases of mkinfit calls [2.3 s]
-────────────────────────────────────────────────────────────────────────────────
-test_mkinfit_errors.R:64: failure: We get reproducible output if quiet = FALSE
-Results have changed from known value recorded in 'DFOP_FOCUS_C_messages.txt'.
-2/165 mismatches
-x[84]: "Sum of squared residuals at call 57: 4.364077"
-y[84]: "Sum of squared residuals at call 57: 4.364078"
-
-x[105]: "85.00134 -0.7776046 -4.025878 1.248775 "
-y[105]: "85.00135 -0.7776046 -4.025878 1.248775 "
-────────────────────────────────────────────────────────────────────────────────
+✔ |  12       | Special cases of mkinfit calls [2.5 s]
 ✔ |   9       | mkinmod model generation and printing [0.2 s]
-✔ |   3       | Model predictions with mkinpredict [0.3 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.3 s]
-✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
+✔ |   3       | Model predictions with mkinpredict [0.4 s]
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.4 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
 ✔ |   3       | Summary
-✖ |  10 1     | Plotting [0.6 s]
-────────────────────────────────────────────────────────────────────────────────
-test_plots_summary_twa.R:118: failure: Plotting mkinfit and mmkin objects is reproducible
-Figures don't match: plot-errmod-with-sfo-lin-a-obs.svg
-
-────────────────────────────────────────────────────────────────────────────────
+✔ |  11       | Plotting [0.6 s]
 ✔ |   4       | AIC calculation
 ✔ |   2       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.6 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.7 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.4 s]
-✔ |   7     1 | Hypothesis tests [33.6 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.7 s]
+✔ |   7     1 | Hypothesis tests [35.7 s]
 ────────────────────────────────────────────────────────────────────────────────
 test_tests.R:60: skip: We can do a likelihood ratio test using an update specification
 Reason: This errors out if called by testthat while it works in a normal R session
 ────────────────────────────────────────────────────────────────────────────────
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 117.3 s
+Duration: 123.0 s
 
-OK:       136
-Failed:   2
+OK:       138
+Failed:   0
 Warnings: 0
 Skipped:  1