From 89cd81cf47c9f05831e854d5185b5cc599745db4 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 15 May 2015 13:31:28 +0200 Subject: Update of vignettes during staticdoc documentation --- vignettes/FOCUS_L.html | 122 ++++++++++++++++++++++++------------------------- vignettes/FOCUS_Z.pdf | Bin 214499 -> 215014 bytes vignettes/mkin.pdf | Bin 160335 -> 160260 bytes 3 files changed, 61 insertions(+), 61 deletions(-) diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index b5228532..a06f360e 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -236,17 +236,17 @@ given in the FOCUS report.

summary(m.L1.SFO) -
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:49 2014 
-## Date of summary: Thu Dec 18 09:52:49 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:55 2015 
+## Date of summary: Fri May 15 13:29:55 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.214 s
+## Fitted with method Port using 37 model solutions performed in 0.082 s
 ## 
 ## Weighting: none
 ## 
@@ -323,13 +323,13 @@ summary(m.L1.SFO)
 
plot(m.L1.SFO)
 

 
-
plot of chunk unnamed-chunk-4 
+
plot of chunk unnamed-chunk-4 
 The residual plot can be easily obtained by

 
 
mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
 

 
-
plot of chunk unnamed-chunk-5 

+
plot of chunk unnamed-chunk-5 

 
 
For comparison, the FOMC model is fitted as well, and the chi2 error level
 is checked.

@@ -344,10 +344,10 @@ is checked.

 
summary(m.L1.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:50 2014 
-## Date of summary: Thu Dec 18 09:52:50 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:55 2015 
+## Date of summary: Fri May 15 13:29:55 2015 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -359,7 +359,7 @@ is checked.

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 1.085 s
+## Fitted with method Port using 188 model solutions performed in 0.412 s
 ## 
 ## Weighting: none
 ## 
@@ -443,17 +443,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
 summary(m.L2.SFO)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:51 2014 
-## Date of summary: Thu Dec 18 09:52:51 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:56 2015 
+## Date of summary: Fri May 15 13:29:56 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.238 s
+## Fitted with method Port using 41 model solutions performed in 0.091 s
 ## 
 ## Weighting: none
 ## 
@@ -527,7 +527,7 @@ plot(m.L2.SFO)
 mkinresplot(m.L2.SFO)
 

 
-
plot of chunk unnamed-chunk-9 

+
plot of chunk unnamed-chunk-9 

 
 
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
@@ -548,22 +548,22 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)
 

 
-
plot of chunk unnamed-chunk-10 

+
plot of chunk unnamed-chunk-10 

 
 
summary(m.L2.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:51 2014 
-## Date of summary: Thu Dec 18 09:52:51 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:56 2015 
+## Date of summary: Fri May 15 13:29:56 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.464 s
+## Fitted with method Port using 81 model solutions performed in 0.192 s
 ## 
 ## Weighting: none
 ## 
@@ -622,7 +622,7 @@ experimental error has to be assumed in order to explain the data.

 plot(m.L2.DFOP)
 

 
-
plot of chunk unnamed-chunk-11 

+
plot of chunk unnamed-chunk-11 

 
 
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
@@ -634,15 +634,15 @@ parameters.

 plot(m.L2.DFOP)
 

 
-
plot of chunk unnamed-chunk-12 

+
plot of chunk unnamed-chunk-12 

 
 
summary(m.L2.DFOP, data = FALSE)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:56 2014 
-## Date of summary: Thu Dec 18 09:52:56 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:58 2015 
+## Date of summary: Fri May 15 13:29:58 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -651,7 +651,7 @@ plot(m.L2.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 1.986 s
+## Fitted with method Port using 336 model solutions performed in 0.775 s
 ## 
 ## Weighting: none
 ## 
@@ -723,22 +723,22 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
 plot(m.L3.SFO)
 

 
-
plot of chunk unnamed-chunk-14 

+
plot of chunk unnamed-chunk-14 

 
 
summary(m.L3.SFO)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:56 2014 
-## Date of summary: Thu Dec 18 09:52:56 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:58 2015 
+## Date of summary: Fri May 15 13:29:58 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.246 s
+## Fitted with method Port using 43 model solutions performed in 0.099 s
 ## 
 ## Weighting: none
 ## 
@@ -809,22 +809,22 @@ does not fit very well. 

 plot(m.L3.FOMC)
 

 
-
plot of chunk unnamed-chunk-15 

+
plot of chunk unnamed-chunk-15 

 
 
summary(m.L3.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:57 2014 
-## Date of summary: Thu Dec 18 09:52:57 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:58 2015 
+## Date of summary: Fri May 15 13:29:58 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.475 s
+## Fitted with method Port using 83 model solutions performed in 0.186 s
 ## 
 ## Weighting: none
 ## 
@@ -882,15 +882,15 @@ considerably:

 plot(m.L3.DFOP)
 

 
-
plot of chunk unnamed-chunk-16 

+
plot of chunk unnamed-chunk-16 

 
 
summary(m.L3.DFOP, data = FALSE)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:58 2014 
-## Date of summary: Thu Dec 18 09:52:58 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:59 2015 
+## Date of summary: Fri May 15 13:29:59 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -899,7 +899,7 @@ plot(m.L3.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.813 s
+## Fitted with method Port using 137 model solutions performed in 0.314 s
 ## 
 ## Weighting: none
 ## 
@@ -980,22 +980,22 @@ FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
 plot(m.L4.SFO)
 

 
-
plot of chunk unnamed-chunk-18 

+
plot of chunk unnamed-chunk-18 

 
 
summary(m.L4.SFO, data = FALSE)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:58 2014 
-## Date of summary: Thu Dec 18 09:52:58 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:59 2015 
+## Date of summary: Fri May 15 13:29:59 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.264 s
+## Fitted with method Port using 46 model solutions performed in 0.109 s
 ## 
 ## Weighting: none
 ## 
@@ -1055,22 +1055,22 @@ fits very well. 

 plot(m.L4.FOMC)
 

 
-
plot of chunk unnamed-chunk-19 

+
plot of chunk unnamed-chunk-19 

 
 
summary(m.L4.FOMC, data = FALSE)
 

 
-
## mkin version:    0.9.34 
-## R version:       3.1.2 
-## Date of fit:     Thu Dec 18 09:52:59 2014 
-## Date of summary: Thu Dec 18 09:52:59 2014 
+
## mkin version:    0.9.35 
+## R version:       3.2.0 
+## Date of fit:     Fri May 15 13:29:59 2015 
+## Date of summary: Fri May 15 13:29:59 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.375 s
+## Fitted with method Port using 66 model solutions performed in 0.146 s
 ## 
 ## Weighting: none
 ## 
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