Reduce check time for CRAN, releasev1.1.0

6 files changed, 20 insertions, 16 deletions

diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index ca982688..17a35806 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index de2d61aa..ddd3a0d7 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
index f8bf10bb..fa29fc43 100644
--- a/docs/reference/Rplot003.png
+++ b/docs/reference/Rplot003.png
diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html
index 57516fba..2516edff 100644
--- a/docs/reference/create_deg_func.html
+++ b/docs/reference/create_deg_func.html
@@ -111,8 +111,8 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
 <span class="r-in"><span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># to avoid warnings</span></span>
 <span class="r-in"><span class="va">fit_1</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_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">fit_2</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_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span class="r-in"><span class="co"># \dontrun{</span></span>
+<span class="r-in"><span class="va">fit_2</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_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span></span>
 <span class="r-in">  <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span>
 <span class="r-in">    analytical <span class="op">=</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_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
@@ -120,8 +120,8 @@
 <span class="r-in">    replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         test replications elapsed relative user.self sys.self user.child</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.406    1.000     0.407    0.000          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   0.698    1.719     0.695    0.003          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.394    1.000     0.393        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   0.678    1.721     0.677        0          0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   sys.child</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1         0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2         0</span>
@@ -134,8 +134,8 @@
 <span class="r-in">    deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span class="r-in">    replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         test replications elapsed relative user.self sys.self user.child</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.855    1.000     0.856        0          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   1.588    1.857     1.587        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.829    1.000     0.829        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   1.559    1.881     1.559        0          0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   sys.child</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1         0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2         0</span>
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 4b59afed..1f071ffa 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -97,7 +97,7 @@ have been obtained by fitting the same model to a list of datasets.</p>
   data <span class="op">=</span> <span class="st">"auto"</span>,
   fixed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span>
     <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,
-  random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,
+  random <span class="op">=</span> <span class="fu">pdDiag</span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,
   <span class="va">groups</span>,
   start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,
   correlation <span class="op">=</span> <span class="cn">NULL</span>,
@@ -187,12 +187,11 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
     <h2>Examples</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span>
 <span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></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/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
-<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f_nlme_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span>
 <span class="r-in"></span>
 <span class="r-in"><span class="co"># \dontrun{</span></span>
-<span class="r-in"></span>
+<span class="r-in">  <span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
+<span class="r-in">  <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span>
+<span class="r-in">  <span class="va">f_nlme_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span>
 <span class="r-in">  <span class="va">f_nlme_dfop</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span>
 <span class="r-in">  <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             Model df      AIC      BIC    logLik   Test  L.Ratio p-value</span>
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html
index d2ed2a86..3f98bec7 100644
--- a/docs/reference/summary.nlme.mmkin.html
+++ b/docs/reference/summary.nlme.mmkin.html
@@ -96,7 +96,7 @@ endpoints such as formation fractions and DT50 values. Optionally
 
     <div id="ref-usage">
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for nlme.mmkin</span>
-<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span>
+<span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span>
   <span class="va">object</span>,
   data <span class="op">=</span> <span class="cn">FALSE</span>,
   verbose <span class="op">=</span> <span class="cn">FALSE</span>,
@@ -193,16 +193,20 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-in">    n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span>
 <span class="r-in"><span class="op">}</span><span class="op">)</span></span>
 <span class="r-in"></span>
+<span class="r-in"><span class="co"># \dontrun{</span></span>
 <span class="r-in"><span class="co"># Evaluate using mmkin and nlme</span></span>
 <span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span>
 <span class="r-in"><span class="va">f_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo_syn</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Optimisation did not converge:</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> iteration limit reached without convergence (10)</span>
 <span class="r-in"><span class="va">f_nlme</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span>
+<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> nlme version used for fitting:      3.1.155 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.1.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Mar  7 13:15:33 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Mar  7 13:15:33 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.1.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Mar 14 08:58:29 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Mar 14 08:58:29 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
@@ -212,7 +216,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.528 s using 4 iterations</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.527 s using 4 iterations</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -352,6 +356,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   90     20.8    22.692  -1.89165 1.7926    -1.055273</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent  120     13.4    13.768  -0.36790 1.0876    -0.338259</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent  120     13.8    13.768   0.03210 1.0876     0.029517</span>
+<span class="r-in"><span class="co"># }</span></span>
 <span class="r-in"></span>
 </code></pre></div>
     </div>