Prepare for v1.0.0v1.0.0

- Improve authorship and copyright information
- Prepare pkgdown config
- Remove dependence on saemix as we need the development version which
is not ready for CRAN
- Temporarily remove saemix interface to check code coverage of the rest

1 files changed, 20 insertions, 27 deletions

diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 17f38938..035a21f9 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." />
       </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">0.9.50.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span>
       </span>
     </div>
 
@@ -123,7 +123,7 @@ kinetic parameters and initial values for the state variables." />
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -151,19 +151,7 @@ kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, u
 kinetic parameters and initial values for the state variables.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>mkinpredict</span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  <span class='va'>odeparms</span>,
-  <span class='va'>odeini</span>,
-  outtimes <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>120</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
-  solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>,
-  use_compiled <span class='op'>=</span> <span class='st'>"auto"</span>,
-  method.ode <span class='op'>=</span> <span class='st'>"lsoda"</span>,
-  atol <span class='op'>=</span> <span class='fl'>1e-08</span>,
-  rtol <span class='op'>=</span> <span class='fl'>1e-10</span>,
-  map_output <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  <span class='va'>...</span>
-<span class='op'>)</span>
+    <pre class="usage"><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>odeparms</span>, <span class='va'>odeini</span>, <span class='va'>outtimes</span>, <span class='va'>...</span><span class='op'>)</span>
 
 <span class='co'># S3 method for mkinmod</span>
 <span class='fu'>mkinpredict</span><span class='op'>(</span>
@@ -177,6 +165,7 @@ kinetic parameters and initial values for the state variables.</p>
   atol <span class='op'>=</span> <span class='fl'>1e-08</span>,
   rtol <span class='op'>=</span> <span class='fl'>1e-10</span>,
   map_output <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  na_stop <span class='op'>=</span> <span class='cn'>TRUE</span>,
   <span class='va'>...</span>
 <span class='op'>)</span>
 
@@ -222,6 +211,11 @@ observed variables, for example in the case of the SFORB model.</p></td>
 predictions should be generated.</p></td>
     </tr>
     <tr>
+      <th>...</th>
+      <td><p>Further arguments passed to the ode solver in case such a
+solver is used.</p></td>
+    </tr>
+    <tr>
       <th>solution_type</th>
       <td><p>The method that should be used for producing the
 predictions. This should generally be "analytical" if there is only one
@@ -258,9 +252,8 @@ FALSE). Setting this to FALSE has no effect for analytical solutions,
 as these always return mapped output.</p></td>
     </tr>
     <tr>
-      <th>...</th>
-      <td><p>Further arguments passed to the ode solver in case such a
-solver is used.</p></td>
+      <th>na_stop</th>
+      <td><p>Should it be an error if deSolve::ode returns NaN values</p></td>
     </tr>
     </table>
 
@@ -273,7 +266,7 @@ solver is used.</p></td>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
-<span class='va'>SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+<span class='va'>SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
 <span class='co'># Compare solution types</span>
 <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
       solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span>
@@ -395,7 +388,7 @@ solver is used.</p></td>
 <span class='co'># Comparison of the performance of solution types</span>
 <span class='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
                   m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span><span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='kw'>if</span><span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
   <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>replications <span class='op'>=</span> <span class='fl'>10</span>, order <span class='op'>=</span> <span class='st'>"relative"</span>, columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"test"</span>, <span class='st'>"relative"</span>, <span class='st'>"elapsed"</span><span class='op'>)</span>,
     eigen <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>,
       <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>,
@@ -415,10 +408,10 @@ solver is used.</p></td>
       solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span><span class='op'>)</span>
 <span class='op'>}</span>
 </div><div class='output co'>#&gt;               test relative elapsed
+#&gt; 2 deSolve_compiled      1.0   0.005
 #&gt; 4       analytical      1.0   0.005
-#&gt; 2 deSolve_compiled      1.2   0.006
 #&gt; 1            eigen      4.0   0.020
-#&gt; 3          deSolve     45.6   0.228</div><div class='input'>
+#&gt; 3          deSolve     44.6   0.223</div><div class='input'>
 <span class='co'># \dontrun{</span>
   <span class='co'># Predict from a fitted model</span>
   <span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@@ -426,11 +419,11 @@ solver is used.</p></td>
   <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span><span class='op'>)</span>
 </div><div class='output co'>#&gt;     time   parent       m1
 #&gt; 0    0.0 82.49216 0.000000
-#&gt; 0.1  0.1 80.00562 1.236198
-#&gt; 0.2  0.2 77.59404 2.422818
-#&gt; 0.3  0.3 75.25514 3.561476
-#&gt; 0.4  0.4 72.98675 4.653740
-#&gt; 0.5  0.5 70.78673 5.701130</div><div class='input'><span class='co'># }</span>
+#&gt; 0.1  0.1 80.00562 1.236394
+#&gt; 0.2  0.2 77.59404 2.423201
+#&gt; 0.3  0.3 75.25514 3.562040
+#&gt; 0.4  0.4 72.98675 4.654478
+#&gt; 0.5  0.5 70.78673 5.702033</div><div class='input'><span class='co'># }</span>
 
 </div></pre>
   </div>