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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-08 02:59:07 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-08 02:59:07 +0100
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+<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters
+for fixed effects (population), random effects (deviations from the
+population mean) and residual error model, as well as the resulting
+endpoints such as formation fractions and DT50 values. Optionally
+(default is FALSE), the data are listed in full." />
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+ <div class="page-header">
+ <h1>Summary method for class "saem.mmkin"</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/summary.saem.mmkin.R'><code>R/summary.saem.mmkin.R</code></a></small>
+ <div class="hidden name"><code>summary.saem.mmkin.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Lists model equations, initial parameter values, optimised parameters
+for fixed effects (population), random effects (deviations from the
+population mean) and residual error model, as well as the resulting
+endpoints such as formation fractions and DT50 values. Optionally
+(default is FALSE), the data are listed in full.</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
+
+<span class='co'># S3 method for summary.saem.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</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">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>an object of class <a href='saem.html'>saem.mmkin</a></p></td>
+ </tr>
+ <tr>
+ <th>data</th>
+ <td><p>logical, indicating whether the full data should be included in
+the summary.</p></td>
+ </tr>
+ <tr>
+ <th>verbose</th>
+ <td><p>Should the summary be verbose?</p></td>
+ </tr>
+ <tr>
+ <th>distimes</th>
+ <td><p>logical, indicating whether DT50 and DT90 values should be
+included.</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>optional arguments passed to methods like <code>print</code>.</p></td>
+ </tr>
+ <tr>
+ <th>x</th>
+ <td><p>an object of class summary.saem.mmkin</p></td>
+ </tr>
+ <tr>
+ <th>digits</th>
+ <td><p>Number of digits to use for printing</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The summary function returns a list based on the <a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a>
+obtained in the fit, with at least the following additional components</p>
+<dt>saemixversion, mkinversion, Rversion</dt><dd><p>The saemix, mkin and R versions used</p></dd>
+<dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were
+produced</p></dd>
+<dt>diffs</dt><dd><p>The differential equations used in the degradation model</p></dd>
+<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd>
+<dt>data</dt><dd><p>The data</p></dd>
+<dt>confint_trans</dt><dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd>
+<dt>confint_back</dt><dd><p>Backtransformed parameters, with confidence intervals if available</p></dd>
+<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted
+model.</p></dd>
+<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
+<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
+The print method is called for its side effect, i.e. printing the summary.
+
+ <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+ <p>Johannes Ranke for the mkin specific parts
+saemix authors for the parts inherited from saemix.</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># Generate five datasets following SFO kinetics</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_pop</span> <span class='op'>&lt;-</span> <span class='fl'>50</span>
+<span class='va'>k_in_pop</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_pop</span>
+<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</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/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='va'>k_in_pop</span><span class='op'>)</span>, <span class='fl'>0.5</span><span class='op'>)</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/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</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'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</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='co'># \dontrun{</span>
+<span class='co'># Evaluate using mmkin and saem</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='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, 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'>1</span><span class='op'>)</span>
+<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_mmkin</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Sun Nov 8 02:58:03 2020"
+#&gt; ....
+#&gt; Minimisation finished
+#&gt; [1] "Sun Nov 8 02:58:07 2020"</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</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: 0.9.50.4
+#&gt; R version used for fitting: 4.0.3
+#&gt; Date of fit: Sun Nov 8 02:58:07 2020
+#&gt; Date of summary: Sun Nov 8 02:58:07 2020
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt;
+#&gt; Data:
+#&gt; 90 observations of 1 variable(s) grouped in 5 datasets
+#&gt;
+#&gt; Model predictions using solution type analytical
+#&gt;
+#&gt; Fitted in 4.175 s using 300, 100 iterations
+#&gt;
+#&gt; Variance model: Two-component variance function
+#&gt;
+#&gt; Mean of starting values for individual parameters:
+#&gt; parent_0 log_k_parent
+#&gt; 97.849556 -4.455036
+#&gt;
+#&gt; Fixed degradation parameter values:
+#&gt; None
+#&gt;
+#&gt; Results:
+#&gt;
+#&gt; Likelihood computed by importance sampling
+#&gt; AIC BIC logLik
+#&gt; 555.6718 553.3284 -271.8359
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; est. lower upper
+#&gt; parent_0 97.840291 94.701895 100.978686
+#&gt; log_k_parent -4.464246 -5.001413 -3.927078
+#&gt;
+#&gt; Correlation:
+#&gt; prnt_0
+#&gt; log_k_parent 0.022
+#&gt;
+#&gt; Random effects:
+#&gt; est. lower upper
+#&gt; SD.parent_0 3.0805465 0.4960170 5.6650760
+#&gt; SD.log_k_parent 0.6109508 0.2301398 0.9917617
+#&gt;
+#&gt; Variance model:
+#&gt; est. lower upper
+#&gt; a.1 1.06249961 0.23012265 1.89487657
+#&gt; b.1 0.04649661 0.03060849 0.06238473
+#&gt;
+#&gt; Backtransformed parameters with asymmetric confidence intervals:
+#&gt; est. lower upper
+#&gt; parent_0 97.84029088 94.701895315 100.97868644
+#&gt; k_parent 0.01151338 0.006728434 0.01970115
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 60.2 200
+#&gt;
+#&gt; Data:
+#&gt; ds name time observed predicted residual standardized
+#&gt; ds 1 parent 0 103.6 97.303 6.297361 -1.12720
+#&gt; ds 1 parent 0 95.9 97.303 -1.402639 0.25107
+#&gt; ds 1 parent 1 95.4 96.599 -1.198705 0.21583
+#&gt; ds 1 parent 1 95.3 96.599 -1.298705 0.23383
+#&gt; ds 1 parent 3 91.6 95.206 -3.606076 0.65693
+#&gt; ds 1 parent 3 94.5 95.206 -0.706076 0.12863
+#&gt; ds 1 parent 7 88.1 92.481 -4.380761 0.81692
+#&gt; ds 1 parent 7 89.6 92.481 -2.880761 0.53720
+#&gt; ds 1 parent 14 90.3 87.898 2.402166 -0.46649
+#&gt; ds 1 parent 14 96.0 87.898 8.102166 -1.57340
+#&gt; ds 1 parent 28 80.2 79.402 0.797948 -0.16783
+#&gt; ds 1 parent 28 77.9 79.402 -1.502052 0.31593
+#&gt; ds 1 parent 60 59.3 62.940 -3.639829 0.91247
+#&gt; ds 1 parent 60 59.6 62.940 -3.339829 0.83726
+#&gt; ds 1 parent 90 59.4 50.620 8.779547 -2.56999
+#&gt; ds 1 parent 90 51.0 50.620 0.379547 -0.11110
+#&gt; ds 1 parent 120 38.8 40.712 -1.912380 0.64706
+#&gt; ds 1 parent 120 38.9 40.712 -1.812380 0.61323
+#&gt; ds 2 parent 0 103.2 97.185 6.015158 -1.07774
+#&gt; ds 2 parent 0 95.1 97.185 -2.084842 0.37354
+#&gt; ds 2 parent 1 88.3 95.609 -7.309466 1.32706
+#&gt; ds 2 parent 1 102.4 95.609 6.790534 -1.23285
+#&gt; ds 2 parent 3 88.4 92.535 -4.134911 0.77071
+#&gt; ds 2 parent 3 95.2 92.535 2.665089 -0.49675
+#&gt; ds 2 parent 7 83.5 86.679 -3.179231 0.62426
+#&gt; ds 2 parent 7 96.4 86.679 9.720769 -1.90873
+#&gt; ds 2 parent 14 77.3 77.309 -0.009268 0.00199
+#&gt; ds 2 parent 14 76.0 77.309 -1.309268 0.28113
+#&gt; ds 2 parent 28 61.7 61.499 0.201491 -0.05137
+#&gt; ds 2 parent 28 56.5 61.499 -4.998509 1.27449
+#&gt; ds 2 parent 60 35.1 36.454 -1.353571 0.49087
+#&gt; ds 2 parent 60 32.2 36.454 -4.253571 1.54256
+#&gt; ds 2 parent 90 21.2 22.326 -1.125996 0.53604
+#&gt; ds 2 parent 90 23.3 22.326 0.974004 -0.46368
+#&gt; ds 2 parent 120 14.1 13.674 0.426440 -0.25110
+#&gt; ds 2 parent 120 16.9 13.674 3.226440 -1.89983
+#&gt; ds 3 parent 0 92.4 93.838 -1.437848 0.26501
+#&gt; ds 3 parent 0 94.0 93.838 0.162152 -0.02989
+#&gt; ds 3 parent 1 95.7 91.709 3.991384 -0.74932
+#&gt; ds 3 parent 1 90.8 91.709 -0.908616 0.17058
+#&gt; ds 3 parent 3 86.7 87.594 -0.893997 0.17409
+#&gt; ds 3 parent 3 85.8 87.594 -1.793997 0.34934
+#&gt; ds 3 parent 7 77.1 79.910 -2.810299 0.58817
+#&gt; ds 3 parent 7 81.5 79.910 1.589701 -0.33271
+#&gt; ds 3 parent 14 69.1 68.050 1.050102 -0.24845
+#&gt; ds 3 parent 14 62.4 68.050 -5.649898 1.33675
+#&gt; ds 3 parent 28 49.1 49.349 -0.248837 0.07412
+#&gt; ds 3 parent 28 47.2 49.349 -2.148837 0.64010
+#&gt; ds 3 parent 60 21.9 23.676 -1.775776 0.82085
+#&gt; ds 3 parent 60 23.6 23.676 -0.075776 0.03503
+#&gt; ds 3 parent 90 12.4 11.892 0.507660 -0.31425
+#&gt; ds 3 parent 90 13.8 11.892 1.907660 -1.18088
+#&gt; ds 3 parent 120 4.9 5.974 -1.073521 0.80099
+#&gt; ds 3 parent 120 7.5 5.974 1.526479 -1.13895
+#&gt; ds 4 parent 0 91.8 102.087 -10.287197 1.77084
+#&gt; ds 4 parent 0 104.6 102.087 2.512803 -0.43256
+#&gt; ds 4 parent 1 117.5 101.632 15.867689 -2.74145
+#&gt; ds 4 parent 1 99.3 101.632 -2.332311 0.40295
+#&gt; ds 4 parent 3 94.0 100.729 -6.728610 1.17100
+#&gt; ds 4 parent 3 98.7 100.729 -2.028610 0.35304
+#&gt; ds 4 parent 7 109.2 98.945 10.254756 -1.81080
+#&gt; ds 4 parent 7 89.2 98.945 -9.745244 1.72083
+#&gt; ds 4 parent 14 103.3 95.900 7.400009 -1.34021
+#&gt; ds 4 parent 14 103.0 95.900 7.100009 -1.28588
+#&gt; ds 4 parent 28 90.8 90.088 0.712227 -0.13563
+#&gt; ds 4 parent 28 88.7 90.088 -1.387773 0.26427
+#&gt; ds 4 parent 60 74.8 78.091 -3.291273 0.70124
+#&gt; ds 4 parent 60 75.3 78.091 -2.791273 0.59471
+#&gt; ds 4 parent 90 71.1 68.300 2.800407 -0.66075
+#&gt; ds 4 parent 90 78.0 68.300 9.700407 -2.28880
+#&gt; ds 4 parent 120 59.1 59.736 -0.635668 0.16554
+#&gt; ds 4 parent 120 53.8 59.736 -5.935668 1.54574
+#&gt; ds 5 parent 0 94.9 98.353 -3.452694 0.61266
+#&gt; ds 5 parent 0 101.8 98.353 3.447306 -0.61171
+#&gt; ds 5 parent 1 96.1 96.722 -0.621996 0.11187
+#&gt; ds 5 parent 1 97.1 96.722 0.378004 -0.06799
+#&gt; ds 5 parent 3 93.8 93.541 0.258738 -0.04781
+#&gt; ds 5 parent 3 85.8 93.541 -7.741262 1.43043
+#&gt; ds 5 parent 7 87.6 87.490 0.109848 -0.02141
+#&gt; ds 5 parent 7 94.0 87.490 6.509848 -1.26885
+#&gt; ds 5 parent 14 82.5 77.827 4.672679 -0.99818
+#&gt; ds 5 parent 14 81.7 77.827 3.872679 -0.82728
+#&gt; ds 5 parent 28 60.0 61.585 -1.585419 0.40382
+#&gt; ds 5 parent 28 61.0 61.585 -0.585419 0.14911
+#&gt; ds 5 parent 60 32.5 36.068 -3.568284 1.30251
+#&gt; ds 5 parent 60 35.5 36.068 -0.568284 0.20744
+#&gt; ds 5 parent 90 21.8 21.842 -0.042136 0.02028
+#&gt; ds 5 parent 90 24.4 21.842 2.557864 -1.23088
+#&gt; ds 5 parent 120 14.1 13.227 0.872898 -0.52035
+#&gt; ds 5 parent 120 12.1 13.227 -1.127102 0.67189</div><div class='input'><span class='co'># }</span>
+
+</div></pre>
+ </div>
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+ <h2 data-toc-skip>Contents</h2>
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+ <p>Developed by Johannes Ranke.</p>
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+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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