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-rw-r--r--vignettes/FOCUS_L.html135
-rw-r--r--vignettes/FOCUS_Z.pdfbin220198 -> 220189 bytes
2 files changed, 73 insertions, 62 deletions
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 60c5132a..82bbd2c7 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -244,15 +244,15 @@ summary(m.L1.SFO)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:33 2014
-## Date of summary: Tue Oct 14 22:03:33 2014
+## Date of fit: Wed Oct 15 00:58:15 2014
+## Date of summary: Wed Oct 15 00:58:15 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 14 model solutions performed in 0.081 s
+## Fitted with method Port using 37 model solutions performed in 0.203 s
##
## Weighting: none
##
@@ -272,7 +272,7 @@ summary(m.L1.SFO)
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
## parent_0 92.50 1.3700 89.60 95.40 67.6 4.34e-21
-## log_k_parent_sink -2.35 0.0406 -2.43 -2.26 -57.9 5.16e-20
+## log_k_parent_sink -2.35 0.0406 -2.43 -2.26 -57.9 5.15e-20
## Pr(&gt;t)
## parent_0 2.17e-21
## log_k_parent_sink 2.58e-20
@@ -341,20 +341,31 @@ The residual plot can be easily obtained by</p>
is checked.</p>
<pre><code class="r">m.L1.FOMC &lt;- mkinfit(&quot;FOMC&quot;, FOCUS_2006_L1_mkin, quiet=TRUE)
-summary(m.L1.FOMC, data = FALSE)
+</code></pre>
+
+<pre><code>## Warning: Optimisation by method Port did not converge.
+## Convergence code is 1
+</code></pre>
+
+<pre><code class="r">summary(m.L1.FOMC, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:34 2014
-## Date of summary: Tue Oct 14 22:03:34 2014
+## Date of fit: Wed Oct 15 00:58:16 2014
+## Date of summary: Wed Oct 15 00:58:16 2014
+##
+##
+## Warning: Optimisation by method Port did not converge.
+## Convergence code is 1
+##
##
## Equations:
## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 53 model solutions performed in 0.289 s
+## Fitted with method Port using 188 model solutions performed in 1.011 s
##
## Weighting: none
##
@@ -375,23 +386,23 @@ summary(m.L1.FOMC, data = FALSE)
##
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 92.5 1.45 89.40 95.6 63.60 1.17e-19 5.85e-20
-## log_alpha 14.9 10.60 -7.75 37.5 1.40 1.82e-01 9.08e-02
-## log_beta 17.2 10.60 -5.38 39.8 1.62 1.25e-01 6.26e-02
+## parent_0 92.5 1.42 89.4 95.5 65.00 8.32e-20 4.16e-20
+## log_alpha 15.4 15.10 -16.7 47.6 1.02 3.22e-01 1.61e-01
+## log_beta 17.8 15.10 -14.4 49.9 1.18 2.57e-01 1.28e-01
##
## Parameter correlation:
## parent_0 log_alpha log_beta
-## parent_0 1.000 0.24 0.238
-## log_alpha 0.240 1.00 1.000
-## log_beta 0.238 1.00 1.000
+## parent_0 1.000 0.113 0.111
+## log_alpha 0.113 1.000 1.000
+## log_beta 0.111 1.000 1.000
##
## Residual standard error: 3.05 on 15 degrees of freedom
##
## Backtransformed parameters:
## Estimate Lower Upper
-## parent_0 9.25e+01 8.94e+01 9.56e+01
-## alpha 2.85e+06 4.32e-04 1.88e+16
-## beta 2.98e+07 4.59e-03 1.93e+17
+## parent_0 9.25e+01 8.94e+01 9.55e+01
+## alpha 5.04e+06 5.51e-08 4.62e+20
+## beta 5.28e+07 5.73e-07 4.86e+21
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -440,15 +451,15 @@ summary(m.L2.SFO)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:35 2014
-## Date of summary: Tue Oct 14 22:03:35 2014
+## Date of fit: Wed Oct 15 00:58:17 2014
+## Date of summary: Wed Oct 15 00:58:17 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 29 model solutions performed in 0.154 s
+## Fitted with method Port using 41 model solutions performed in 0.22 s
##
## Weighting: none
##
@@ -500,10 +511,10 @@ summary(m.L2.SFO)
##
## Data:
## time variable observed predicted residual
-## 0 parent 96.1 9.15e+01 4.635
-## 0 parent 91.8 9.15e+01 0.335
-## 1 parent 41.4 4.71e+01 -5.740
-## 1 parent 38.7 4.71e+01 -8.440
+## 0 parent 96.1 9.15e+01 4.634
+## 0 parent 91.8 9.15e+01 0.334
+## 1 parent 41.4 4.71e+01 -5.739
+## 1 parent 38.7 4.71e+01 -8.439
## 3 parent 19.3 1.25e+01 6.779
## 3 parent 22.3 1.25e+01 9.779
## 7 parent 4.6 8.83e-01 3.717
@@ -522,7 +533,7 @@ plot(m.L2.SFO)
mkinresplot(m.L2.SFO)
</code></pre>
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alt="plot of chunk unnamed-chunk-9"/> </p>
<p>In the FOCUS kinetics report, it is stated that there is no apparent systematic
error observed from the residual plot up to the measured DT90 (approximately at
@@ -543,22 +554,22 @@ plot(m.L2.FOMC)
mkinresplot(m.L2.FOMC)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-10"/> </p>
<pre><code class="r">summary(m.L2.FOMC, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:36 2014
-## Date of summary: Tue Oct 14 22:03:36 2014
+## Date of fit: Wed Oct 15 00:58:17 2014
+## Date of summary: Wed Oct 15 00:58:17 2014
##
## Equations:
## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 35 model solutions performed in 0.192 s
+## Fitted with method Port using 81 model solutions performed in 0.438 s
##
## Weighting: none
##
@@ -617,7 +628,7 @@ experimental error has to be assumed in order to explain the data.</p>
plot(m.L2.DFOP)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-11"/> </p>
<p>Here, the default starting parameters for the DFOP model obviously do not lead
to a reasonable solution. Therefore the fit is repeated with different starting
@@ -629,15 +640,15 @@ parameters.</p>
plot(m.L2.DFOP)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-12"/> </p>
<pre><code class="r">summary(m.L2.DFOP, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:36 2014
-## Date of summary: Tue Oct 14 22:03:36 2014
+## Date of fit: Wed Oct 15 00:58:21 2014
+## Date of summary: Wed Oct 15 00:58:21 2014
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -646,7 +657,7 @@ plot(m.L2.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 43 model solutions performed in 0.24 s
+## Fitted with method Port using 336 model solutions performed in 1.844 s
##
## Weighting: none
##
@@ -669,8 +680,8 @@ plot(m.L2.DFOP)
##
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 94.000 NA NA NA NA NA NA
-## log_k1 6.160 NA NA NA NA NA NA
+## parent_0 93.900 NA NA NA NA NA NA
+## log_k1 3.120 NA NA NA NA NA NA
## log_k2 -1.090 NA NA NA NA NA NA
## g_ilr -0.282 NA NA NA NA NA NA
##
@@ -681,8 +692,8 @@ plot(m.L2.DFOP)
##
## Backtransformed parameters:
## Estimate Lower Upper
-## parent_0 94.000 NA NA
-## k1 476.000 NA NA
+## parent_0 93.900 NA NA
+## k1 22.700 NA NA
## k2 0.337 NA NA
## g 0.402 NA NA
##
@@ -693,7 +704,7 @@ plot(m.L2.DFOP)
##
## Estimated disappearance times:
## DT50 DT90 DT50_k1 DT50_k2
-## parent NA NA 0.00146 2.06
+## parent NA NA 0.0306 2.06
</code></pre>
<p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the
@@ -718,22 +729,22 @@ FOCUS_2006_L3_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L3)
plot(m.L3.SFO)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-14"/> </p>
+<p><img 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alt="plot of chunk unnamed-chunk-14"/> </p>
<pre><code class="r">summary(m.L3.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:37 2014
-## Date of summary: Tue Oct 14 22:03:37 2014
+## Date of fit: Wed Oct 15 00:58:22 2014
+## Date of summary: Wed Oct 15 00:58:22 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 44 model solutions performed in 0.237 s
+## Fitted with method Port using 43 model solutions performed in 0.232 s
##
## Weighting: none
##
@@ -785,14 +796,14 @@ plot(m.L3.SFO)
##
## Data:
## time variable observed predicted residual
-## 0 parent 97.8 74.87 22.9274
-## 3 parent 60.0 69.41 -9.4065
+## 0 parent 97.8 74.87 22.9281
+## 3 parent 60.0 69.41 -9.4061
## 7 parent 51.0 62.73 -11.7340
-## 14 parent 43.0 52.56 -9.5634
-## 30 parent 35.0 35.08 -0.0828
-## 60 parent 22.0 16.44 5.5614
-## 91 parent 15.0 7.51 7.4896
-## 120 parent 12.0 3.61 8.3908
+## 14 parent 43.0 52.56 -9.5638
+## 30 parent 35.0 35.08 -0.0839
+## 60 parent 22.0 16.44 5.5602
+## 91 parent 15.0 7.51 7.4887
+## 120 parent 12.0 3.61 8.3903
</code></pre>
<p>The chi<sup>2</sup> error level of 21% as well as the plot suggest that the model
@@ -811,15 +822,15 @@ plot(m.L3.FOMC)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:37 2014
-## Date of summary: Tue Oct 14 22:03:37 2014
+## Date of fit: Wed Oct 15 00:58:22 2014
+## Date of summary: Wed Oct 15 00:58:22 2014
##
## Equations:
## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 26 model solutions performed in 0.139 s
+## Fitted with method Port using 83 model solutions performed in 0.442 s
##
## Weighting: none
##
@@ -884,8 +895,8 @@ plot(m.L3.DFOP)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:37 2014
-## Date of summary: Tue Oct 14 22:03:37 2014
+## Date of fit: Wed Oct 15 00:58:23 2014
+## Date of summary: Wed Oct 15 00:58:23 2014
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -894,7 +905,7 @@ plot(m.L3.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 37 model solutions performed in 0.207 s
+## Fitted with method Port using 137 model solutions performed in 0.778 s
##
## Weighting: none
##
@@ -982,15 +993,15 @@ plot(m.L4.SFO)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:38 2014
-## Date of summary: Tue Oct 14 22:03:38 2014
+## Date of fit: Wed Oct 15 00:58:24 2014
+## Date of summary: Wed Oct 15 00:58:24 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 20 model solutions performed in 0.106 s
+## Fitted with method Port using 46 model solutions performed in 0.246 s
##
## Weighting: none
##
@@ -1057,15 +1068,15 @@ plot(m.L4.FOMC)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:38 2014
-## Date of summary: Tue Oct 14 22:03:38 2014
+## Date of fit: Wed Oct 15 00:58:24 2014
+## Date of summary: Wed Oct 15 00:58:24 2014
##
## Equations:
## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 48 model solutions performed in 0.26 s
+## Fitted with method Port using 66 model solutions performed in 0.359 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index b5898b7c..0013cd5e 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ

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