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, 42 insertions, 21 deletions

diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 7a01313f..20134030 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -75,7 +75,7 @@ datasets specified in its first two arguments." />
       </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>
 
@@ -124,7 +124,7 @@ datasets specified in its first two arguments." />
       <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>
@@ -155,7 +155,7 @@ datasets specified in its first two arguments.</p>
     <pre class="usage"><span class='fu'>mmkin</span><span class='op'>(</span>
   models <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'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>,
   <span class='va'>datasets</span>,
-  cores <span class='op'>=</span> <span class='fu'>detectCores</span><span class='op'>(</span><span class='op'>)</span>,
+  cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>,
   cluster <span class='op'>=</span> <span class='cn'>NULL</span>,
   <span class='va'>...</span>
 <span class='op'>)</span></pre>
@@ -210,37 +210,36 @@ plotting.</p></div>
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
 <span class='co'># \dontrun{</span>
-<span class='va'>m_synth_SFO_lin</span> <span class='op'>&lt;-</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>,
-                           M1 <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='st'>"M2"</span><span class='op'>)</span>,
-                           M2 <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>, 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='va'>m_synth_FOMC_lin</span> <span class='op'>&lt;-</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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"M1"</span><span class='op'>)</span>,
-                            M1 <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='st'>"M2"</span><span class='op'>)</span>,
-                            M2 <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>, 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='va'>m_synth_SFO_lin</span> <span class='op'>&lt;-</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='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>,
+                           M1 <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='st'>"M2"</span><span class='op'>)</span>,
+                           M2 <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>, 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'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
+<span class='va'>m_synth_FOMC_lin</span> <span class='op'>&lt;-</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='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"M1"</span><span class='op'>)</span>,
+                            M1 <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='st'>"M2"</span><span class='op'>)</span>,
+                            M2 <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>, 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'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
 <span class='va'>models</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>SFO_lin <span class='op'>=</span> <span class='va'>m_synth_SFO_lin</span>, FOMC_lin <span class='op'>=</span> <span class='va'>m_synth_FOMC_lin</span><span class='op'>)</span>
 <span class='va'>datasets</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span>
 <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>datasets</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span>
 
 <span class='va'>time_default</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>fits.0</span> <span class='op'>&lt;-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='va'>models</span>, <span class='va'>datasets</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
 <span class='va'>time_1</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>fits.4</span> <span class='op'>&lt;-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='va'>models</span>, <span class='va'>datasets</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
-#&gt; <span class='warning'>false convergence (8)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0117</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0174</span></div><div class='input'>
+
 <span class='va'>time_default</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   4.828   0.413   1.467 </div><div class='input'><span class='va'>time_1</span>
+#&gt;   4.869   0.357   1.415 </div><div class='input'><span class='va'>time_1</span>
 </div><div class='output co'>#&gt;    user  system elapsed 
-#&gt;   5.228   0.000   5.231 </div><div class='input'>
+#&gt;   5.502   0.002   5.507 </div><div class='input'>
 <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
 #&gt;   parent_M1 parent_sink       M1_M2     M1_sink 
-#&gt;   0.7340478   0.2659522   0.7505691   0.2494309 
+#&gt;   0.7340478   0.2659522   0.7505687   0.2494313 
 #&gt; 
 #&gt; $distimes
-#&gt;              DT50       DT90
-#&gt; parent  0.8777688   2.915885
-#&gt; M1      2.3257466   7.725963
-#&gt; M2     33.7200800 112.015681
+#&gt;             DT50       DT90
+#&gt; parent  0.877769   2.915885
+#&gt; M1      2.325746   7.725960
+#&gt; M2     33.720083 112.015691
 #&gt; </div><div class='input'>
 <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span>
@@ -253,7 +252,29 @@ plotting.</p></div>
 <span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
 <span class='co'># allow to plot the observed variables separately</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='co'># On Windows, we can use multiple cores by making a cluster using the parallel</span>
+<span class='co'># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span>
+<span class='va'>cl</span> <span class='op'>&lt;-</span> <span class='fu'>makePSOCKcluster</span><span class='op'>(</span><span class='fl'>12</span><span class='op'>)</span>
+<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'>mmkin</span><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'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>,
+  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>A <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span>, D <span class='op'>=</span> <span class='va'>FOCUS_2006_D</span><span class='op'>)</span>,
+  cluster <span class='op'>=</span> <span class='va'>cl</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; &lt;mmkin&gt; object
+#&gt; Status of individual fits:
+#&gt; 
+#&gt;       dataset
+#&gt; model  A  B  C  D 
+#&gt;   SFO  OK OK OK OK
+#&gt;   FOMC C  OK OK OK
+#&gt;   DFOP OK OK OK OK
+#&gt; 
+#&gt; OK: No warnings
+#&gt; C: Optimisation did not converge:
+#&gt; false convergence (8)</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span>
+<span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span>
+<span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span>
+<span class='co'># }</span>
 
 </div></pre>
   </div>