Merge branch 'main' into custom_lsoda_call

1 files changed, 20 insertions, 7 deletions

diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 73382cba..131b168b 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -19,7 +19,7 @@ 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">1.2.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -113,7 +113,7 @@ Expectation Maximisation algorithm (SAEM).</p>
 <span>  covariates <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  error.init <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">3</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
+<span>  error.init <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">1</span>, <span class="fl">1</span><span class="op">)</span>,</span>
 <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">300</span>, <span class="fl">100</span><span class="op">)</span>,</span>
 <span>  control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span>
 <span>    save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
@@ -430,10 +430,10 @@ 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:  1.2.0 </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> R version used for fitting:         4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Tue Nov 15 00:45:58 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Tue Nov 15 00:45:58 2022 </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> </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 +448,12 @@ 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 9.189 s</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> 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 +462,19 @@ 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>