From f52fffd9eab13b7902bf767dd9cd7f0e7abf8069 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2016 17:47:17 +0100 Subject: Improve yaml header, remove trailing whitespace Now the year is showing in the reference, and the TOC is not collapsed. --- vignettes/FOCUS_L.html | 106 +++++++++++++++++++++++++++---------------------- 1 file changed, 58 insertions(+), 48 deletions(-) (limited to 'vignettes/FOCUS_L.html') diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index ab25f2f1..bcdee8df 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -11,7 +11,7 @@ - + Example evaluation of FOCUS Laboratory Data L1 to L3 @@ -24,10 +24,11 @@ + + + - - @@ -216,7 +223,7 @@ div.tocify {

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2016-10-22

+

2016-11-17

@@ -227,7 +234,7 @@ div.tocify { 
library("mkin", quietly = TRUE)
 FOCUS_2006_L1 = data.frame(
   t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
-  parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, 
+  parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
              72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
              27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
 FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
@@ -235,17 +242,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version:    0.9.44 
-## R version:       3.3.1 
-## Date of fit:     Sat Oct 22 17:54:39 2016 
-## Date of summary: Sat Oct 22 17:54:39 2016 
+
## mkin version:    0.9.44.9000 
+## R version:       3.3.2 
+## Date of fit:     Thu Nov 17 17:46:04 2016 
+## Date of summary: Thu Nov 17 17:46:04 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.09 s
+## Fitted with method Port using 37 model solutions performed in 0.093 s
 ## 
 ## Weighting: none
 ## 
@@ -328,10 +335,10 @@ summary(m.L1.SFO)

 
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

 

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

-
## mkin version:    0.9.44 
-## R version:       3.3.1 
-## Date of fit:     Sat Oct 22 17:54:40 2016 
-## Date of summary: Sat Oct 22 17:54:40 2016 
+
## mkin version:    0.9.44.9000 
+## R version:       3.3.2 
+## Date of fit:     Thu Nov 17 17:46:05 2016 
+## Date of summary: Thu Nov 17 17:46:05 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -343,7 +350,7 @@ summary(m.L1.SFO)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 0.417 s
+## Fitted with method Port using 188 model solutions performed in 0.456 s
 ## 
 ## Weighting: none
 ## 
@@ -395,7 +402,7 @@ summary(m.L1.SFO)

 ## parent 7.25 24.08     7.25

We get a warning that the default optimisation algorithm Port did not converge, which is an indication that the model is overparameterised, i.e. contains too many parameters that are ill-defined as a consequence.

And in fact, due to the higher number of parameters, and the lower number of degrees of freedom of the fit, the χ2 error level is actually higher for the FOMC model (3.6%) than for the SFO model (3.4%). Additionally, the parameters log_alpha and log_beta internally fitted in the model have excessive confidence intervals, that span more than 25 orders of magnitude (!) when backtransformed to the scale of alpha and beta. Also, the t-test for significant difference from zero does not indicate such a significant difference, with p-values greater than 0.1, and finally, the parameter correlation of log_alpha and log_beta is 1.000, clearly indicating that the model is overparameterised.

-

The χ2 error levels reported in Appendix 3 and Appendix 7 to the FOCUS kinetics report are rounded to integer percentages and partly deviate by one percentage point from the results calculated by mkin. The reason for this is not known. However, mkin gives the same χ2 error levels as the kinfit package and the calculation routines of the kinfit package have been extensively compared to the results obtained by the KinGUI software, as documented in the kinfit package vignette. KinGUI was the first widely used standard package in this field. Also, the calculation of χ2 error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt (Ranke, n.d.).

+

The χ2 error levels reported in Appendix 3 and Appendix 7 to the FOCUS kinetics report are rounded to integer percentages and partly deviate by one percentage point from the results calculated by mkin. The reason for this is not known. However, mkin gives the same χ2 error levels as the kinfit package and the calculation routines of the kinfit package have been extensively compared to the results obtained by the KinGUI software, as documented in the kinfit package vignette. KinGUI was the first widely used standard package in this field. Also, the calculation of χ2 error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt (Ranke 2014).

Laboratory Data L2

@@ -410,7 +417,7 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)

SFO fit for L2

Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument show_residuals to the plot command.

m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
-plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE, 
+plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - SFO")

The χ2 error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.

@@ -425,17 +432,17 @@ plot(m.L2.FOMC, show_residuals = TRUE, main = "FOCUS L2 - FOMC") 

summary(m.L2.FOMC, data = FALSE)
-
## mkin version:    0.9.44 
-## R version:       3.3.1 
-## Date of fit:     Sat Oct 22 17:54:40 2016 
-## Date of summary: Sat Oct 22 17:54:40 2016 
+
## mkin version:    0.9.44.9000 
+## R version:       3.3.2 
+## Date of fit:     Thu Nov 17 17:46:06 2016 
+## Date of summary: Thu Nov 17 17:46:06 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.179 s
+## Fitted with method Port using 81 model solutions performed in 0.227 s
 ## 
 ## Weighting: none
 ## 
@@ -495,10 +502,10 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

 

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

-
## mkin version:    0.9.44 
-## R version:       3.3.1 
-## Date of fit:     Sat Oct 22 17:54:41 2016 
-## Date of summary: Sat Oct 22 17:54:41 2016 
+
## mkin version:    0.9.44.9000 
+## R version:       3.3.2 
+## Date of fit:     Thu Nov 17 17:46:07 2016 
+## Date of summary: Thu Nov 17 17:46:07 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -507,7 +514,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.759 s
+## Fitted with method Port using 336 model solutions performed in 0.935 s
 ## 
 ## Weighting: none
 ## 
@@ -584,10 +591,10 @@ plot(mm.L3)

 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

 
We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

 
summary(mm.L3[["DFOP", 1]])

-
## mkin version:    0.9.44 
-## R version:       3.3.1 
-## Date of fit:     Sat Oct 22 17:54:42 2016 
-## Date of summary: Sat Oct 22 17:54:42 2016 
+
## mkin version:    0.9.44.9000 
+## R version:       3.3.2 
+## Date of fit:     Thu Nov 17 17:46:08 2016 
+## Date of summary: Thu Nov 17 17:46:08 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -596,7 +603,7 @@ plot(mm.L3)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.309 s
+## Fitted with method Port using 137 model solutions performed in 0.332 s
 ## 
 ## Weighting: none
 ## 
@@ -678,23 +685,23 @@ FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)

 
Fits of the SFO and FOMC models, plots and summaries are produced below:

 
# Only use one core here, not to offend the CRAN checks
 mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
-               list("FOCUS L4" = FOCUS_2006_L4_mkin), 
+               list("FOCUS L4" = FOCUS_2006_L4_mkin),
                quiet = TRUE)
 plot(mm.L4)

 

 
The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
summary(mm.L4[["SFO", 1]], data = FALSE)

-
## mkin version:    0.9.44 
-## R version:       3.3.1 
-## Date of fit:     Sat Oct 22 17:54:42 2016 
-## Date of summary: Sat Oct 22 17:54:43 2016 
+
## mkin version:    0.9.44.9000 
+## R version:       3.3.2 
+## Date of fit:     Thu Nov 17 17:46:08 2016 
+## Date of summary: Thu Nov 17 17:46:08 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.101 s
+## Fitted with method Port using 46 model solutions performed in 0.131 s
 ## 
 ## Weighting: none
 ## 
@@ -744,17 +751,17 @@ plot(mm.L4)

 ##        DT50 DT90
 ## parent  106  352

 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version:    0.9.44 
-## R version:       3.3.1 
-## Date of fit:     Sat Oct 22 17:54:43 2016 
-## Date of summary: Sat Oct 22 17:54:43 2016 
+
## mkin version:    0.9.44.9000 
+## R version:       3.3.2 
+## Date of fit:     Thu Nov 17 17:46:08 2016 
+## Date of summary: Thu Nov 17 17:46:08 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.144 s
+## Fitted with method Port using 66 model solutions performed in 0.167 s
 ## 
 ## Weighting: none
 ## 
@@ -809,7 +816,7 @@ plot(mm.L4)

 
References

 

 

-
Ranke, Johannes. n.d. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.

+
Ranke, Johannes. 2014. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.
@@ -824,8 +831,11 @@ plot(mm.L4)