Update static docs

1 files changed, 11 insertions, 7 deletions

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>
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