diff options
Diffstat (limited to 'vignettes')
| -rw-r--r-- | vignettes/FOCUS_L.html | 135 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 220198 -> 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(>|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(>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 <- mkinfit("FOMC", 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(>|t|) Pr(>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> -<p><img 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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><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(>|t|) Pr(>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 <- 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> <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 Binary files differindex b5898b7c..0013cd5e 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf |