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1 files changed, 18 insertions, 196 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index ffccd3d5..86ba7566 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.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>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • 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> @@ -40,7 +40,8 @@ <!-- 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> @@ -56,14 +57,15 @@ <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> @@ -153,192 +155,13 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), - <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), - <span class='kw'>anisole</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'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 12:27:54 2018 -#> Date of summary: Mon Nov 26 12:27:54 2018 -#> -#> Equations: -#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 -#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - -#> k_phenol_anisole * phenol -#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole -#> -#> Model predictions using solution type deSolve -#> -#> Fitted with method Port using 574 model solutions performed in 3.654 s -#> -#> Weighting: none -#> -#> Starting values for parameters to be optimised: -#> value type -#> T245_0 100.9000 state -#> k_T245_sink 0.1000 deparm -#> k_T245_phenol 0.1001 deparm -#> k_phenol_sink 0.1002 deparm -#> k_phenol_anisole 0.1003 deparm -#> k_anisole_sink 0.1004 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> T245_0 100.900000 -Inf Inf -#> log_k_T245_sink -2.302585 -Inf Inf -#> log_k_T245_phenol -2.301586 -Inf Inf -#> log_k_phenol_sink -2.300587 -Inf Inf -#> log_k_phenol_anisole -2.299590 -Inf Inf -#> log_k_anisole_sink -2.298593 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> phenol_0 0 state -#> anisole_0 0 state -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> T245_0 103.9000 NA NA NA -#> log_k_T245_sink -4.1130 NA NA NA -#> log_k_T245_phenol -3.6120 NA NA NA -#> log_k_phenol_sink -25.0800 NA NA NA -#> log_k_phenol_anisole -0.9037 NA NA NA -#> log_k_anisole_sink -5.0090 NA NA NA -#> -#> Parameter correlation:</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#> Could not estimate covariance matrix; singular system: -#> -#> Residual standard error: 2.78 on 18 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 -#> T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA -#> k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA -#> k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA -#> k_phenol_sink 1.286e-11 4.575e-11 5.000e-01 NA NA -#> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA -#> k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 10.070 6 16 -#> T245 7.908 3 5 -#> phenol 106.445 2 5 -#> anisole 5.379 1 6 -#> -#> Resulting formation fractions: -#> ff -#> T245_sink 3.772e-01 -#> T245_phenol 6.228e-01 -#> phenol_sink 3.175e-11 -#> phenol_anisole 1.000e+00 -#> anisole_sink 1.000e+00 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> T245 15.982 53.091 -#> phenol 1.711 5.685 -#> anisole 103.784 344.763</div><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span> + <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</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>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), + <span class='kw'>phenol</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>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), + <span class='kw'>anisole</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(T245 = list(type = "SFO", to = "phenol"), phenol = list(type = "SFO", to = "anisole"), anisole = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</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_SFO, subset(mccall81_245T, soil == "Commerce"), 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.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.1, data = FALSE): Objekt 'fit.1' nicht gefunden</span></div><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span> - <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), - <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), - <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 12:27:56 2018 -#> Date of summary: Mon Nov 26 12:27:56 2018 -#> -#> Equations: -#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 -#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - -#> k_phenol_anisole * phenol -#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole -#> -#> Model predictions using solution type deSolve -#> -#> Fitted with method Port using 246 model solutions performed in 1.629 s -#> -#> Weighting: none -#> -#> Starting values for parameters to be optimised: -#> value type -#> T245_0 100.9000 state -#> k_T245_sink 0.1000 deparm -#> k_T245_phenol 0.1001 deparm -#> k_phenol_anisole 0.1002 deparm -#> k_anisole_sink 0.1003 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> T245_0 100.900000 -Inf Inf -#> log_k_T245_sink -2.302585 -Inf Inf -#> log_k_T245_phenol -2.301586 -Inf Inf -#> log_k_phenol_anisole -2.300587 -Inf Inf -#> log_k_anisole_sink -2.299590 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> phenol_0 0 state -#> anisole_0 0 state -#> k_phenol_sink 0 deparm -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> T245_0 103.9000 2.35200 98.930 108.8000 -#> log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350 -#> log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070 -#> log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637 -#> log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750 -#> -#> Parameter correlation: -#> T245_0 log_k_T245_sink log_k_T245_phenol -#> T245_0 1.00000 0.63761 -0.1742 -#> log_k_T245_sink 0.63761 1.00000 -0.3831 -#> log_k_T245_phenol -0.17416 -0.38313 1.0000 -#> log_k_phenol_anisole -0.05948 0.08745 -0.3047 -#> log_k_anisole_sink -0.16208 -0.60469 0.5227 -#> log_k_phenol_anisole log_k_anisole_sink -#> T245_0 -0.05948 -0.1621 -#> log_k_T245_sink 0.08745 -0.6047 -#> log_k_T245_phenol -0.30470 0.5227 -#> log_k_phenol_anisole 1.00000 -0.1774 -#> log_k_anisole_sink -0.17744 1.0000 -#> -#> Residual standard error: 2.706 on 19 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 -#> T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000 -#> k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159 -#> k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999 -#> k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820 -#> k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844 -#> -#> Chi2 error levels in percent: -#> err.min n.optim df -#> All data 9.831 5 17 -#> T245 7.908 3 5 -#> phenol 99.808 1 6 -#> anisole 5.379 1 6 -#> -#> Resulting formation fractions: -#> ff -#> T245_sink 0.3772 -#> T245_phenol 0.6228 -#> phenol_anisole 1.0000 -#> phenol_sink 0.0000 -#> anisole_sink 1.0000 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> T245 15.982 53.091 -#> phenol 1.711 5.685 -#> anisole 103.784 344.763</div><div class='input'> </div></pre> + <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</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_SFO, subset(mccall81_245T, soil == "Commerce"), parms.ini = c(k_phenol_sink = 0), fixed_parms = "k_phenol_sink", 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.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.2, data = FALSE): Objekt 'fit.2' nicht gefunden</span></div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -360,9 +183,8 @@ </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> |