Merge branch 'v1.2.3_pkgdown'

1 files changed, 70 insertions, 29 deletions

diff --git a/docs/reference/saem.html b/docs/reference/saem.html
index 957c098e..e308af61 100644
--- a/docs/reference/saem.html
+++ b/docs/reference/saem.html
@@ -19,13 +19,13 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/
       </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">1.2.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released 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)."><!-- mathjax --><script src="https:/
   <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)."><!-- mathjax --><script src="https:/
       <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)."><!-- mathjax --><script src="https:/
     <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>
@@ -143,10 +160,7 @@ Expectation Maximisation algorithm (SAEM).</p>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
-<span></span>
-<span><span class="co"># S3 method for saem.mmkin</span></span>
-<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -257,11 +271,6 @@ and the end of the optimisation process?</p></dd>
 <dt>digits</dt>
 <dd><p>Number of digits to use for printing</p></dd>
 
-
-<dt>ci</dt>
-<dd><p>Should a matrix with estimates and confidence interval boundaries
-be returned? If FALSE (default), a vector of estimates is returned.</p></dd>
-
 </dl></div>
     <div id="value">
     <h2>Value</h2>
@@ -430,10 +439,10 @@ 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:  1.2.1 </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:     Fri Nov 18 19:19:25 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Nov 18 19:19:25 2022 </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:         4.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Apr 20 07:34:38 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Apr 20 07:34:38 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>
@@ -448,12 +457,12 @@ 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 9.068 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 3.757 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Mean of starting values for individual parameters:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for degradation parameters:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        parent_0        log_k_A1 f_parent_qlogis          log_k1          log_k2 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         93.8102         -5.3734         -0.9711         -1.8799         -4.2708 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        g_qlogis </span>
@@ -462,6 +471,19 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Fixed degradation parameter values:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> None</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for random effects (square root of initial entries in omega):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>                 parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0           4.941    0.000          0.0000  0.000  0.000   0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_A1           0.000    2.551          0.0000  0.000  0.000   0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis    0.000    0.000          0.7251  0.000  0.000   0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k1             0.000    0.000          0.0000  1.449  0.000   0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k2             0.000    0.000          0.0000  0.000  2.228   0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g_qlogis           0.000    0.000          0.0000  0.000  0.000   0.7814</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for error model parameters:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   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> Results:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood computed by importance sampling</span>
@@ -698,12 +720,31 @@ 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 = lsoda_func,  : </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>
@@ -724,7 +765,7 @@ 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>
 </div>
 
       </footer></div>