Move mkin::twa to pfm::max_twa.mkinfit

- Add max_twa.mkinfit() recently introduced to mkin as mkin::twa() but
  never released with it
- Add a test to check max_twa.one_box() against analytical solutions in
  max_twa.mkinfit().
- Clean up R CMD check
- Update docs

7 files changed, 53 insertions, 8 deletions

diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html
index 4bb1be9..f78da58 100644
--- a/docs/reference/max_twa.html
+++ b/docs/reference/max_twa.html
@@ -70,7 +70,11 @@
     </div>
 
     
-    <p>The maximum time weighted average concentration for a moving window</p>
+    <p>If you generate your time series using <code><a href='sawtooth.html'>sawtooth</a></code>,
+you need to make sure that the length of the time series allows
+for finding the maximum. It is therefore recommended to check this using
+<code><a href='plot.one_box.html'>plot.one_box</a></code> using the window size for the argument
+<code>max_twa</code>.</p>
     
 
     <pre><span class='fu'>max_twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre>
@@ -83,19 +87,56 @@
       <dd>The size of the moving window</dd>
     </dl>
     
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>The method working directly on fitted <code>mkinfit</code> objects uses the
+equations given in the PEC soil section of the FOCUS guidance and is restricted
+SFO, FOMC and DFOP models and to the parent compound</p>
+    
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
+  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+  Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+  <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+    
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <p><code><a href='twa.html'>twa</a></code></p>
     
 
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>),
+  <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>1</span>)))
+<span class='fu'>max_twa</span>(<span class='no'>pred</span>)</div><div class='output co'>#&gt; $max
+#&gt;    parent 
+#&gt; 0.9537545 
+#&gt; 
+#&gt; $window_start
+#&gt; parent 
+#&gt;      0 
+#&gt; 
+#&gt; $window_end
+#&gt; parent 
+#&gt;     21 
+#&gt; </div><div class='input'><span class='no'>pred_FOMC</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>max_twa</span>(<span class='no'>pred_FOMC</span>)</div><div class='output co'>#&gt;       21 
+#&gt; 18.22124 </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="#arguments">Arguments</a></li>
       
+      <li><a href="#details">Details</a></li>
+
+      <li><a href="#references">References</a></li>
+
       <li><a href="#see-also">See also</a></li>
-          </ul>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
 
   </div>
 </div>
diff --git a/docs/reference/one_box-4.png b/docs/reference/one_box-4.png
index 10ebb35..3c6dadb 100644
--- a/docs/reference/one_box-4.png
+++ b/docs/reference/one_box-4.png
diff --git a/docs/reference/one_box-8.png b/docs/reference/one_box-8.png
index 31e2f4b..897737e 100644
--- a/docs/reference/one_box-8.png
+++ b/docs/reference/one_box-8.png
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 698f887..cb49c02 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -74,22 +74,26 @@
 This does not create objects of type <code>ts</code>.</p>
     
 
-    <pre><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+    <pre><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>ini</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
 
 <span class='co'># S3 method for numeric</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
 
 <span class='co'># S3 method for character</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+  <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
 
 <span class='co'># S3 method for mkinfit</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre>
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"model"</span>, <span class='fl'>1</span>), <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+  <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <dl class="dl-horizontal">
       <dt>x</dt>
       <dd>When numeric, this is the half-life to be used for an exponential
 decline. If x is an mkinfit object, the decline is calculated from this object</dd>
+      <dt>ini</dt>
+      <dd>The initial amount for each compound</dd>
       <dt>...</dt>
       <dd>Further arguments passed to methods</dd>
       <dt>t_end</dt>
diff --git a/docs/reference/plot.one_box-8.png b/docs/reference/plot.one_box-8.png
index 161ecb4..f534444 100644
--- a/docs/reference/plot.one_box-8.png
+++ b/docs/reference/plot.one_box-8.png
diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png
index 161ecb4..f534444 100644
--- a/docs/reference/sawtooth-6.png
+++ b/docs/reference/sawtooth-6.png
diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html
index cf33630..216f64a 100644
--- a/docs/reference/sawtooth.html
+++ b/docs/reference/sawtooth.html
@@ -102,8 +102,8 @@ the corresponding amounts applied in the second column.</dd>
 <span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)
 <span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><img src='sawtooth-6.png' alt='' width='540' height='400' /><div class='input'>
 <span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#&gt; $max
-#&gt;    parent        m1 
-#&gt; 0.6627707 0.8542785 
+#&gt;   parent       m1 
+#&gt; 66.01096 85.08484 
 #&gt; 
 #&gt; $window_start
 #&gt; parent     m1