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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
commit8d1a84ac2190538ed3bac53a303064e281595868 (patch)
treeacb894d85ab7ec87c4911c355a5264a77e08e34b /docs/dev/reference/saem.html
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/dev/reference/saem.html')
-rw-r--r--docs/dev/reference/saem.html27
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>

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