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Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 957 |
1 files changed, 41 insertions, 916 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 4ed354f0..bd691770 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -9,17 +9,17 @@ <title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title> <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" /> <!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> <!-- sticky kit --> <script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> @@ -48,7 +48,8 @@ <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -64,14 +65,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.47.6</span> </span> </div> @@ -136,7 +138,7 @@ <p>This function uses the Flexible Modelling Environment package <code>FME</code> to create a function calculating the model cost, i.e. the deviation between the kinetic model and the observed data. This model cost is - then minimised using the Port algorithm <code>nlminb</code>, + then minimised using the Port algorithm <code><a href='https://www.rdocumentation.org/packages/stats/topics/nlminb'>nlminb</a></code>, using the specified initial or fixed parameters and starting values. Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators. @@ -150,19 +152,19 @@ <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'>names</span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>), <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Port"</span>, <span class='st'>"Marq"</span>, <span class='st'>"SANN"</span>, <span class='st'>"Nelder-Mead"</span>, <span class='st'>"BFGS"</span>, <span class='st'>"CG"</span>, <span class='st'>"L-BFGS-B"</span>), + <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Port"</span>, <span class='st'>"Marq"</span>, <span class='st'>"SANN"</span>, <span class='st'>"Nelder-Mead"</span>, <span class='st'>"BFGS"</span>, <span class='st'>"CG"</span>, <span class='st'>"L-BFGS-B"</span>), <span class='kw'>maxit.modFit</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>control.modFit</span> <span class='kw'>=</span> <span class='fu'>list</span>(), + <span class='kw'>control.modFit</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(), <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>weight</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"none"</span>, <span class='st'>"manual"</span>, <span class='st'>"std"</span>, <span class='st'>"mean"</span>, <span class='st'>"tc"</span>), - <span class='kw'>tc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>sigma_low</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>rsd_high</span> <span class='kw'>=</span> <span class='fl'>0.07</span>), + <span class='kw'>weight</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"none"</span>, <span class='st'>"manual"</span>, <span class='st'>"std"</span>, <span class='st'>"mean"</span>, <span class='st'>"tc"</span>), + <span class='kw'>tc</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>sigma_low</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>rsd_high</span> <span class='kw'>=</span> <span class='fl'>0.07</span>), <span class='kw'>scaleVar</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, @@ -406,7 +408,7 @@ <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> -<p>Comparisons of models fitted to the same data can be made using <code>AIC</code> +<p>Comparisons of models fitted to the same data can be made using <code><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></code> by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p> <p>Fitting of several models to several datasets in a single call to <code><a href='mmkin.html'>mmkin</a></code>.</p></div> @@ -433,914 +435,40 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 -#> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 12:27:59 2018 -#> Date of summary: Mon Nov 26 12:27:59 2018 -#> -#> Equations: -#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent -#> -#> Model predictions using solution type analytical -#> -#> Fitted with method Port using 64 model solutions performed in 0.155 s -#> -#> Weighting: none -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 85.1 state -#> alpha 1.0 deparm -#> beta 10.0 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 85.100000 -Inf Inf -#> log_alpha 0.000000 -Inf Inf -#> log_beta 2.302585 -Inf Inf -#> -#> Fixed parameter values: -#> None -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 85.87000 2.2460 80.38000 91.3700 -#> log_alpha 0.05192 0.1605 -0.34080 0.4446 -#> log_beta 0.65100 0.2801 -0.03452 1.3360 -#> -#> Parameter correlation: -#> parent_0 log_alpha log_beta -#> parent_0 1.0000 -0.2033 -0.3624 -#> log_alpha -0.2033 1.0000 0.9547 -#> log_beta -0.3624 0.9547 1.0000 -#> -#> Residual standard error: 2.275 on 6 degrees of freedom -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 85.870 38.230 1.069e-08 80.3800 91.370 -#> alpha 1.053 6.231 3.953e-04 0.7112 1.560 -#> beta 1.917 3.570 5.895e-03 0.9661 3.806 -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.657 3 6 -#> parent 6.657 3 6 -#> -#> Estimated disappearance times: -#> DT50 DT90 DT50back -#> parent 1.785 15.15 4.56 -#> -#> Data: -#> time variable observed predicted residual -#> 0 parent 85.1 85.875 -0.7749 -#> 1 parent 57.9 55.191 2.7091 -#> 3 parent 29.9 31.845 -1.9452 -#> 7 parent 14.6 17.012 -2.4124 -#> 14 parent 9.7 9.241 0.4590 -#> 28 parent 6.6 4.754 1.8460 -#> 63 parent 4.0 2.102 1.8977 -#> 91 parent 3.9 1.441 2.4590 -#> 119 parent 0.6 1.092 -0.4919</div><div class='input'> +<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'> <span class='co'># One parent compound, one metabolite, both single first order.</span> <span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span> <span class='no'>SFO_SFO</span> <span class='kw'><-</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'>"m1"</span>), - <span class='kw'>m1</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'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> User System verstrichen -#> 1.002 0.000 1.003 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff -#> parent_sink parent_m1 m1_sink -#> 0.485524 0.514476 1.000000 -#> -#> $SFORB -#> logical(0) -#> -#> $distimes -#> DT50 DT90 -#> parent 7.022929 23.32967 -#> m1 131.760712 437.69961 -#> </div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> -<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> Model cost at call 1 : 18915.53 -#> Model cost at call 2 : 18915.53 -#> Model cost at call 6 : 11424.02 -#> Model cost at call 10 : 11424 -#> Model cost at call 12 : 4094.396 -#> Model cost at call 16 : 4094.396 -#> Model cost at call 19 : 1340.595 -#> Model cost at call 20 : 1340.593 -#> Model cost at call 25 : 1072.239 -#> Model cost at call 28 : 1072.236 -#> Model cost at call 30 : 874.2615 -#> Model cost at call 33 : 874.2611 -#> Model cost at call 35 : 616.2377 -#> Model cost at call 37 : 616.2372 -#> Model cost at call 40 : 467.4386 -#> Model cost at call 42 : 467.4381 -#> Model cost at call 46 : 398.2914 -#> Model cost at call 48 : 398.2914 -#> Model cost at call 49 : 398.2913 -#> Model cost at call 51 : 395.0712 -#> Model cost at call 54 : 395.0711 -#> Model cost at call 56 : 378.3298 -#> Model cost at call 59 : 378.3298 -#> Model cost at call 62 : 376.9812 -#> Model cost at call 64 : 376.9811 -#> Model cost at call 67 : 375.2085 -#> Model cost at call 69 : 375.2085 -#> Model cost at call 70 : 375.2085 -#> Model cost at call 71 : 375.2085 -#> Model cost at call 72 : 374.5723 -#> Model cost at call 74 : 374.5723 -#> Model cost at call 77 : 374.0075 -#> Model cost at call 79 : 374.0075 -#> Model cost at call 80 : 374.0075 -#> Model cost at call 82 : 373.1711 -#> Model cost at call 84 : 373.1711 -#> Model cost at call 87 : 372.6445 -#> Model cost at call 88 : 372.1614 -#> Model cost at call 90 : 372.1614 -#> Model cost at call 91 : 372.1614 -#> Model cost at call 94 : 371.6464 -#> Model cost at call 99 : 371.4299 -#> Model cost at call 101 : 371.4299 -#> Model cost at call 104 : 371.4071 -#> Model cost at call 106 : 371.4071 -#> Model cost at call 107 : 371.4071 -#> Model cost at call 109 : 371.2524 -#> Model cost at call 113 : 371.2524 -#> Model cost at call 114 : 371.2136 -#> Model cost at call 115 : 371.2136 -#> Model cost at call 116 : 371.2136 -#> Model cost at call 119 : 371.2134 -#> Model cost at call 120 : 371.2134 -#> Model cost at call 122 : 371.2134 -#> Model cost at call 123 : 371.2134 -#> Model cost at call 125 : 371.2134 -#> Model cost at call 126 : 371.2134 -#> Model cost at call 135 : 371.2134 -#> Model cost at call 146 : 371.2134 -#> Optimisation by method Port successfully terminated. -#> User System verstrichen -#> 0.794 0.000 0.793 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff -#> parent_sink parent_m1 m1_sink -#> 0.485524 0.514476 1.000000 -#> -#> $SFORB -#> logical(0) -#> -#> $distimes -#> DT50 DT90 -#> parent 7.022929 23.32967 -#> m1 131.760711 437.69961 -#> </div><div class='input'> + <span class='kw'>m1</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'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in coef(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in endpoints(fit): konnte Funktion "endpoints" nicht finden</span></div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve"): konnte Funktion "mkinfit" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> <span class='error'>Error in coef(fit.deSolve): Objekt 'fit.deSolve' nicht gefunden</span></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> <span class='error'>Error in endpoints(fit.deSolve): konnte Funktion "endpoints" nicht finden</span></div><div class='input'> # Use stepwise fitting, using optimised parameters from parent only fit, FOMC </div><div class='input'><span class='no'>FOMC_SFO</span> <span class='kw'><-</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'>"FOMC"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</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'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='co'># Use starting parameters from parent only FOMC fit</span> -<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>) - + <span class='kw'>m1</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'>#> <span class='error'>Error in mkinmod(parent = mkinsub("FOMC", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='co'># Use starting parameters from parent only FOMC fit</span> +<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span> <span class='no'>SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( - <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFORB"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span> -<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='input'> + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFORB"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFORB", to = "m1", sink = TRUE), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span> +<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> </div><div class='input'><span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</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'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 -#> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 12:28:11 2018 -#> Date of summary: Mon Nov 26 12:28:11 2018 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -#> -#> Model predictions using solution type deSolve -#> -#> Fitted with method Port using 186 model solutions performed in 0.824 s -#> -#> Weighting: none -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> m1_0 0 state -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.60000 1.61400 96.3300 102.9000 -#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 -#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 -#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 -#> parent_0 1.0000 0.5178 -0.1701 -0.5489 -#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 -#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 -#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000 -#> -#> Residual standard error: 3.211 on 36 degrees of freedom -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 -#> k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01 -#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 -#> f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01 -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.398 4 15 -#> parent 6.459 2 7 -#> m1 4.690 2 8 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.5145 -#> parent_sink 0.4855 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 7.023 23.33 -#> m1 131.761 437.70 -#> -#> Data: -#> time variable observed predicted residual -#> 0 parent 99.46 99.59848 -1.385e-01 -#> 0 parent 102.04 99.59848 2.442e+00 -#> 1 parent 93.50 90.23787 3.262e+00 -#> 1 parent 92.50 90.23787 2.262e+00 -#> 3 parent 63.23 74.07319 -1.084e+01 -#> 3 parent 68.99 74.07319 -5.083e+00 -#> 7 parent 52.32 49.91206 2.408e+00 -#> 7 parent 55.13 49.91206 5.218e+00 -#> 14 parent 27.27 25.01257 2.257e+00 -#> 14 parent 26.64 25.01257 1.627e+00 -#> 21 parent 11.50 12.53462 -1.035e+00 -#> 21 parent 11.64 12.53462 -8.946e-01 -#> 35 parent 2.85 3.14787 -2.979e-01 -#> 35 parent 2.91 3.14787 -2.379e-01 -#> 50 parent 0.69 0.71624 -2.624e-02 -#> 50 parent 0.63 0.71624 -8.624e-02 -#> 75 parent 0.05 0.06074 -1.074e-02 -#> 75 parent 0.06 0.06074 -7.381e-04 -#> 0 m1 0.00 0.00000 0.000e+00 -#> 0 m1 0.00 0.00000 0.000e+00 -#> 1 m1 4.84 4.80296 3.704e-02 -#> 1 m1 5.64 4.80296 8.370e-01 -#> 3 m1 12.91 13.02400 -1.140e-01 -#> 3 m1 12.96 13.02400 -6.400e-02 -#> 7 m1 22.97 25.04476 -2.075e+00 -#> 7 m1 24.47 25.04476 -5.748e-01 -#> 14 m1 41.69 36.69002 5.000e+00 -#> 14 m1 33.21 36.69002 -3.480e+00 -#> 21 m1 44.37 41.65310 2.717e+00 -#> 21 m1 46.44 41.65310 4.787e+00 -#> 35 m1 41.22 43.31312 -2.093e+00 -#> 35 m1 37.95 43.31312 -5.363e+00 -#> 50 m1 41.19 41.21831 -2.831e-02 -#> 50 m1 40.01 41.21831 -1.208e+00 -#> 75 m1 40.09 36.44703 3.643e+00 -#> 75 m1 33.85 36.44703 -2.597e+00 -#> 100 m1 31.04 31.98163 -9.416e-01 -#> 100 m1 33.13 31.98163 1.148e+00 -#> 120 m1 25.15 28.78984 -3.640e+00 -#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 -#> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 12:28:13 2018 -#> Date of summary: Mon Nov 26 12:28:13 2018 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -#> -#> Model predictions using solution type deSolve -#> -#> Fitted with method Port using 551 model solutions performed in 2.458 s -#> -#> Weighting: none -#> -#> Iterative reweighting with method obs -#> Final mean squared residuals of observed variables: -#> parent m1 -#> 11.573407 7.407845 -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> m1_0 0 state -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.67000 1.79200 96.04000 103.300 -#> log_k_parent -2.31200 0.04560 -2.40400 -2.219 -#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 -#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 -#> parent_0 1.0000 0.5083 -0.1979 -0.6148 -#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 -#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 -#> f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000 -#> -#> Residual standard error: 1.054 on 36 degrees of freedom -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 99.67000 55.630 8.185e-37 96.040000 1.033e+02 -#> k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01 -#> k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03 -#> f_parent_to_m1 0.51340 23.000 2.038e-23 0.468100 5.584e-01 -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.399 4 15 -#> parent 6.466 2 7 -#> m1 4.679 2 8 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.5134 -#> parent_sink 0.4866 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 6.997 23.24 -#> m1 132.282 439.43 -#> -#> Data: -#> time variable observed predicted residual err -#> 0 parent 99.46 99.67218 -2.122e-01 3.402 -#> 0 parent 102.04 99.67218 2.368e+00 3.402 -#> 1 parent 93.50 90.27153 3.228e+00 3.402 -#> 1 parent 92.50 90.27153 2.228e+00 3.402 -#> 3 parent 63.23 74.04648 -1.082e+01 3.402 -#> 3 parent 68.99 74.04648 -5.056e+00 3.402 -#> 7 parent 52.32 49.82092 2.499e+00 3.402 -#> 7 parent 55.13 49.82092 5.309e+00 3.402 -#> 14 parent 27.27 24.90288 2.367e+00 3.402 -#> 14 parent 26.64 24.90288 1.737e+00 3.402 -#> 21 parent 11.50 12.44765 -9.476e-01 3.402 -#> 21 parent 11.64 12.44765 -8.076e-01 3.402 -#> 35 parent 2.85 3.11002 -2.600e-01 3.402 -#> 35 parent 2.91 3.11002 -2.000e-01 3.402 -#> 50 parent 0.69 0.70374 -1.374e-02 3.402 -#> 50 parent 0.63 0.70374 -7.374e-02 3.402 -#> 75 parent 0.05 0.05913 -9.134e-03 3.402 -#> 75 parent 0.06 0.05913 8.662e-04 3.402 -#> 0 m1 0.00 0.00000 0.000e+00 2.722 -#> 0 m1 0.00 0.00000 0.000e+00 2.722 -#> 1 m1 4.84 4.81328 2.672e-02 2.722 -#> 1 m1 5.64 4.81328 8.267e-01 2.722 -#> 3 m1 12.91 13.04779 -1.378e-01 2.722 -#> 3 m1 12.96 13.04779 -8.779e-02 2.722 -#> 7 m1 22.97 25.07615 -2.106e+00 2.722 -#> 7 m1 24.47 25.07615 -6.062e-01 2.722 -#> 14 m1 41.69 36.70729 4.983e+00 2.722 -#> 14 m1 33.21 36.70729 -3.497e+00 2.722 -#> 21 m1 44.37 41.65050 2.720e+00 2.722 -#> 21 m1 46.44 41.65050 4.790e+00 2.722 -#> 35 m1 41.22 43.28866 -2.069e+00 2.722 -#> 35 m1 37.95 43.28866 -5.339e+00 2.722 -#> 50 m1 41.19 41.19339 -3.386e-03 2.722 -#> 50 m1 40.01 41.19339 -1.183e+00 2.722 -#> 75 m1 40.09 36.43820 3.652e+00 2.722 -#> 75 m1 33.85 36.43820 -2.588e+00 2.722 -#> 100 m1 31.04 31.98971 -9.497e-01 2.722 -#> 100 m1 33.13 31.98971 1.140e+00 2.722 -#> 120 m1 25.15 28.80898 -3.659e+00 2.722 -#> 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 -#> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 12:28:14 2018 -#> Date of summary: Mon Nov 26 12:28:14 2018 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -#> -#> Model predictions using solution type deSolve -#> -#> Fitted with method Port using 155 model solutions performed in 0.69 s -#> -#> Weighting: mean -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> m1_0 0 state -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.7300 1.93200 95.81000 103.6000 -#> log_k_parent -2.3090 0.04837 -2.40700 -2.2110 -#> log_k_m1 -5.2550 0.12070 -5.49900 -5.0100 -#> f_parent_ilr_1 0.0354 0.06344 -0.09327 0.1641 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 -#> parent_0 1.0000 0.5004 -0.2143 -0.6514 -#> log_k_parent 0.5004 1.0000 -0.4282 -0.6383 -#> log_k_m1 -0.2143 -0.4282 1.0000 0.7390 -#> f_parent_ilr_1 -0.6514 -0.6383 0.7390 1.0000 -#> -#> Residual standard error: 0.09829 on 36 degrees of freedom -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 99.730000 51.630 1.166e-35 95.81000 1.036e+02 -#> k_parent 0.099360 20.670 7.304e-22 0.09007 1.096e-01 -#> k_m1 0.005224 8.287 3.649e-10 0.00409 6.672e-03 -#> f_parent_to_m1 0.512500 22.860 2.497e-23 0.46710 5.578e-01 -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.401 4 15 -#> parent 6.473 2 7 -#> m1 4.671 2 8 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.5125 -#> parent_sink 0.4875 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 6.976 23.18 -#> m1 132.696 440.81 -#> -#> Data: -#> time variable observed predicted residual -#> 0 parent 99.46 99.73057 -0.270570 -#> 0 parent 102.04 99.73057 2.309430 -#> 1 parent 93.50 90.29805 3.201945 -#> 1 parent 92.50 90.29805 2.201945 -#> 3 parent 63.23 74.02503 -10.795028 -#> 3 parent 68.99 74.02503 -5.035028 -#> 7 parent 52.32 49.74838 2.571618 -#> 7 parent 55.13 49.74838 5.381618 -#> 14 parent 27.27 24.81588 2.454124 -#> 14 parent 26.64 24.81588 1.824124 -#> 21 parent 11.50 12.37885 -0.878849 -#> 21 parent 11.64 12.37885 -0.738849 -#> 35 parent 2.85 3.08022 -0.230219 -#> 35 parent 2.91 3.08022 -0.170219 -#> 50 parent 0.69 0.69396 -0.003958 -#> 50 parent 0.63 0.69396 -0.063958 -#> 75 parent 0.05 0.05789 -0.007888 -#> 75 parent 0.06 0.05789 0.002112 -#> 0 m1 0.00 0.00000 0.000000 -#> 0 m1 0.00 0.00000 0.000000 -#> 1 m1 4.84 4.82149 0.018512 -#> 1 m1 5.64 4.82149 0.818512 -#> 3 m1 12.91 13.06669 -0.156692 -#> 3 m1 12.96 13.06669 -0.106692 -#> 7 m1 22.97 25.10106 -2.131058 -#> 7 m1 24.47 25.10106 -0.631058 -#> 14 m1 41.69 36.72092 4.969077 -#> 14 m1 33.21 36.72092 -3.510923 -#> 21 m1 44.37 41.64835 2.721647 -#> 21 m1 46.44 41.64835 4.791647 -#> 35 m1 41.22 43.26923 -2.049225 -#> 35 m1 37.95 43.26923 -5.319225 -#> 50 m1 41.19 41.17364 0.016361 -#> 50 m1 40.01 41.17364 -1.163639 -#> 75 m1 40.09 36.43122 3.658776 -#> 75 m1 33.85 36.43122 -2.581224 -#> 100 m1 31.04 31.99612 -0.956124 -#> 100 m1 33.13 31.99612 1.133876 -#> 120 m1 25.15 28.82413 -3.674128 -#> 120 m1 33.31 28.82413 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 -#> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 12:28:15 2018 -#> Date of summary: Mon Nov 26 12:28:15 2018 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -#> -#> Model predictions using solution type deSolve -#> -#> Fitted with method Port using 174 model solutions performed in 0.774 s -#> -#> Weighting: manual -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> m1_0 0 state -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.6600 2.712000 94.14000 105.2000 -#> log_k_parent -2.2980 0.008118 -2.31500 -2.2820 -#> log_k_m1 -5.2410 0.096690 -5.43800 -5.0450 -#> f_parent_ilr_1 0.0231 0.057990 -0.09474 0.1409 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 -#> parent_0 1.00000 0.6843 -0.08687 -0.7564 -#> log_k_parent 0.68435 1.0000 -0.12695 -0.5812 -#> log_k_m1 -0.08687 -0.1269 1.00000 0.5195 -#> f_parent_ilr_1 -0.75644 -0.5812 0.51952 1.0000 -#> -#> Residual standard error: 0.08396 on 34 degrees of freedom -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 99.660000 36.75 2.957e-29 94.14000 1.052e+02 -#> k_parent 0.100400 123.20 5.927e-47 0.09878 1.021e-01 -#> k_m1 0.005295 10.34 2.447e-12 0.00435 6.444e-03 -#> f_parent_to_m1 0.508200 24.79 1.184e-23 0.46660 5.497e-01 -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.461 4 15 -#> parent 6.520 2 7 -#> m1 4.744 2 8 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.5082 -#> parent_sink 0.4918 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 6.902 22.93 -#> m1 130.916 434.89 -#> -#> Data: -#> time variable observed predicted residual err -#> 0 parent 99.46 99.65571 -0.195715 99.46 -#> 0 parent 102.04 99.65571 2.384285 102.04 -#> 1 parent 93.50 90.13383 3.366170 93.50 -#> 1 parent 92.50 90.13383 2.366170 92.50 -#> 3 parent 63.23 73.73252 -10.502518 63.23 -#> 3 parent 68.99 73.73252 -4.742518 68.99 -#> 7 parent 52.32 49.34027 2.979728 52.32 -#> 7 parent 55.13 49.34027 5.789728 55.13 -#> 14 parent 27.27 24.42873 2.841271 27.27 -#> 14 parent 26.64 24.42873 2.211271 26.64 -#> 21 parent 11.50 12.09484 -0.594842 11.50 -#> 21 parent 11.64 12.09484 -0.454842 11.64 -#> 35 parent 2.85 2.96482 -0.114824 2.85 -#> 35 parent 2.91 2.96482 -0.054824 2.91 -#> 50 parent 0.69 0.65733 0.032670 0.69 -#> 50 parent 0.63 0.65733 -0.027330 0.63 -#> 75 parent 0.05 0.05339 -0.003386 0.05 -#> 75 parent 0.06 0.05339 0.006614 0.06 -#> 1 m1 4.84 4.82570 0.014301 4.84 -#> 1 m1 5.64 4.82570 0.814301 5.64 -#> 3 m1 12.91 13.06402 -0.154020 12.91 -#> 3 m1 12.96 13.06402 -0.104020 12.96 -#> 7 m1 22.97 25.04656 -2.076564 22.97 -#> 7 m1 24.47 25.04656 -0.576564 24.47 -#> 14 m1 41.69 36.53601 5.153988 41.69 -#> 14 m1 33.21 36.53601 -3.326012 33.21 -#> 21 m1 44.37 41.34639 3.023609 44.37 -#> 21 m1 46.44 41.34639 5.093609 46.44 -#> 35 m1 41.22 42.82669 -1.606690 41.22 -#> 35 m1 37.95 42.82669 -4.876690 37.95 -#> 50 m1 41.19 40.67342 0.516578 41.19 -#> 50 m1 40.01 40.67342 -0.663422 40.01 -#> 75 m1 40.09 35.91105 4.178947 40.09 -#> 75 m1 33.85 35.91105 -2.061053 33.85 -#> 100 m1 31.04 31.48161 -0.441612 31.04 -#> 100 m1 33.13 31.48161 1.648388 33.13 -#> 120 m1 25.15 28.32018 -3.170181 25.15 -#> 120 m1 33.31 28.32018 4.989819 33.31</div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.noweight): Objekt 'f.noweight' nicht gefunden</span></div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.irls): Objekt 'f.irls' nicht gefunden</span></div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.w.mean): Objekt 'f.w.mean' nicht gefunden</span></div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.w.value): Objekt 'f.w.value' nicht gefunden</span></div><div class='input'> </div><div class='input'><span class='co'># Manual weighting</span> <span class='no'>dw</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> -<span class='no'>errors</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>) +<span class='no'>errors</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'><-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>] -<span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 -#> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 12:28:16 2018 -#> Date of summary: Mon Nov 26 12:28:16 2018 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -#> -#> Model predictions using solution type deSolve -#> -#> Fitted with method Port using 270 model solutions performed in 1.205 s -#> -#> Weighting: manual -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> m1_0 0 state -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.49000 1.33200 96.7800 102.2000 -#> log_k_parent -2.32100 0.03550 -2.3930 -2.2490 -#> log_k_m1 -5.24100 0.21280 -5.6730 -4.8100 -#> f_parent_ilr_1 0.04571 0.08966 -0.1361 0.2275 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 -#> parent_0 1.00000 0.5312 -0.09456 -0.3351 -#> log_k_parent 0.53123 1.0000 -0.17800 -0.3360 -#> log_k_m1 -0.09456 -0.1780 1.00000 0.7616 -#> f_parent_ilr_1 -0.33514 -0.3360 0.76156 1.0000 -#> -#> Residual standard error: 2.628 on 36 degrees of freedom -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 99.490000 74.69 2.221e-41 96.780000 1.022e+02 -#> k_parent 0.098140 28.17 2.012e-26 0.091320 1.055e-01 -#> k_m1 0.005292 4.70 1.873e-05 0.003437 8.148e-03 -#> f_parent_to_m1 0.516200 16.30 1.686e-18 0.452000 5.798e-01 -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.400 4 15 -#> parent 6.454 2 7 -#> m1 4.708 2 8 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.5162 -#> parent_sink 0.4838 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 7.063 23.46 -#> m1 130.971 435.08 -#> -#> Data: -#> time variable observed predicted residual err -#> 0 parent 99.46 99.48598 -0.025979 1 -#> 0 parent 102.04 99.48598 2.554021 1 -#> 1 parent 93.50 90.18612 3.313880 1 -#> 1 parent 92.50 90.18612 2.313880 1 -#> 3 parent 63.23 74.11316 -10.883163 1 -#> 3 parent 68.99 74.11316 -5.123163 1 -#> 7 parent 52.32 50.05030 2.269705 1 -#> 7 parent 55.13 50.05030 5.079705 1 -#> 14 parent 27.27 25.17975 2.090250 1 -#> 14 parent 26.64 25.17975 1.460250 1 -#> 21 parent 11.50 12.66765 -1.167654 1 -#> 21 parent 11.64 12.66765 -1.027654 1 -#> 35 parent 2.85 3.20616 -0.356164 1 -#> 35 parent 2.91 3.20616 -0.296164 1 -#> 50 parent 0.69 0.73562 -0.045619 1 -#> 50 parent 0.63 0.73562 -0.105619 1 -#> 75 parent 0.05 0.06326 -0.013256 1 -#> 75 parent 0.06 0.06326 -0.003256 1 -#> 0 m1 0.00 0.00000 0.000000 2 -#> 0 m1 0.00 0.00000 0.000000 2 -#> 1 m1 4.84 4.78729 0.052713 2 -#> 1 m1 5.64 4.78729 0.852713 2 -#> 3 m1 12.91 12.98785 -0.077848 2 -#> 3 m1 12.96 12.98785 -0.027848 2 -#> 7 m1 22.97 24.99695 -2.026946 2 -#> 7 m1 24.47 24.99695 -0.526946 2 -#> 14 m1 41.69 36.66353 5.026472 2 -#> 14 m1 33.21 36.66353 -3.453528 2 -#> 21 m1 44.37 41.65681 2.713186 2 -#> 21 m1 46.44 41.65681 4.783186 2 -#> 35 m1 41.22 43.35031 -2.130314 2 -#> 35 m1 37.95 43.35031 -5.400314 2 -#> 50 m1 41.19 41.25637 -0.066368 2 -#> 50 m1 40.01 41.25637 -1.246368 2 -#> 75 m1 40.09 36.46057 3.629429 2 -#> 75 m1 33.85 36.46057 -2.610571 2 -#> 100 m1 31.04 31.96929 -0.929293 2 -#> 100 m1 33.13 31.96929 1.160707 2 -#> 120 m1 25.15 28.76062 -3.610621 2 -#> 120 m1 33.31 28.76062 4.549379 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 -#> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 12:28:19 2018 -#> Date of summary: Mon Nov 26 12:28:19 2018 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -#> -#> Model predictions using solution type deSolve -#> -#> Fitted with method Port using 692 model solutions performed in 3.1 s -#> -#> Weighting: manual -#> -#> Iterative reweighting with method obs -#> Final mean squared residuals of observed variables: -#> parent m1 -#> 11.573406 7.407846 -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> m1_0 0 state -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.67000 1.79200 96.04000 103.300 -#> log_k_parent -2.31200 0.04560 -2.40400 -2.220 -#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 -#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 -#> parent_0 1.0000 0.5083 -0.1979 -0.6148 -#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 -#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 -#> f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000 -#> -#> Residual standard error: 1.054 on 36 degrees of freedom -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 99.67000 55.630 8.185e-37 96.040000 1.033e+02 -#> k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01 -#> k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03 -#> f_parent_to_m1 0.51340 23.000 2.039e-23 0.468100 5.584e-01 -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.399 4 15 -#> parent 6.466 2 7 -#> m1 4.679 2 8 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.5134 -#> parent_sink 0.4866 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 6.997 23.24 -#> m1 132.282 439.43 -#> -#> Data: -#> time variable observed predicted residual err.ini err -#> 0 parent 99.46 99.67217 -2.122e-01 1 3.402 -#> 0 parent 102.04 99.67217 2.368e+00 1 3.402 -#> 1 parent 93.50 90.27152 3.228e+00 1 3.402 -#> 1 parent 92.50 90.27152 2.228e+00 1 3.402 -#> 3 parent 63.23 74.04648 -1.082e+01 1 3.402 -#> 3 parent 68.99 74.04648 -5.056e+00 1 3.402 -#> 7 parent 52.32 49.82092 2.499e+00 1 3.402 -#> 7 parent 55.13 49.82092 5.309e+00 1 3.402 -#> 14 parent 27.27 24.90288 2.367e+00 1 3.402 -#> 14 parent 26.64 24.90288 1.737e+00 1 3.402 -#> 21 parent 11.50 12.44765 -9.477e-01 1 3.402 -#> 21 parent 11.64 12.44765 -8.077e-01 1 3.402 -#> 35 parent 2.85 3.11002 -2.600e-01 1 3.402 -#> 35 parent 2.91 3.11002 -2.000e-01 1 3.402 -#> 50 parent 0.69 0.70375 -1.375e-02 1 3.402 -#> 50 parent 0.63 0.70375 -7.375e-02 1 3.402 -#> 75 parent 0.05 0.05913 -9.134e-03 1 3.402 -#> 75 parent 0.06 0.05913 8.661e-04 1 3.402 -#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 -#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 -#> 1 m1 4.84 4.81328 2.672e-02 2 2.722 -#> 1 m1 5.64 4.81328 8.267e-01 2 2.722 -#> 3 m1 12.91 13.04779 -1.378e-01 2 2.722 -#> 3 m1 12.96 13.04779 -8.779e-02 2 2.722 -#> 7 m1 22.97 25.07615 -2.106e+00 2 2.722 -#> 7 m1 24.47 25.07615 -6.062e-01 2 2.722 -#> 14 m1 41.69 36.70729 4.983e+00 2 2.722 -#> 14 m1 33.21 36.70729 -3.497e+00 2 2.722 -#> 21 m1 44.37 41.65050 2.719e+00 2 2.722 -#> 21 m1 46.44 41.65050 4.789e+00 2 2.722 -#> 35 m1 41.22 43.28866 -2.069e+00 2 2.722 -#> 35 m1 37.95 43.28866 -5.339e+00 2 2.722 -#> 50 m1 41.19 41.19339 -3.387e-03 2 2.722 -#> 50 m1 40.01 41.19339 -1.183e+00 2 2.722 -#> 75 m1 40.09 36.43820 3.652e+00 2 2.722 -#> 75 m1 33.85 36.43820 -2.588e+00 2 2.722 -#> 100 m1 31.04 31.98971 -9.497e-01 2 2.722 -#> 100 m1 33.13 31.98971 1.140e+00 2 2.722 -#> 120 m1 25.15 28.80897 -3.659e+00 2 2.722 -#> 120 m1 33.31 28.80897 4.501e+00 2 2.722</div></pre> +<span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.w.man): Objekt 'f.w.man' nicht gefunden</span></div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE, reweight.method = "obs"): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.w.man.irls): Objekt 'f.w.man.irls' nicht gefunden</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -1361,9 +489,7 @@ </ul> <h2>Author</h2> - - Johannes Ranke - + <p>Johannes Ranke</p> </div> </div> @@ -1373,9 +499,8 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> - </footer> </div> |