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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-01 14:16:21 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-01 14:16:21 +0100
commit630e657f1794ea441afc9ff10663309fec5e847e (patch)
tree6f09ad8413f0a8c23f0b21e5067b4fccb183056e /docs/dev/reference/saem.html
parenta787e5266628f859fd70454c5419721efa494887 (diff)
Update online docs
Diffstat (limited to 'docs/dev/reference/saem.html')
-rw-r--r--docs/dev/reference/saem.html18
1 files changed, 12 insertions, 6 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index c8a7504f..8ea0ef6e 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">1.1.2</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span>
</span>
</div>
@@ -100,6 +100,7 @@ Expectation Maximisation algorithm (SAEM).</p>
<span><span class="fu">saem</span><span class="op">(</span></span>
<span> <span class="va">object</span>,</span>
<span> transformations <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="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span>
+<span> error_model <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span>
@@ -124,6 +125,7 @@ Expectation Maximisation algorithm (SAEM).</p>
<span> <span class="va">object</span>,</span>
<span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span> transformations <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="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span>
+<span> error_model <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -160,6 +162,10 @@ SFO, FOMC, DFOP and HS without fixing <code>parent_0</code>, and SFO or DFOP wit
one SFO metabolite.</p></dd>
+<dt>error_model</dt>
+<dd><p>Possibility to override the error model used in the mmkin object</p></dd>
+
+
<dt>degparms_start</dt>
<dd><p>Parameter values given as a named numeric vector will
be used to override the starting values obtained from the 'mmkin' object.</p></dd>
@@ -409,10 +415,10 @@ 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: 1.1.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Wed Oct 26 09:20:37 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Oct 26 09:20:37 2022 </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> 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 1 14:12:07 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Tue Nov 1 14:12:07 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>
@@ -427,7 +433,7 @@ 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 8.902 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 8.45 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>

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