Update static docs

16 files changed, 34 insertions, 12 deletions

diff --git a/docs/news/index.html b/docs/news/index.html
index 13b82597..4776f207 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -83,7 +83,11 @@
 
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.1.1" id="mkin-111">mkin 1.1.1<a class="anchor" aria-label="anchor" href="#mkin-111"></a></h2>
-<ul><li>‘dimethenamid_2018’: Update example code to use saemix</li>
+<ul><li><p>‘dimethenamid_2018’: Update example code to use saemix</p></li>
+<li><p>‘CAKE_export’: Check for validity of the map argument, updates</p></li>
+<li><p>‘saem()’: Slightly improve speed in the case that no analytical solution for saemix is implemented, activate a test of the respective code</p></li>
+<li><p>‘mean_degparms’: New argument ‘default_log_parms’ that makes it possible to supply a surrogate value (default) for log parameters that fail the t-test</p></li>
+<li><p>‘plot.mixed.mmkin’: Pass the frame argument also to residual plots, take the ‘default_log_parms’ argument for ‘mean_degparms’ used for constructing approximate population curves, plot population curve last to avoid that it is covered by data</p></li>
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.1.0" id="mkin-110-2022-03-14">mkin 1.1.0 (2022-03-14)<a class="anchor" aria-label="anchor" href="#mkin-110-2022-03-14"></a></h2>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 3e26de5b..b94f7f0e 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
   dimethenamid_2018: web_only/dimethenamid_2018.html
-last_built: 2022-03-16T13:42Z
+last_built: 2022-04-09T15:50Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html
index 44297d1b..f16a9e6c 100644
--- a/docs/reference/CAKE_export.html
+++ b/docs/reference/CAKE_export.html
@@ -96,11 +96,11 @@ specified as well.</p>
   filename <span class="op">=</span> <span class="st">"CAKE_export.csf"</span>,
   path <span class="op">=</span> <span class="st">"."</span>,
   overwrite <span class="op">=</span> <span class="cn">FALSE</span>,
-  study <span class="op">=</span> <span class="st">"Codlemone aerobic soil degradation"</span>,
+  study <span class="op">=</span> <span class="st">"Degradinol aerobic soil degradation"</span>,
   description <span class="op">=</span> <span class="st">""</span>,
   time_unit <span class="op">=</span> <span class="st">"days"</span>,
   res_unit <span class="op">=</span> <span class="st">"% AR"</span>,
-  comment <span class="op">=</span> <span class="st">"Created using mkin::CAKE_export"</span>,
+  comment <span class="op">=</span> <span class="st">""</span>,
   date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>,
   optimiser <span class="op">=</span> <span class="st">"IRLS"</span>
 <span class="op">)</span></code></pre></div>
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index 26efcdd2..fa5f3834 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index 065f21f6..3caf465f 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
index 50a52a1c..88ebd2d4 100644
--- a/docs/reference/Rplot003.png
+++ b/docs/reference/Rplot003.png
diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png
index 0f3d8214..7e87d63d 100644
--- a/docs/reference/Rplot004.png
+++ b/docs/reference/Rplot004.png
diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png
index be59fc90..4300b0c0 100644
--- a/docs/reference/dimethenamid_2018-1.png
+++ b/docs/reference/dimethenamid_2018-1.png
diff --git a/docs/reference/dimethenamid_2018-2.png b/docs/reference/dimethenamid_2018-2.png
index 0bbb14d8..36db063c 100644
--- a/docs/reference/dimethenamid_2018-2.png
+++ b/docs/reference/dimethenamid_2018-2.png
diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png
index 71087e85..efb89bdb 100644
--- a/docs/reference/dimethenamid_2018-3.png
+++ b/docs/reference/dimethenamid_2018-3.png
diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html
index 85e954ac..d2ed8647 100644
--- a/docs/reference/dimethenamid_2018.html
+++ b/docs/reference/dimethenamid_2018.html
@@ -186,20 +186,25 @@ specific pieces of information in the comments.</p>
 <span class="r-in"><span class="co"># between these variants</span></span>
 <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span class="r-plt img"><img src="dimethenamid_2018-2.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="co"># Therefore we use nonlinear mixed-effects models</span></span>
+<span class="r-in"><span class="co"># We can also specify a default value for the failing</span></span>
+<span class="r-in"><span class="co"># log parameters, to mimic FOCUS guidance</span></span>
+<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span class="r-in">  default_log_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span></span>
+<span class="r-plt img"><img src="dimethenamid_2018-3.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span class="co"># As these attempts are not satisfying, we use nonlinear mixed-effects models</span></span>
 <span class="r-in"><span class="co"># f_dmta_nlme_tc &lt;- nlme(dmta_sfo_sfo3p_tc)</span></span>
 <span class="r-in"><span class="co"># nlme reaches maxIter = 50 without convergence</span></span>
 <span class="r-in"><span class="va">f_dmta_saem_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span></span>
 <span class="r-in"><span class="co"># I am commenting out the convergence plot as rendering them</span></span>
-<span class="r-in"><span class="co"># with pkgdown fails (at least without further tweaks to the </span></span>
+<span class="r-in"><span class="co"># with pkgdown fails (at least without further tweaks to the</span></span>
 <span class="r-in"><span class="co"># graphics device used)</span></span>
 <span class="r-in"><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></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_dmta_saem_tc</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.0 </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:         4.1.3 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed Mar 16 14:32:04 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Mar 16 14:32:04 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Sat Apr  9 18:03:34 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Sat Apr  9 18:03:34 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_DMTA/dt = - k_DMTA * DMTA</span>
@@ -212,7 +217,7 @@ specific pieces of information in the comments.</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 deSolve </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 927.963 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 787.836 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 9 chains</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>
@@ -300,8 +305,7 @@ specific pieces of information in the comments.</p>
 <span class="r-in"><span class="co">#   covariance.model = diag(c(0, rep(1, 7))))</span></span>
 <span class="r-in"><span class="co"># saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence")</span></span>
 <span class="r-in"><span class="co"># This does not perform better judged by AIC and BIC</span></span>
-<span class="r-in"><span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_dmta_saem_tc_2</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so):</span> object 'f_dmta_saem_tc_2' not found</span>
+<span class="r-in"><span class="co"># saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so)</span></span>
 <span class="r-in"><span class="co"># }</span></span>
 </code></pre></div>
     </div>
diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html
index aaeb44ea..efe91b6f 100644
--- a/docs/reference/mean_degparms.html
+++ b/docs/reference/mean_degparms.html
@@ -87,7 +87,13 @@
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mean_degparms</span><span class="op">(</span><span class="va">object</span>, random <span class="op">=</span> <span class="cn">FALSE</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>, conf.level <span class="op">=</span> <span class="fl">0.6</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mean_degparms</span><span class="op">(</span>
+  <span class="va">object</span>,
+  random <span class="op">=</span> <span class="cn">FALSE</span>,
+  test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,
+  conf.level <span class="op">=</span> <span class="fl">0.6</span>,
+  default_log_parms <span class="op">=</span> <span class="cn">NA</span>
+<span class="op">)</span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -103,6 +109,10 @@ rate constants) pass the t-test for significant difference from zero.</p></dd>
 <dt>conf.level</dt>
 <dd><p>Possibility to adjust the required confidence level
 for parameter that are tested if requested by 'test_log_parms'.</p></dd>
+<dt>default_log_parms</dt>
+<dd><p>If set to a numeric value, this is used
+as a default value for the tested log parameters that failed the
+t-test.</p></dd>
 </dl></div>
     <div id="value">
     <h2>Value</h2>
diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png
index 67c9b8ab..8678c166 100644
--- a/docs/reference/plot.mixed.mmkin-2.png
+++ b/docs/reference/plot.mixed.mmkin-2.png
diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png
index 0840c7da..9bd01852 100644
--- a/docs/reference/plot.mixed.mmkin-3.png
+++ b/docs/reference/plot.mixed.mmkin-3.png
diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png
index a78087bb..d2fa1ae1 100644
--- a/docs/reference/plot.mixed.mmkin-4.png
+++ b/docs/reference/plot.mixed.mmkin-4.png
diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html
index b405b84a..52971427 100644
--- a/docs/reference/plot.mixed.mmkin.html
+++ b/docs/reference/plot.mixed.mmkin.html
@@ -99,6 +99,7 @@
   pred_over <span class="op">=</span> <span class="cn">NULL</span>,
   test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,
   conf.level <span class="op">=</span> <span class="fl">0.6</span>,
+  default_log_parms <span class="op">=</span> <span class="cn">NA</span>,
   ymax <span class="op">=</span> <span class="st">"auto"</span>,
   maxabs <span class="op">=</span> <span class="st">"auto"</span>,
   ncol.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">&lt;=</span> <span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">&lt;=</span> <span class="fl">8</span>, <span class="fl">3</span>, <span class="fl">4</span><span class="op">)</span><span class="op">)</span>,
@@ -143,6 +144,9 @@ from <a href="mkinpredict.html">mkinpredict</a> with a compatible <a href="mkinm
 <dt>conf.level</dt>
 <dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an
 <a href="mixed.html">mixed.mmkin</a> object</p></dd>
+<dt>default_log_parms</dt>
+<dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an
+<a href="mixed.html">mixed.mmkin</a> object</p></dd>
 <dt>ymax</dt>
 <dd><p>Vector of maximum y axis values</p></dd>
 <dt>maxabs</dt>