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1 files changed, 242 insertions, 8 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 4314c84e..7b294129 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -111,19 +111,253 @@
<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'> <span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span>
-<span class='co'># summary(fit.1, data = FALSE)</span>
-<span class='co'># </span>
-<span class='co'>## ---------------------------------------------</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'>
+ <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>))</div><div class='output co'>#&gt; Model cost at call 1 : 13655.2
+#&gt; Model cost at call 2 : 13655.2
+#&gt; Model cost at call 8 : 9191.59
+#&gt; Model cost at call 16 : 5663.584
+#&gt; Model cost at call 17 : 5663.582
+#&gt; Model cost at call 18 : 5663.566
+#&gt; Model cost at call 19 : 5663.55
+#&gt; Model cost at call 23 : 3035.567
+#&gt; Model cost at call 24 : 3035.566
+#&gt; Model cost at call 26 : 3035.561
+#&gt; Model cost at call 27 : 3035.559
+#&gt; Model cost at call 28 : 3035.558
+#&gt; Model cost at call 30 : 2252.97
+#&gt; Model cost at call 31 : 2252.965
+#&gt; Model cost at call 32 : 2252.965
+#&gt; Model cost at call 36 : 2252.958
+#&gt; Model cost at call 37 : 1220.201
+#&gt; Model cost at call 38 : 1220.2
+#&gt; Model cost at call 39 : 1220.199
+#&gt; Model cost at call 41 : 1220.183
+#&gt; Model cost at call 45 : 507.1358
+#&gt; Model cost at call 48 : 507.1353
+#&gt; Model cost at call 52 : 198.5695
+#&gt; Model cost at call 55 : 198.5694
+#&gt; Model cost at call 60 : 175.8239
+#&gt; Model cost at call 63 : 175.8239
+#&gt; Model cost at call 67 : 170.6316
+#&gt; Model cost at call 69 : 170.6316
+#&gt; Model cost at call 74 : 165.881
+#&gt; Model cost at call 77 : 165.881
+#&gt; Model cost at call 81 : 161.6423
+#&gt; Model cost at call 84 : 161.6423
+#&gt; Model cost at call 88 : 158.2953
+#&gt; Model cost at call 91 : 158.2953
+#&gt; Model cost at call 95 : 156.7311
+#&gt; Model cost at call 97 : 156.731
+#&gt; Model cost at call 103 : 155.998
+#&gt; Model cost at call 106 : 155.998
+#&gt; Model cost at call 110 : 155.6263
+#&gt; Model cost at call 113 : 155.6262
+#&gt; Model cost at call 116 : 155.6262
+#&gt; Model cost at call 117 : 155.1202
+#&gt; Model cost at call 120 : 155.1202
+#&gt; Model cost at call 124 : 154.4133
+#&gt; Model cost at call 125 : 153.8489
+#&gt; Model cost at call 126 : 152.7413
+#&gt; Model cost at call 129 : 152.7413
+#&gt; Model cost at call 132 : 152.7413
+#&gt; Model cost at call 133 : 150.3995
+#&gt; Model cost at call 134 : 148.7256
+#&gt; Model cost at call 135 : 147.2618
+#&gt; Model cost at call 137 : 147.2618
+#&gt; Model cost at call 139 : 147.2618
+#&gt; Model cost at call 142 : 145.115
+#&gt; Model cost at call 144 : 145.115
+#&gt; Model cost at call 145 : 145.115
+#&gt; Model cost at call 146 : 145.115
+#&gt; Model cost at call 147 : 145.115
+#&gt; Model cost at call 150 : 143.7878
+#&gt; Model cost at call 157 : 142.8531
+#&gt; Model cost at call 160 : 142.8531
+#&gt; Model cost at call 164 : 142.7325
+#&gt; Model cost at call 167 : 142.7325
+#&gt; Model cost at call 169 : 142.7325
+#&gt; Model cost at call 172 : 141.8393
+#&gt; Model cost at call 173 : 141.8393
+#&gt; Model cost at call 174 : 141.8393
+#&gt; Model cost at call 179 : 141.3446
+#&gt; Model cost at call 180 : 141.3446
+#&gt; Model cost at call 181 : 141.3446
+#&gt; Model cost at call 186 : 141.1111
+#&gt; Model cost at call 193 : 140.7786
+#&gt; Model cost at call 200 : 140.451
+#&gt; Model cost at call 207 : 140.1395
+#&gt; Model cost at call 214 : 139.7903
+#&gt; Model cost at call 221 : 139.5476
+#&gt; Model cost at call 228 : 139.4441
+#&gt; Model cost at call 235 : 139.3204
+#&gt; Model cost at call 242 : 139.2508
+#&gt; Model cost at call 249 : 139.1891
+#&gt; Model cost at call 256 : 139.1561
+#&gt; Model cost at call 263 : 139.137
+#&gt; Model cost at call 270 : 139.1278
+#&gt; Model cost at call 271 : 139.1278
+#&gt; Model cost at call 279 : 139.1211
+#&gt; Model cost at call 280 : 139.1211
+#&gt; Model cost at call 281 : 139.1211
+#&gt; Model cost at call 282 : 139.1211
+#&gt; Model cost at call 286 : 139.1179
+#&gt; Model cost at call 287 : 139.1179
+#&gt; Model cost at call 291 : 139.1179
+#&gt; Model cost at call 294 : 139.1179
+#&gt; Model cost at call 298 : 139.1158
+#&gt; Model cost at call 299 : 139.1158
+#&gt; Model cost at call 302 : 139.1158
+#&gt; Model cost at call 310 : 139.1148
+#&gt; Model cost at call 311 : 139.1148
+#&gt; Model cost at call 315 : 139.1148
+#&gt; Model cost at call 322 : 139.1143
+#&gt; Model cost at call 323 : 139.1143
+#&gt; Model cost at call 326 : 139.1143
+#&gt; Model cost at call 334 : 139.114
+#&gt; Model cost at call 335 : 139.114
+#&gt; Model cost at call 338 : 139.114
+#&gt; Model cost at call 339 : 139.114
+#&gt; Model cost at call 346 : 139.1139
+#&gt; Model cost at call 347 : 139.1139
+#&gt; Model cost at call 350 : 139.1139
+#&gt; Model cost at call 351 : 139.1139
+#&gt; Model cost at call 358 : 139.1139
+#&gt; Model cost at call 359 : 139.1139
+#&gt; Model cost at call 362 : 139.1139
+#&gt; Model cost at call 363 : 139.1139
+#&gt; Model cost at call 370 : 139.1138
+#&gt; Model cost at call 382 : 139.1138
+#&gt; Model cost at call 390 : 139.1138
+#&gt; Model cost at call 395 : 139.1138
+#&gt; Model cost at call 403 : 139.1138
+#&gt; Model cost at call 408 : 139.1138
+#&gt; Model cost at call 416 : 139.1138
+#&gt; Model cost at call 421 : 139.1138
+#&gt; Model cost at call 429 : 139.1138
+#&gt; Model cost at call 434 : 139.1138
+#&gt; Model cost at call 442 : 139.1138
+#&gt; Model cost at call 447 : 139.1138
+#&gt; Model cost at call 455 : 139.1138
+#&gt; Model cost at call 460 : 139.1138
+#&gt; Model cost at call 468 : 139.1138
+#&gt; Model cost at call 473 : 139.1138
+#&gt; Model cost at call 481 : 139.1138
+#&gt; Model cost at call 486 : 139.1138
+#&gt; Model cost at call 494 : 139.1138
+#&gt; Model cost at call 499 : 139.1138
+#&gt; Model cost at call 507 : 139.1138
+#&gt; Model cost at call 512 : 139.1138
+#&gt; Model cost at call 519 : 139.1138
+#&gt; Model cost at call 520 : 139.1138
+#&gt; Model cost at call 525 : 139.1138
+#&gt; Model cost at call 538 : 139.1138
+#&gt; Model cost at call 545 : 139.1138
+#&gt; Model cost at call 546 : 139.1138
+#&gt; Model cost at call 551 : 139.1138
+#&gt; Model cost at call 558 : 139.1138
+#&gt; Model cost at call 559 : 139.1138
+#&gt; Model cost at call 564 : 139.1138
+#&gt; Model cost at call 571 : 139.1138
+#&gt; Model cost at call 580 : 139.1138
+#&gt; Model cost at call 588 : 139.1138 </div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
+#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'> <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: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 15:19:33 2016
+#&gt; Date of summary: Fri Nov 18 15:19:33 2016
+#&gt;
+#&gt;
+#&gt; Warning: Optimisation by method Port did not converge.
+#&gt; Convergence code is 1
+#&gt;
+#&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 590 model solutions performed in 3.45 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 -26.3900 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 3.457e-12 1.230e-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 8.534e-12
+#&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 covariance matrix and 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: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Thu Nov 17 22:56:55 2016
-#&gt; Date of summary: Thu Nov 17 22:56:55 2016
+#&gt; Date of fit: Fri Nov 18 15:19:35 2016
+#&gt; Date of summary: Fri Nov 18 15:19:35 2016
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -133,7 +367,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.457 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.477 s
#&gt;
#&gt; Weighting: none
#&gt;

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