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-rw-r--r--docs/reference/mccall81_245T.html111
1 files changed, 96 insertions, 15 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index cea92155..ac2adf1e 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -63,7 +63,7 @@
</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">0.9.47.3</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span>
</span>
</div>
@@ -155,19 +155,11 @@
<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'>&lt;-</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'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><span class='co'># NOT RUN {</span>
- <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'>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>)
-
-<span class='co'># }</span><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'>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'>#&gt; mkin version used for fitting: 0.9.47.3
+ <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'>#&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'>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'>#&gt; mkin version used for fitting: 0.9.47.4
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 06:39:07 2018
-#&gt; Date of summary: Fri Sep 14 06:39:07 2018
+#&gt; Date of fit: Fri Sep 14 11:34:50 2018
+#&gt; Date of summary: Fri Sep 14 11:34:50 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -177,7 +169,96 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.423 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.33 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:</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#&gt; Could not estimate covariance matrix; singular system:
+#&gt;
+#&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='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'>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'>#&gt; mkin version used for fitting: 0.9.47.4
+#&gt; R version used for fitting: 3.5.1
+#&gt; Date of fit: Fri Sep 14 11:34:51 2018
+#&gt; Date of summary: Fri Sep 14 11:34:51 2018
+#&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 1.417 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -257,7 +338,7 @@
#&gt; DT50 DT90
#&gt; T245 15.982 53.091
#&gt; phenol 1.711 5.685
-#&gt; anisole 103.784 344.763</div></pre>
+#&gt; anisole 103.784 344.763</div><div class='input'> </div></pre>
</div>
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