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Optionally +(default is FALSE), the data are listed in full.</p> + </div> + + <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/base/summary.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>, + alpha <span class='op'>=</span> <span class='fl'>0.05</span>, + <span class='va'>...</span> +<span class='op'>)</span> + +<span class='co'># S3 method for summary.nlme.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='nlme.mmkin.html'>nlme.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>alpha</th> + <td><p>error level for confidence interval estimation from the t +distribution</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.nlme.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/nlme/man/nlme.html'>nlme</a> object +obtained in the fit, with at least the following additional components</p> +<dt>nlmeversion, mkinversion, Rversion</dt><dd><p>The nlme, 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 +José Pinheiro and Douglas Bates for the components inherited from nlme</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'><-</span> <span class='fl'>50</span> +<span class='va'>k_in_pop</span> <span class='op'><-</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'><-</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'><-</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'><-</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'><-</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'><-</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'><-</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'># Evaluate using mmkin and nlme</span> +<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> +<span class='va'>f_mmkin</span> <span class='op'><-</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> +</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00371</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> nlme version used for fitting: 3.1.150.1 +#> mkin version used for pre-fitting: 0.9.50.4 +#> R version used for fitting: 4.0.3 +#> Date of fit: Tue Oct 27 15:25:23 2020 +#> Date of summary: Tue Oct 27 15:25:23 2020 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> +#> Data: +#> 90 observations of 1 variable(s) grouped in 5 datasets +#> +#> Model predictions using solution type analytical +#> +#> Fitted in 0.581 s using 5 iterations +#> +#> Variance model: Two-component variance function +#> +#> Mean of starting values for individual parameters: +#> parent_0 log_k_parent +#> 97.849556 -4.455036 +#> +#> Fixed degradation parameter values: +#> None +#> +#> Results: +#> +#> AIC BIC logLik +#> 555.792 570.7908 -271.896 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> lower est. upper +#> parent_0 94.701336 97.763446 100.82556 +#> log_k_parent -5.007574 -4.461767 -3.91596 +#> +#> Correlation: +#> prnt_0 +#> log_k_parent 0.024 +#> +#> Backtransformed parameters with asymmetric confidence intervals: +#> lower est. upper +#> parent_0 94.701335804 97.76344625 100.82555670 +#> k_parent 0.006687109 0.01154195 0.01992142 +#> Random effects: +#> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) +#> Level: ds +#> Structure: Diagonal +#> parent_0 log_k_parent Residual +#> StdDev: 16.65969 3.516961 5.709013 +#> +#> Variance function: +#> Structure: Constant plus proportion of variance covariate +#> Formula: ~fitted(.) +#> Parameter estimates: +#> const prop +#> 1.55075176 0.05680853 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 60.05 199.5 +#> +#> Data: +#> ds name time observed predicted residual std standardized +#> ds 1 parent 0 103.6 97.42 6.17540 5.748 1.074413 +#> ds 1 parent 0 95.9 97.42 -1.52460 5.748 -0.265253 +#> ds 1 parent 1 95.4 96.72 -1.31719 5.709 -0.230721 +#> ds 1 parent 1 95.3 96.72 -1.41719 5.709 -0.248237 +#> ds 1 parent 3 91.6 95.32 -3.71774 5.633 -0.660046 +#> ds 1 parent 3 94.5 95.32 -0.81774 5.633 -0.145181 +#> ds 1 parent 7 88.1 92.58 -4.47930 5.483 -0.816920 +#> ds 1 parent 7 89.6 92.58 -2.97930 5.483 -0.543355 +#> ds 1 parent 14 90.3 87.97 2.32502 5.233 0.444318 +#> ds 1 parent 14 96.0 87.97 8.02502 5.233 1.533602 +#> ds 1 parent 28 80.2 79.44 0.75809 4.772 0.158862 +#> ds 1 parent 28 77.9 79.44 -1.54191 4.772 -0.323118 +#> ds 1 parent 60 59.3 62.92 -3.61742 3.896 -0.928458 +#> ds 1 parent 60 59.6 62.92 -3.31742 3.896 -0.851459 +#> ds 1 parent 90 59.4 50.56 8.83825 3.264 2.707613 +#> ds 1 parent 90 51.0 50.56 0.43825 3.264 0.134260 +#> ds 1 parent 120 38.8 40.63 -1.83247 2.781 -0.658968 +#> ds 1 parent 120 38.9 40.63 -1.73247 2.781 -0.623007 +#> ds 2 parent 0 103.2 97.17 6.02995 5.734 1.051655 +#> ds 2 parent 0 95.1 97.17 -2.07005 5.734 -0.361027 +#> ds 2 parent 1 88.3 95.59 -7.28901 5.647 -1.290694 +#> ds 2 parent 1 102.4 95.59 6.81099 5.647 1.206048 +#> ds 2 parent 3 88.4 92.50 -4.10371 5.479 -0.748984 +#> ds 2 parent 3 95.2 92.50 2.69629 5.479 0.492110 +#> ds 2 parent 7 83.5 86.63 -3.12863 5.160 -0.606349 +#> ds 2 parent 7 96.4 86.63 9.77137 5.160 1.893751 +#> ds 2 parent 14 77.3 77.23 0.06920 4.653 0.014871 +#> ds 2 parent 14 76.0 77.23 -1.23080 4.653 -0.264497 +#> ds 2 parent 28 61.7 61.38 0.31692 3.816 0.083043 +#> ds 2 parent 28 56.5 61.38 -4.88308 3.816 -1.279513 +#> ds 2 parent 60 35.1 36.31 -1.21343 2.581 -0.470178 +#> ds 2 parent 60 32.2 36.31 -4.11343 2.581 -1.593868 +#> ds 2 parent 90 21.2 22.20 -0.99906 1.999 -0.499832 +#> ds 2 parent 90 23.3 22.20 1.10094 1.999 0.550800 +#> ds 2 parent 120 14.1 13.57 0.52931 1.732 0.305638 +#> ds 2 parent 120 16.9 13.57 3.32931 1.732 1.922443 +#> ds 3 parent 0 92.4 94.12 -1.71979 5.567 -0.308917 +#> ds 3 parent 0 94.0 94.12 -0.11979 5.567 -0.021517 +#> ds 3 parent 1 95.7 91.97 3.72634 5.450 0.683712 +#> ds 3 parent 1 90.8 91.97 -1.17366 5.450 -0.215343 +#> ds 3 parent 3 86.7 87.83 -1.12709 5.225 -0.215720 +#> ds 3 parent 3 85.8 87.83 -2.02709 5.225 -0.387976 +#> ds 3 parent 7 77.1 80.09 -2.98635 4.807 -0.621300 +#> ds 3 parent 7 81.5 80.09 1.41365 4.807 0.294104 +#> ds 3 parent 14 69.1 68.15 0.95467 4.170 0.228922 +#> ds 3 parent 14 62.4 68.15 -5.74533 4.170 -1.377682 +#> ds 3 parent 28 49.1 49.34 -0.23911 3.203 -0.074644 +#> ds 3 parent 28 47.2 49.34 -2.13911 3.203 -0.667787 +#> ds 3 parent 60 21.9 23.58 -1.68477 2.049 -0.822090 +#> ds 3 parent 60 23.6 23.58 0.01523 2.049 0.007431 +#> ds 3 parent 90 12.4 11.81 0.59388 1.690 0.351500 +#> ds 3 parent 90 13.8 11.81 1.99388 1.690 1.180112 +#> ds 3 parent 120 4.9 5.91 -1.00993 1.587 -0.636506 +#> ds 3 parent 120 7.5 5.91 1.59007 1.587 1.002137 +#> ds 4 parent 0 91.8 101.72 -9.92097 5.983 -1.658171 +#> ds 4 parent 0 104.6 101.72 2.87903 5.983 0.481194 +#> ds 4 parent 1 117.5 101.27 16.23017 5.958 2.723944 +#> ds 4 parent 1 99.3 101.27 -1.96983 5.958 -0.330602 +#> ds 4 parent 3 94.0 100.37 -6.37355 5.909 -1.078583 +#> ds 4 parent 3 98.7 100.37 -1.67355 5.909 -0.283212 +#> ds 4 parent 7 109.2 98.60 10.59529 5.812 1.822915 +#> ds 4 parent 7 89.2 98.60 -9.40471 5.812 -1.618075 +#> ds 4 parent 14 103.3 95.58 7.71609 5.647 1.366386 +#> ds 4 parent 14 103.0 95.58 7.41609 5.647 1.313261 +#> ds 4 parent 28 90.8 89.82 0.98290 5.333 0.184310 +#> ds 4 parent 28 88.7 89.82 -1.11710 5.333 -0.209477 +#> ds 4 parent 60 74.8 77.91 -3.10870 4.690 -0.662879 +#> ds 4 parent 60 75.3 77.91 -2.60870 4.690 -0.556262 +#> ds 4 parent 90 71.1 68.18 2.91738 4.172 0.699234 +#> ds 4 parent 90 78.0 68.18 9.81738 4.172 2.353017 +#> ds 4 parent 120 59.1 59.67 -0.57073 3.728 -0.153107 +#> ds 4 parent 120 53.8 59.67 -5.87073 3.728 -1.574902 +#> ds 5 parent 0 94.9 98.38 -3.48183 5.800 -0.600307 +#> ds 5 parent 0 101.8 98.38 3.41817 5.800 0.589332 +#> ds 5 parent 1 96.1 96.75 -0.65141 5.711 -0.114065 +#> ds 5 parent 1 97.1 96.75 0.34859 5.711 0.061040 +#> ds 5 parent 3 93.8 93.57 0.22881 5.537 0.041323 +#> ds 5 parent 3 85.8 93.57 -7.77119 5.537 -1.403444 +#> ds 5 parent 7 87.6 87.52 0.07909 5.208 0.015186 +#> ds 5 parent 7 94.0 87.52 6.47909 5.208 1.244026 +#> ds 5 parent 14 82.5 77.86 4.64101 4.687 0.990182 +#> ds 5 parent 14 81.7 77.86 3.84101 4.687 0.819498 +#> ds 5 parent 28 60.0 61.62 -1.61729 3.829 -0.422433 +#> ds 5 parent 28 61.0 61.62 -0.61729 3.829 -0.161236 +#> ds 5 parent 60 32.5 36.10 -3.59608 2.571 -1.398750 +#> ds 5 parent 60 35.5 36.10 -0.59608 2.571 -0.231854 +#> ds 5 parent 90 21.8 21.86 -0.06415 1.987 -0.032287 +#> ds 5 parent 90 24.4 21.86 2.53585 1.987 1.276317 +#> ds 5 parent 120 14.1 13.24 0.85643 1.724 0.496877 +#> ds 5 parent 120 12.1 13.24 -1.14357 1.724 -0.663473</div><div class='input'> +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav 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