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)

## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 17:13:56 2016 -## Date of summary: Fri Nov 4 17:13:56 2016 +## Date of fit: Thu Nov 17 22:58:18 2016 +## Date of summary: Thu Nov 17 22:58:18 2016 ## ## Equations: -## d_parent = - k_parent_sink * parent +## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.089 s +## Fitted with method Port using 37 model solutions performed in 0.103 s ## ## Weighting: none ## @@ -156,8 +156,8 @@ FOCUS_2006_L1_mkin <-summary(m.L1.FOMC, data = FALSE) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 17:13:57 2016 -## Date of summary: Fri Nov 4 17:13:57 2016 +## Date of fit: Thu Nov 17 22:58:19 2016 +## Date of summary: Thu Nov 17 22:58:19 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -165,11 +165,11 @@ FOCUS_2006_L1_mkin <- \(\chi^2\) 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 \(\chi^2\) 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 \(\chi^2\) 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 \(\chi^2\) error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt (Ranke, n.d.). +The \(\chi^2\) 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 \(\chi^2\) 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 \(\chi^2\) error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt (Ranke 2014). Laboratory Data L2 @@ -236,7 +236,7 @@ FOCUS_2006_L2_mkin <- 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 \(\chi^2\) 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. @@ -253,15 +253,15 @@ FOCUS_2006_L2_mkin <- summary(m.L2.FOMC, data = FALSE) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 17:13:58 2016 -## Date of summary: Fri Nov 4 17:13:58 2016 +## Date of fit: Thu Nov 17 22:58:20 2016 +## Date of summary: Thu Nov 17 22:58:20 2016 ## ## Equations: -## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent +## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.194 s +## Fitted with method Port using 81 model solutions performed in 0.195 s ## ## Weighting: none ## @@ -323,17 +323,17 @@ FOCUS_2006_L2_mkin <- summary(m.L2.DFOP, data = FALSE) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 17:13:59 2016 -## Date of summary: Fri Nov 4 17:13:59 2016 +## Date of fit: Thu Nov 17 22:58:21 2016 +## Date of summary: Thu Nov 17 22:58:21 2016 ## ## Equations: -## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * -## time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * -## time))) * parent +## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * +## exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * +## exp(-k2 * time))) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.82 s +## Fitted with method Port using 336 model solutions performed in 0.882 s ## ## Weighting: none ## @@ -412,17 +412,17 @@ mm.L3 <- summary(mm.L3[["DFOP", 1]]) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 17:14:00 2016 -## Date of summary: Fri Nov 4 17:14:00 2016 +## Date of fit: Thu Nov 17 22:58:22 2016 +## Date of summary: Thu Nov 17 22:58:22 2016 ## ## Equations: -## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * -## time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * -## time))) * parent +## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * +## exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * +## exp(-k2 * time))) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.336 s +## Fitted with method Port using 137 model solutions performed in 0.338 s ## ## Weighting: none ## @@ -504,7 +504,7 @@ FOCUS_2006_L4_mkin <- # 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) @@ -512,11 +512,11 @@ mm.L4 <- summary(mm.L4[["SFO", 1]], data = FALSE) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 17:14:01 2016 -## Date of summary: Fri Nov 4 17:14:01 2016 +## Date of fit: Thu Nov 17 22:58:22 2016 +## Date of summary: Thu Nov 17 22:58:23 2016 ## ## Equations: -## d_parent = - k_parent_sink * parent +## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## @@ -572,15 +572,15 @@ mm.L4 <- summary(mm.L4[["FOMC", 1]], data = FALSE) ## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Fri Nov 4 17:14:01 2016 -## Date of summary: Fri Nov 4 17:14:01 2016 +## Date of fit: Thu Nov 17 22:58:23 2016 +## Date of summary: Thu Nov 17 22:58:23 2016 ## ## Equations: -## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent +## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.162 s +## Fitted with method Port using 66 model solutions performed in 0.151 s ## ## Weighting: none ## @@ -635,7 +635,7 @@ 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. -- cgit v1.2.1

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

2016-11-04

2016-11-17

Laboratory Data L2