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<pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</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'>#&gt; <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'>&lt;-</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'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.48.1
-#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:00 2019
-#&gt; Date of summary: Mon Mar 4 10:08:00 2019
-#&gt;
-#&gt; Equations:
-#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
-#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
-#&gt; k_phenol_anisole * phenol
-#&gt; d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 574 model solutions performed in 3.762 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; T245_0 100.9000 state
-#&gt; k_T245_sink 0.1000 deparm
-#&gt; k_T245_phenol 0.1001 deparm
-#&gt; k_phenol_sink 0.1002 deparm
-#&gt; k_phenol_anisole 0.1003 deparm
-#&gt; k_anisole_sink 0.1004 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; T245_0 100.900000 -Inf Inf
-#&gt; log_k_T245_sink -2.302585 -Inf Inf
-#&gt; log_k_T245_phenol -2.301586 -Inf Inf
-#&gt; log_k_phenol_sink -2.300587 -Inf Inf
-#&gt; log_k_phenol_anisole -2.299590 -Inf Inf
-#&gt; log_k_anisole_sink -2.298593 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; phenol_0 0 state
-#&gt; anisole_0 0 state
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; T245_0 103.9000 NA NA NA
-#&gt; log_k_T245_sink -4.1130 NA NA NA
-#&gt; log_k_T245_phenol -3.6120 NA NA NA
-#&gt; log_k_phenol_sink -25.0800 NA NA NA
-#&gt; log_k_phenol_anisole -0.9037 NA NA NA
-#&gt; log_k_anisole_sink -5.0090 NA NA NA
-#&gt;
-#&gt; Parameter correlation:
-#&gt; Could not estimate covariance matrix; singular system.
-#&gt; Residual standard error: 2.78 on 18 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA
-#&gt; k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA
-#&gt; k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA
-#&gt; k_phenol_sink 1.286e-11 4.575e-11 5.000e-01 NA NA
-#&gt; k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA
-#&gt; k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 10.070 6 16
-#&gt; T245 7.908 3 5
-#&gt; phenol 106.445 2 5
-#&gt; anisole 5.379 1 6
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; T245_sink 3.772e-01
-#&gt; T245_phenol 6.228e-01
-#&gt; phenol_sink 3.175e-11
-#&gt; phenol_anisole 1.000e+00
-#&gt; anisole_sink 1.000e+00
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; T245 15.982 53.091
-#&gt; phenol 1.711 5.685
-#&gt; 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'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; T245_0 1.038550e+02 2.4256088519 4.281607e+01 7.235908e-20 NA
+#&gt; k_T245_sink 1.636106e-02 0.0183803090 8.901408e-01 1.925667e-01 NA
+#&gt; k_T245_phenol 2.700936e-02 0.0179604385 1.503825e+00 7.498498e-02 NA
+#&gt; k_phenol_sink 1.286034e-11 0.2810970202 4.575054e-11 5.000000e-01 NA
+#&gt; k_phenol_anisole 4.050581e-01 0.1608928349 2.517564e+00 1.075371e-02 NA
+#&gt; k_anisole_sink 6.678742e-03 0.0008199239 8.145563e+00 9.469402e-08 NA
+#&gt; Upper
+#&gt; T245_0 NA
+#&gt; k_T245_sink NA
+#&gt; k_T245_phenol NA
+#&gt; k_phenol_sink NA
+#&gt; k_phenol_anisole NA
+#&gt; 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'>#&gt; $ff
+#&gt; T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
+#&gt; 3.772401e-01 6.227599e-01 3.174937e-11 1.000000e+00 1.000000e+00
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; T245 15.982025 53.09114
+#&gt; phenol 1.711229 5.68458
+#&gt; anisole 103.784093 344.76330
+#&gt; </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'>&lt;-</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'>#&gt; mkin version used for fitting: 0.9.48.1
-#&gt; R version used for fitting: 3.5.2
-#&gt; Date of fit: Mon Mar 4 10:08:02 2019
-#&gt; Date of summary: Mon Mar 4 10:08:02 2019
-#&gt;
-#&gt; Equations:
-#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
-#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
-#&gt; k_phenol_anisole * phenol
-#&gt; d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
-#&gt;
-#&gt; Model predictions using solution type deSolve
-#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.598 s
-#&gt;
-#&gt; Weighting: none
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; T245_0 100.9000 state
-#&gt; k_T245_sink 0.1000 deparm
-#&gt; k_T245_phenol 0.1001 deparm
-#&gt; k_phenol_anisole 0.1002 deparm
-#&gt; k_anisole_sink 0.1003 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; T245_0 100.900000 -Inf Inf
-#&gt; log_k_T245_sink -2.302585 -Inf Inf
-#&gt; log_k_T245_phenol -2.301586 -Inf Inf
-#&gt; log_k_phenol_anisole -2.300587 -Inf Inf
-#&gt; log_k_anisole_sink -2.299590 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; phenol_0 0 state
-#&gt; anisole_0 0 state
-#&gt; k_phenol_sink 0 deparm
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; T245_0 103.9000 2.35200 98.930 108.8000
-#&gt; log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350
-#&gt; log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070
-#&gt; log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637
-#&gt; log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750
-#&gt;
-#&gt; Parameter correlation:
-#&gt; T245_0 log_k_T245_sink log_k_T245_phenol
-#&gt; T245_0 1.00000 0.63761 -0.1742
-#&gt; log_k_T245_sink 0.63761 1.00000 -0.3831
-#&gt; log_k_T245_phenol -0.17416 -0.38313 1.0000
-#&gt; log_k_phenol_anisole -0.05948 0.08745 -0.3047
-#&gt; log_k_anisole_sink -0.16208 -0.60469 0.5227
-#&gt; log_k_phenol_anisole log_k_anisole_sink
-#&gt; T245_0 -0.05948 -0.1621
-#&gt; log_k_T245_sink 0.08745 -0.6047
-#&gt; log_k_T245_phenol -0.30470 0.5227
-#&gt; log_k_phenol_anisole 1.00000 -0.1774
-#&gt; log_k_anisole_sink -0.17744 1.0000
-#&gt;
-#&gt; Residual standard error: 2.706 on 19 degrees of freedom
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; Confidence intervals for internally transformed parameters are asymmetric.
-#&gt; t-test (unrealistically) based on the assumption of normal distribution
-#&gt; for estimators of untransformed parameters.
-#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000
-#&gt; k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159
-#&gt; k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999
-#&gt; k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820
-#&gt; k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844
-#&gt;
-#&gt; Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 9.831 5 17
-#&gt; T245 7.908 3 5
-#&gt; phenol 99.808 1 6
-#&gt; anisole 5.379 1 6
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; T245_sink 0.3772
-#&gt; T245_phenol 0.6228
-#&gt; phenol_anisole 1.0000
-#&gt; phenol_sink 0.0000
-#&gt; anisole_sink 1.0000
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; T245 15.982 53.091
-#&gt; phenol 1.711 5.685
-#&gt; 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'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; T245_0 1.038550e+02 2.3517950656 44.159900 6.461715e-21 98.932670927
+#&gt; k_T245_sink 1.636106e-02 0.0021685502 7.544701 1.978480e-07 0.012397413
+#&gt; k_T245_phenol 2.700936e-02 0.0013511301 19.990199 1.606634e-14 0.024324422
+#&gt; k_phenol_anisole 4.050581e-01 0.1238660786 3.270129 2.013627e-03 0.213574853
+#&gt; k_anisole_sink 6.678742e-03 0.0007468908 8.942059 1.543812e-08 0.005284957
+#&gt; Upper
+#&gt; T245_0 1.087774e+02
+#&gt; k_T245_sink 2.159195e-02
+#&gt; k_T245_phenol 2.999066e-02
+#&gt; k_phenol_anisole 7.682180e-01
+#&gt; 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'>#&gt; $ff
+#&gt; T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
+#&gt; 3.772401e-01 6.227599e-01 3.174937e-11 1.000000e+00 1.000000e+00
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; T245 15.982025 53.09114
+#&gt; phenol 1.711229 5.68458
+#&gt; anisole 103.784093 344.76330
+#&gt; </div><div class='input'> </div></pre>
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