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| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-03-04 14:09:45 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-03-04 14:09:45 +0100 |
| commit | 9d6a975a0e3850a36889a18b5d9929d27b901ab3 (patch) | |
| tree | 2130084703b45ba08a7f94e0d446a081a4ba2894 /docs/reference/mccall81_245T.html | |
| parent | d0b124992232dde30fbff83dd4eeae8fc977d3ba (diff) | |
Make some example output more reproducible
In order to avoid some unnecessary documentation rebuilds
Diffstat (limited to 'docs/reference/mccall81_245T.html')
| -rw-r--r-- | docs/reference/mccall81_245T.html | 229 |
1 files changed, 50 insertions, 179 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 5fbbc962..47fa6482 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -161,189 +161,60 @@ <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='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'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 -#> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:00 2019 -#> Date of summary: Mon Mar 4 10:08:00 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 3.762 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: -#> 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='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> T245_0 1.038550e+02 2.4256088519 4.281607e+01 7.235908e-20 NA +#> k_T245_sink 1.636106e-02 0.0183803090 8.901408e-01 1.925667e-01 NA +#> k_T245_phenol 2.700936e-02 0.0179604385 1.503825e+00 7.498498e-02 NA +#> k_phenol_sink 1.286034e-11 0.2810970202 4.575054e-11 5.000000e-01 NA +#> k_phenol_anisole 4.050581e-01 0.1608928349 2.517564e+00 1.075371e-02 NA +#> k_anisole_sink 6.678742e-03 0.0008199239 8.145563e+00 9.469402e-08 NA +#> Upper +#> T245_0 NA +#> k_T245_sink NA +#> k_T245_phenol NA +#> k_phenol_sink NA +#> k_phenol_anisole NA +#> k_anisole_sink NA</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff +#> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink +#> 3.772401e-01 6.227599e-01 3.174937e-11 1.000000e+00 1.000000e+00 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> T245 15.982025 53.09114 +#> phenol 1.711229 5.68458 +#> anisole 103.784093 344.76330 +#> </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>) - <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: 0.9.48.1 -#> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:02 2019 -#> Date of summary: Mon Mar 4 10:08:02 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 1.598 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='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> T245_0 1.038550e+02 2.3517950656 44.159900 6.461715e-21 98.932670927 +#> k_T245_sink 1.636106e-02 0.0021685502 7.544701 1.978480e-07 0.012397413 +#> k_T245_phenol 2.700936e-02 0.0013511301 19.990199 1.606634e-14 0.024324422 +#> k_phenol_anisole 4.050581e-01 0.1238660786 3.270129 2.013627e-03 0.213574853 +#> k_anisole_sink 6.678742e-03 0.0007468908 8.942059 1.543812e-08 0.005284957 +#> Upper +#> T245_0 1.087774e+02 +#> k_T245_sink 2.159195e-02 +#> k_T245_phenol 2.999066e-02 +#> k_phenol_anisole 7.682180e-01 +#> k_anisole_sink 8.440105e-03</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff +#> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink +#> 3.772401e-01 6.227599e-01 3.174937e-11 1.000000e+00 1.000000e+00 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> T245 15.982025 53.09114 +#> phenol 1.711229 5.68458 +#> anisole 103.784093 344.76330 +#> </div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |