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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-13 12:40:44 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-13 12:40:44 +0100
commit3dde3b95f1db925c89cd04d19f95c6fc9f68f473 (patch)
treeca6b0bd89374be7dc6597addc25fd5de643fa871 /docs/dev/reference
parentd2d25c51ad95b4344287917574d4c0506bfaf75d (diff)
Update docs
Diffstat (limited to 'docs/dev/reference')
-rw-r--r--docs/dev/reference/endpoints.html2
-rw-r--r--docs/dev/reference/index.html2
-rw-r--r--docs/dev/reference/plot.mixed.mmkin.html6
-rw-r--r--docs/dev/reference/saem.html38
-rw-r--r--docs/dev/reference/summary.saem.mmkin.html14
5 files changed, 31 insertions, 31 deletions
diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html
index a13e11a7..301b454f 100644
--- a/docs/dev/reference/endpoints.html
+++ b/docs/dev/reference/endpoints.html
@@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." />
</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">1.0.1.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span>
</span>
</div>
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 7e98aa50..b52ecb22 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -71,7 +71,7 @@
</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">1.0.1.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span>
</span>
</div>
diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index 601e1554..ef169074 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
+++ b/docs/dev/reference/plot.mixed.mmkin.html
@@ -72,7 +72,7 @@
</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">1.0.1.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span>
</span>
</div>
@@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.</p></td>
</div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span>, transformations <span class='op'>=</span> <span class='st'>"saemix"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:29:17 2021"
+#&gt; [1] "Sat Feb 13 12:33:07 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:29:23 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
+#&gt; [1] "Sat Feb 13 12:33:13 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># We can overlay the two variants if we generate predictions</span>
<span class='va'>pred_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>,
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 4578db2a..02483bec 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." />
</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">1.0.1.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span>
</span>
</div>
@@ -261,27 +261,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:29:26 2021"
+#&gt; [1] "Sat Feb 13 12:33:16 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:29:27 2021"</div><div class='input'>
+#&gt; [1] "Sat Feb 13 12:33:18 2021"</div><div class='input'>
<span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:29:28 2021"
+#&gt; [1] "Sat Feb 13 12:33:19 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:29:30 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Sat Feb 13 12:33:20 2021"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:29:30 2021"
+#&gt; [1] "Sat Feb 13 12:33:20 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:29:32 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Sat Feb 13 12:33:22 2021"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:29:32 2021"
+#&gt; [1] "Sat Feb 13 12:33:23 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:29:35 2021"</div><div class='input'>
+#&gt; [1] "Sat Feb 13 12:33:25 2021"</div><div class='input'>
<span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
<span class='co'># functions from saemix</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
@@ -324,10 +324,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
<span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:29:37 2021"
+#&gt; [1] "Sat Feb 13 12:33:28 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:29:42 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Sat Feb 13 12:33:32 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.</span></div><div class='input'>
<span class='va'>sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
@@ -346,15 +346,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># four minutes</span>
<span class='va'>f_saem_sfo_sfo</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'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:29:44 2021"
+#&gt; [1] "Sat Feb 13 12:33:35 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:29:48 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</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><span class='op'>)</span>
+#&gt; [1] "Sat Feb 13 12:33:39 2021"</div><div class='input'><span class='va'>f_saem_dfop_sfo</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><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:29:49 2021"
+#&gt; [1] "Sat Feb 13 12:33:40 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:29:57 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Sat Feb 13 12:33:48 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by SAEM
#&gt; Structural model:
@@ -395,10 +395,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; SD.g_qlogis 0.44771 -0.86417 1.7596</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
</div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>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>
</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
-#&gt; mkin version used for pre-fitting: 1.0.1.9000
+#&gt; mkin version used for pre-fitting: 1.0.2.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Sat Feb 6 18:29:57 2021
-#&gt; Date of summary: Sat Feb 6 18:29:58 2021
+#&gt; Date of fit: Sat Feb 13 12:33:48 2021
+#&gt; Date of summary: Sat Feb 13 12:33:48 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -413,7 +413,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 8.539 s using 300, 100 iterations
+#&gt; Fitted in 8.875 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
index 93e1365d..81054813 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally
</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">1.0.1.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.2.9000</span>
</span>
</div>
@@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.</p>
quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span>
<span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Sat Feb 6 18:30:00 2021"
+#&gt; [1] "Sat Feb 13 12:33:52 2021"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Sat Feb 6 18:30:11 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>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>
+#&gt; [1] "Sat Feb 13 12:34:03 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>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>
</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
-#&gt; mkin version used for pre-fitting: 1.0.1.9000
+#&gt; mkin version used for pre-fitting: 1.0.2.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Sat Feb 6 18:30:12 2021
-#&gt; Date of summary: Sat Feb 6 18:30:12 2021
+#&gt; Date of fit: Sat Feb 13 12:34:04 2021
+#&gt; Date of summary: Sat Feb 13 12:34:04 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 11.769 s using 300, 100 iterations
+#&gt; Fitted in 11.899 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Two-component variance function
#&gt;

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