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authorJohannes Ranke <jranke@uni-bremen.de>2020-10-15 12:27:40 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-15 12:27:40 +0200
commit272aba066f0d7502e319b7e7f14009318cd44348 (patch)
treec867903e262cb9514be5e92c4115d7e549b0d9e1 /docs/dev/reference/saemix.html
parentfa8623eec46d2c3ab1f405127493beb1846e4f1e (diff)
Updating docs of current dev version
Diffstat (limited to 'docs/dev/reference/saemix.html')
-rw-r--r--docs/dev/reference/saemix.html323
1 files changed, 279 insertions, 44 deletions
diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html
index da28bff1..5b160959 100644
--- a/docs/dev/reference/saemix.html
+++ b/docs/dev/reference/saemix.html
@@ -75,7 +75,7 @@ a list of datasets." />
</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">0.9.50.3</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
</span>
</div>
@@ -123,7 +123,7 @@ a list of datasets." />
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
- <a href="http://github.com/jranke/mkin/">
+ <a href="https://github.com/jranke/mkin/">
<span class="fab fa fab fa-github fa-lg"></span>
</a>
@@ -142,7 +142,7 @@ a list of datasets." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Create saemix models from mmkin row objects</h1>
- <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/saemix.R'><code>R/saemix.R</code></a></small>
<div class="hidden name"><code>saemix.Rd</code></div>
</div>
@@ -153,9 +153,9 @@ list of mkinfit objects that have been obtained by fitting the same model to
a list of datasets.</p>
</div>
- <pre class="usage"><span class='fu'>saemix_model</span>(<span class='no'>object</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span>())
+ <pre class="usage"><span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
-<span class='fu'>saemix_data</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
+<span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -187,14 +187,17 @@ mmkin. Starting variances of the random effects (argument omega.init) are the
variances of the deviations of the parameters from these mean values.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
- <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)]))
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>)
-<span class='no'>sfo_sfo</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"A1"</span>),
- <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># \dontrun{</span>
-<span class='no'>f_mmkin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>sfo_sfo</span>), <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>saemix</span>)</div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
-#&gt; <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='no'>m_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_model</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#&gt;
+ <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
+ <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</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'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
+<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='mkinsub.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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># \dontrun{</span>
+<span class='va'>f_mmkin</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/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>sfo_sfo</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='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>
+</div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
+#&gt; <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='va'>m_saemix</span> <span class='op'>&lt;-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;
#&gt;
#&gt; The following SaemixModel object was successfully created:
#&gt;
@@ -234,8 +237,8 @@ variances of the deviations of the parameters from these mean values.</p>
#&gt; res &lt;- unlist(res_list)
#&gt; return(res)
#&gt; }
-#&gt; &lt;bytecode: 0x55555bbf17c0&gt;
-#&gt; &lt;environment: 0x55555bbec4e0&gt;
+#&gt; &lt;bytecode: 0x55555c1e7720&gt;
+#&gt; &lt;environment: 0x55555c1eff38&gt;
#&gt; Nb of parameters: 4
#&gt; parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
#&gt; distribution:
@@ -250,11 +253,12 @@ variances of the deviations of the parameters from these mean values.</p>
#&gt; log_k_parent 0 1 0 0
#&gt; log_k_A1 0 0 1 0
#&gt; f_parent_ilr_1 0 0 0 1
-#&gt; Error model: constant , initial values: a.1=1
+#&gt; Error model: constant , initial values: a.1=4.97259024646577
#&gt; No covariate in the model.
#&gt; Initial values
#&gt; parent_0 log_k_parent log_k_A1 f_parent_ilr_1
-#&gt; Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449</div><div class='input'><span class='no'>d_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'>saemix_data</span>(<span class='no'>f_mmkin</span>)</div><div class='output co'>#&gt;
+#&gt; Pop.CondInit 86.53449 -3.207005 -3.060308 -1.920449</div><div class='input'><span class='va'>d_saemix</span> <span class='op'>&lt;-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;
#&gt;
#&gt; The following SaemixData object was successfully created:
#&gt;
@@ -262,14 +266,15 @@ variances of the deviations of the parameters from these mean values.</p>
#&gt; longitudinal data for use with the SAEM algorithm
#&gt; Dataset ds_saemix
#&gt; Structured data: value ~ time + name | ds
-#&gt; X variable for graphs: time () </div><div class='input'><span class='no'>saemix_options</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>,
- <span class='kw'>save</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.graphs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>displayProgress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>nbiter.saemix</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>200</span>, <span class='fl'>80</span>))
-<span class='no'>f_saemix</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span>(<span class='no'>m_saemix</span>, <span class='no'>d_saemix</span>, <span class='no'>saemix_options</span>)</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Wed May 27 07:45:07 2020"
+#&gt; X variable for graphs: time () </div><div class='input'><span class='va'>saemix_options</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>seed <span class='op'>=</span> <span class='fl'>123456</span>,
+ save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span> <span class='cn'>FALSE</span>, displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>,
+ nbiter.saemix <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='fl'>200</span>, <span class='fl'>80</span><span class='op'>)</span><span class='op'>)</span>
+<span class='va'>f_saemix</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix</span>, <span class='va'>d_saemix</span>, <span class='va'>saemix_options</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Thu Oct 15 11:55:14 2020"
#&gt; ..
#&gt; Minimisation finished
-#&gt; [1] "Wed May 27 07:51:24 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
+#&gt; [1] "Thu Oct 15 11:57:07 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
#&gt; -----------------------------------
#&gt; ---- Data ----
#&gt; -----------------------------------
@@ -333,8 +338,8 @@ variances of the deviations of the parameters from these mean values.</p>
#&gt; res &lt;- unlist(res_list)
#&gt; return(res)
#&gt; }
-#&gt; &lt;bytecode: 0x55555bbf17c0&gt;
-#&gt; &lt;environment: 0x55555bbec4e0&gt;
+#&gt; &lt;bytecode: 0x55555c1e7720&gt;
+#&gt; &lt;environment: 0x55555c1eff38&gt;
#&gt; Nb of parameters: 4
#&gt; parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
#&gt; distribution:
@@ -349,7 +354,7 @@ variances of the deviations of the parameters from these mean values.</p>
#&gt; log_k_parent 0 1 0 0
#&gt; log_k_A1 0 0 1 0
#&gt; f_parent_ilr_1 0 0 0 1
-#&gt; Error model: constant , initial values: a.1=1
+#&gt; Error model: constant , initial values: a.1=4.97259024646577
#&gt; No covariate in the model.
#&gt; Initial values
#&gt; parent_0 log_k_parent log_k_A1 f_parent_ilr_1
@@ -375,20 +380,20 @@ variances of the deviations of the parameters from these mean values.</p>
#&gt; ----------------------------------------------------
#&gt; ----------------- Fixed effects ------------------
#&gt; ----------------------------------------------------
-#&gt; Parameter Estimate SE CV(%)
-#&gt; [1,] parent_0 86.14 1.61 1.9
-#&gt; [2,] log_k_parent -3.21 0.59 18.5
-#&gt; [3,] log_k_A1 -4.66 0.30 6.4
-#&gt; [4,] f_parent_ilr_1 -0.33 0.30 91.7
-#&gt; [5,] a.1 4.68 0.27 5.8
+#&gt; Parameter Estimate SE CV(%)
+#&gt; parent_0 86.09 1.57 1.8
+#&gt; log_k_parent -3.21 0.59 18.5
+#&gt; log_k_A1 -4.69 0.31 6.6
+#&gt; f_parent_ilr_1 -0.34 0.30 89.2
+#&gt; a a.1 4.69 0.27 5.8
#&gt; ----------------------------------------------------
#&gt; ----------- Variance of random effects -----------
#&gt; ----------------------------------------------------
#&gt; Parameter Estimate SE CV(%)
-#&gt; parent_0 omega2.parent_0 7.71 8.14 106
-#&gt; log_k_parent omega2.log_k_parent 1.76 1.12 63
-#&gt; log_k_A1 omega2.log_k_A1 0.26 0.26 101
-#&gt; f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.28 71
+#&gt; parent_0 omega2.parent_0 7.07 7.72 109
+#&gt; log_k_parent omega2.log_k_parent 1.75 1.11 63
+#&gt; log_k_A1 omega2.log_k_A1 0.28 0.28 99
+#&gt; f_parent_ilr_1 omega2.f_parent_ilr_1 0.39 0.27 71
#&gt; ----------------------------------------------------
#&gt; ------ Correlation matrix of random effects ------
#&gt; ----------------------------------------------------
@@ -406,15 +411,245 @@ variances of the deviations of the parameters from these mean values.</p>
#&gt; --------------- Statistical criteria -------------
#&gt; ----------------------------------------------------
#&gt; Likelihood computed by linearisation
-#&gt; -2LL= 1064.364
-#&gt; AIC = 1082.364
-#&gt; BIC = 1078.848
+#&gt; -2LL= 1064.35
+#&gt; AIC = 1082.35
+#&gt; BIC = 1078.835
#&gt;
#&gt; Likelihood computed by importance sampling
-#&gt; -2LL= 1063.462
-#&gt; AIC = 1081.462
-#&gt; BIC = 1077.947
-#&gt; ----------------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span>(<span class='no'>f_saemix</span>, <span class='kw'>plot.type</span> <span class='kw'>=</span> <span class='st'>"convergence"</span>)</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'># }
+#&gt; -2LL= 1063.475
+#&gt; AIC = 1081.475
+#&gt; BIC = 1077.96
+#&gt; ----------------------------------------------------</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_saemix</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='img'><img src='saemix-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+<span class='co'># Synthetic data with two-component error</span>
+<span class='va'>sampling_times</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='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
+<span class='va'>dt50_sfo_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>800</span>, <span class='fl'>900</span>, <span class='fl'>1000</span>, <span class='fl'>1111.11</span>, <span class='fl'>1250</span><span class='op'>)</span>
+<span class='va'>k_in</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in</span>
+
+<span class='va'>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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+
+<span class='va'>pred_sfo</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span>
+ <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><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>, <span class='va'>sampling_times</span><span class='op'>)</span>
+<span class='op'>}</span>
+
+<span class='va'>ds_sfo_mean</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456L</span><span class='op'>)</span>
+<span class='va'>ds_sfo_syn</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span>
+ <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>,
+ n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>
+ <span class='op'>}</span><span class='op'>)</span>
+<span class='va'>f_mmkin_syn</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='va'>m_saemix_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;
+#&gt;
+#&gt; The following SaemixModel object was successfully created:
+#&gt;
+#&gt; Nonlinear mixed-effects model
+#&gt; Model function: Mixed model generated from mmkin object Model type: structural
+#&gt; function (psi, id, xidep)
+#&gt; {
+#&gt; uid &lt;- unique(id)
+#&gt; res_list &lt;- parallel::mclapply(uid, function(i) {
+#&gt; transparms_optim &lt;- psi[i, ]
+#&gt; names(transparms_optim) &lt;- names(degparms_optim)
+#&gt; odeini_optim &lt;- transparms_optim[odeini_optim_parm_names]
+#&gt; names(odeini_optim) &lt;- gsub("_0$", "", odeini_optim_parm_names)
+#&gt; odeini &lt;- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
+#&gt; ode_transparms_optim_names &lt;- setdiff(names(transparms_optim),
+#&gt; odeini_optim_parm_names)
+#&gt; odeparms_optim &lt;- backtransform_odeparms(transparms_optim[ode_transparms_optim_names],
+#&gt; mkin_model, transform_rates = object[[1]]$transform_rates,
+#&gt; transform_fractions = object[[1]]$transform_fractions)
+#&gt; odeparms &lt;- c(odeparms_optim, odeparms_fixed)
+#&gt; xidep_i &lt;- subset(xidep, id == i)
+#&gt; if (analytical) {
+#&gt; out_values &lt;- mkin_model$deg_func(xidep_i, odeini,
+#&gt; odeparms)
+#&gt; }
+#&gt; else {
+#&gt; i_time &lt;- xidep_i$time
+#&gt; i_name &lt;- xidep_i$name
+#&gt; out_wide &lt;- mkinpredict(mkin_model, odeparms = odeparms,
+#&gt; odeini = odeini, solution_type = object[[1]]$solution_type,
+#&gt; outtimes = sort(unique(i_time)))
+#&gt; out_index &lt;- cbind(as.character(i_time), as.character(i_name))
+#&gt; out_values &lt;- out_wide[out_index]
+#&gt; }
+#&gt; return(out_values)
+#&gt; }, mc.cores = cores)
+#&gt; res &lt;- unlist(res_list)
+#&gt; return(res)
+#&gt; }
+#&gt; &lt;bytecode: 0x55555c1e7720&gt;
+#&gt; &lt;environment: 0x55555be5b848&gt;
+#&gt; Nb of parameters: 2
+#&gt; parameter names: parent_0 log_k_parent
+#&gt; distribution:
+#&gt; Parameter Distribution Estimated
+#&gt; [1,] parent_0 normal Estimated
+#&gt; [2,] log_k_parent normal Estimated
+#&gt; Variance-covariance matrix:
+#&gt; parent_0 log_k_parent
+#&gt; parent_0 1 0
+#&gt; log_k_parent 0 1
+#&gt; Error model: combined , initial values: a.1=2.4206146215511 b.1=0.03831266409084
+#&gt; No covariate in the model.
+#&gt; Initial values
+#&gt; parent_0 log_k_parent
+#&gt; Pop.CondInit 100.2498 -9.33922</div><div class='input'><span class='va'>d_saemix_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>f_mmkin_syn</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;
+#&gt;
+#&gt; The following SaemixData object was successfully created:
+#&gt;
+#&gt; Object of class SaemixData
+#&gt; longitudinal data for use with the SAEM algorithm
+#&gt; Dataset ds_saemix
+#&gt; Structured data: value ~ time + name | ds
+#&gt; X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_tc</span>, <span class='va'>d_saemix_tc</span>, <span class='va'>saemix_options</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Thu Oct 15 11:57:25 2020"
+#&gt; ..
+#&gt; Minimisation finished
+#&gt; [1] "Thu Oct 15 11:58:16 2020"
+#&gt; Error in solve.default(Fth) :
+#&gt; Lapack routine dgesv: system is exactly singular: U[2,2] = 0
+#&gt; Error computing the Fisher Information Matrix: singular system.
+#&gt; Error in solve.default(FO) :
+#&gt; Lapack routine dgesv: system is exactly singular: U[2,2] = 0
+#&gt; Error computing the Fisher Information Matrix: singular system.</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by the SAEM algorithm
+#&gt; -----------------------------------
+#&gt; ---- Data ----
+#&gt; -----------------------------------
+#&gt; Object of class SaemixData
+#&gt; longitudinal data for use with the SAEM algorithm
+#&gt; Dataset ds_saemix
+#&gt; Structured data: value ~ time + name | ds
+#&gt; X variable for graphs: time ()
+#&gt; Dataset characteristics:
+#&gt; number of subjects: 5
+#&gt; number of observations: 90
+#&gt; average/min/max nb obs: 18.00 / 18 / 18
+#&gt; First 10 lines of data:
+#&gt; ds time name value mdv cens occ ytype
+#&gt; 1 1 0 parent 105.9 0 0 1 1
+#&gt; 2 1 0 parent 98.0 0 0 1 1
+#&gt; 3 1 1 parent 97.4 0 0 1 1
+#&gt; 4 1 1 parent 100.5 0 0 1 1
+#&gt; 5 1 3 parent 115.6 0 0 1 1
+#&gt; 6 1 3 parent 105.6 0 0 1 1
+#&gt; 7 1 7 parent 108.6 0 0 1 1
+#&gt; 8 1 7 parent 117.0 0 0 1 1
+#&gt; 9 1 14 parent 107.0 0 0 1 1
+#&gt; 10 1 14 parent 95.8 0 0 1 1
+#&gt; -----------------------------------
+#&gt; ---- Model ----
+#&gt; -----------------------------------
+#&gt; Nonlinear mixed-effects model
+#&gt; Model function: Mixed model generated from mmkin object Model type: structural
+#&gt; function (psi, id, xidep)
+#&gt; {
+#&gt; uid &lt;- unique(id)
+#&gt; res_list &lt;- parallel::mclapply(uid, function(i) {
+#&gt; transparms_optim &lt;- psi[i, ]
+#&gt; names(transparms_optim) &lt;- names(degparms_optim)
+#&gt; odeini_optim &lt;- transparms_optim[odeini_optim_parm_names]
+#&gt; names(odeini_optim) &lt;- gsub("_0$", "", odeini_optim_parm_names)
+#&gt; odeini &lt;- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
+#&gt; ode_transparms_optim_names &lt;- setdiff(names(transparms_optim),
+#&gt; odeini_optim_parm_names)
+#&gt; odeparms_optim &lt;- backtransform_odeparms(transparms_optim[ode_transparms_optim_names],
+#&gt; mkin_model, transform_rates = object[[1]]$transform_rates,
+#&gt; transform_fractions = object[[1]]$transform_fractions)
+#&gt; odeparms &lt;- c(odeparms_optim, odeparms_fixed)
+#&gt; xidep_i &lt;- subset(xidep, id == i)
+#&gt; if (analytical) {
+#&gt; out_values &lt;- mkin_model$deg_func(xidep_i, odeini,
+#&gt; odeparms)
+#&gt; }
+#&gt; else {
+#&gt; i_time &lt;- xidep_i$time
+#&gt; i_name &lt;- xidep_i$name
+#&gt; out_wide &lt;- mkinpredict(mkin_model, odeparms = odeparms,
+#&gt; odeini = odeini, solution_type = object[[1]]$solution_type,
+#&gt; outtimes = sort(unique(i_time)))
+#&gt; out_index &lt;- cbind(as.character(i_time), as.character(i_name))
+#&gt; out_values &lt;- out_wide[out_index]
+#&gt; }
+#&gt; return(out_values)
+#&gt; }, mc.cores = cores)
+#&gt; res &lt;- unlist(res_list)
+#&gt; return(res)
+#&gt; }
+#&gt; &lt;bytecode: 0x55555c1e7720&gt;
+#&gt; &lt;environment: 0x55555be5b848&gt;
+#&gt; Nb of parameters: 2
+#&gt; parameter names: parent_0 log_k_parent
+#&gt; distribution:
+#&gt; Parameter Distribution Estimated
+#&gt; [1,] parent_0 normal Estimated
+#&gt; [2,] log_k_parent normal Estimated
+#&gt; Variance-covariance matrix:
+#&gt; parent_0 log_k_parent
+#&gt; parent_0 1 0
+#&gt; log_k_parent 0 1
+#&gt; Error model: combined , initial values: a.1=2.4206146215511 b.1=0.03831266409084
+#&gt; No covariate in the model.
+#&gt; Initial values
+#&gt; parent_0 log_k_parent
+#&gt; Pop.CondInit 100.2498 -9.33922
+#&gt; -----------------------------------
+#&gt; ---- Key algorithm options ----
+#&gt; -----------------------------------
+#&gt; Estimation of individual parameters (MAP)
+#&gt; Estimation of standard errors and linearised log-likelihood
+#&gt; Estimation of log-likelihood by importance sampling
+#&gt; Number of iterations: K1=200, K2=80
+#&gt; Number of chains: 10
+#&gt; Seed: 123456
+#&gt; Number of MCMC iterations for IS: 5000
+#&gt; Simulations:
+#&gt; nb of simulated datasets used for npde: 1000
+#&gt; nb of simulated datasets used for VPC: 100
+#&gt; Input/output
+#&gt; save the results to a file: FALSE
+#&gt; save the graphs to files: FALSE
+#&gt; ----------------------------------------------------
+#&gt; ---- Results ----
+#&gt; ----------------------------------------------------
+#&gt; ----------------- Fixed effects ------------------
+#&gt; ----------------------------------------------------
+#&gt; Parameter Estimate SE CV(%)
+#&gt; parent_0 97.44 &lt;NA&gt; &lt;NA&gt;
+#&gt; log_k_parent -56.97 &lt;NA&gt; &lt;NA&gt;
+#&gt; a a.1 -7.12 &lt;NA&gt; &lt;NA&gt;
+#&gt; b b.1 0.15 &lt;NA&gt; &lt;NA&gt;
+#&gt; ----------------------------------------------------
+#&gt; ----------- Variance of random effects -----------
+#&gt; ----------------------------------------------------
+#&gt; Parameter Estimate SE CV(%)
+#&gt; parent_0 omega2.parent_0 2.8 NA NA
+#&gt; log_k_parent omega2.log_k_parent 750.3 NA NA
+#&gt; ----------------------------------------------------
+#&gt; ------ Correlation matrix of random effects ------
+#&gt; ----------------------------------------------------
+#&gt; omega2.parent_0 omega2.log_k_parent
+#&gt; omega2.parent_0 1 0
+#&gt; omega2.log_k_parent 0 1
+#&gt; ----------------------------------------------------
+#&gt; --------------- Statistical criteria -------------
+#&gt; ----------------------------------------------------
+#&gt; Likelihood computed by linearisation
+#&gt; -2LL= 623.7744
+#&gt; AIC = 635.7744
+#&gt; BIC = 633.431
+#&gt;
+#&gt; Likelihood computed by importance sampling
+#&gt; -2LL= 621.1909
+#&gt; AIC = 633.1909
+#&gt; BIC = 630.8475
+#&gt; ----------------------------------------------------</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_saemix_tc</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+</div><div class='img'><img src='saemix-3.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Plotting convergence plots</div><div class='img'><img src='saemix-4.png' alt='' width='700' height='433' /></div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -431,7 +666,7 @@ variances of the deviations of the parameters from these mean values.</p>
</div>
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- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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