Update online docs, fix bug that surfaced

1 files changed, 54 insertions, 18 deletions

diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 131b168b..66e5478a 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -19,13 +19,13 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav"><li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../reference/index.html">Reference</a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
@@ -36,6 +36,8 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex
   <ul class="dropdown-menu" role="menu"><li>
       <a href="../articles/mkin.html">Introduction to mkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
     <li>
       <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
     </li>
@@ -43,22 +45,29 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
     <li>
-      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+      <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+      <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
     </li>
     <li>
-      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
     </li>
     <li>
-      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+    </li>
+    <li class="divider">
+    <li class="dropdown-header">Performance</li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
@@ -66,6 +75,14 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex
     <li>
       <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Miscellaneous</li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
   </ul></li>
 <li>
   <a href="../news/index.html">News</a>
@@ -430,10 +447,10 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span>
 <span class="r-in"><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="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.3 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed Dec  7 16:22:26 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Dec  7 16:22:26 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Fri Feb 17 22:22:33 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Feb 17 22:22:33 2023 </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 = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -448,7 +465,7 @@ using <a href="mmkin.html">mmkin</a>.</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 8.508 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 4.212 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 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: Constant variance </span>
@@ -711,12 +728,31 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Dataset 10     A1  120     12.1  12.79238 -0.69238 1.882     -0.36791</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># The following takes about 6 minutes</span></span></span>
-<span class="r-in"><span><span class="co">#f_saem_dfop_sfo_deSolve &lt;- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span></span>
-<span class="r-in"><span><span class="co">#  control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span></span>
+<span class="r-in"><span><span class="va">f_saem_dfop_sfo_deSolve</span> <span class="op">&lt;-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span></span>
+<span class="r-in"><span>  nbiter.saemix <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="fl">200</span>, <span class="fl">80</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DINTDY-  T (=R1) illegal      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, R1 = 70</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       T not in interval TCUR - HU (= R1) to TCUR (=R2)      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, R1 = 53.1122, R2 = 56.6407</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DINTDY-  T (=R1) illegal      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, R1 = 91</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       T not in interval TCUR - HU (= R1) to TCUR (=R2)      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, R1 = 53.1122, R2 = 56.6407</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DLSODA-  Trouble in DINTDY.  ITASK = I1, TOUT = R1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, I1 = 1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, R1 = 91</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Error in deSolve::lsoda(y = odeini, times = outtimes, func = x$symbols,  : </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   illegal input detected before taking any integration steps - see written message</span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co">#saemix::compare.saemix(list(</span></span></span>
-<span class="r-in"><span><span class="co">#  f_saem_dfop_sfo$so,</span></span></span>
-<span class="r-in"><span><span class="co">#  f_saem_dfop_sfo_deSolve$so))</span></span></span>
+<span class="r-in"><span><span class="co">#anova(</span></span></span>
+<span class="r-in"><span><span class="co">#  f_saem_dfop_sfo,</span></span></span>
+<span class="r-in"><span><span class="co">#  f_saem_dfop_sfo_deSolve))</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># If the model supports it, we can also use eigenvalue based solutions, which</span></span></span>
 <span class="r-in"><span><span class="co"># take a similar amount of time</span></span></span>
@@ -737,7 +773,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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