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diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 86ba7566..93d7f197 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -157,11 +157,190 @@ <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'><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='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='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'><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>) + <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'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:05 2019 +#> Date of summary: Thu Jan 31 16:51:05 2019 +#> +#> 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 3.87 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> <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'><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> + <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'><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'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:07 2019 +#> Date of summary: Thu Jan 31 16:51:07 2019 +#> +#> 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 1.618 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> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |