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diff --git a/vignettes/FOCUS_L.Rmd b/vignettes/FOCUS_L.Rmd
deleted file mode 100644
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--- a/vignettes/FOCUS_L.Rmd
+++ /dev/null
@@ -1,243 +0,0 @@
-<!--
-%\VignetteEngine{knitr::knitr}
-%\VignetteIndexEntry{Example evaluation of FOCUS Laboratory Data L1 to L3}
--->
-
-# Example evaluation of FOCUS Laboratory Data L1 to L3
-
-## Laboratory Data L1
-
-The following code defines example dataset L1 from the FOCUS kinetics
-report, p. 284
-
-```{r}
-library("mkin")
-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,
- 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)
-```
-
-The next step is to set up the models used for the kinetic analysis. Note that
-the model definitions contain the names of the observed variables in the data.
-In this case, there is only one variable called `parent`.
-
-```{r}
-SFO <- mkinmod(parent = list(type = "SFO"))
-FOMC <- mkinmod(parent = list(type = "FOMC"))
-DFOP <- mkinmod(parent = list(type = "DFOP"))
-```
-
-The three models cover the first assumption of simple first order (SFO),
-the case of declining rate constant over time (FOMC) and the case of two
-different phases of the kinetics (DFOP). For a more detailed discussion
-of the models, please see the FOCUS kinetics report.
-
-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.
-
-```{r}
-m.L1.SFO <- mkinfit(SFO, FOCUS_2006_L1_mkin, quiet=TRUE)
-summary(m.L1.SFO)
-```
-
-A plot of the fit is obtained with the plot function for mkinfit objects.
-
-```{r fig.width=7, fig.height = 5}
-plot(m.L1.SFO)
-```
-The residual plot can be easily obtained by
-
-```{r fig.width=7, fig.height = 5}
-mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
-```
-
-For comparison, the FOMC model is fitted as well, and the chi^2 error level
-is checked.
-
-```{r}
-m.L1.FOMC <- mkinfit(FOMC, FOCUS_2006_L1_mkin, quiet=TRUE)
-summary(m.L1.FOMC, data = FALSE)
-```
-
-Due to the higher number of parameters, and the lower number of degrees of
-freedom of the fit, the chi^2 error level is actually higher for the FOMC
-model (3.6%) than for the SFO model (3.4%). Additionally, the covariance
-matrix can not be obtained, indicating overparameterisation of the model.
-As a consequence, no standard errors for transformed parameters nor
-confidence intervals for backtransformed parameters are available.
-
-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.
-
-Furthermore, 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 is a widely used standard package in this field.
-Therefore, the reason for the difference was not investigated further.
-
-## Laboratory Data L2
-
-The following code defines example dataset L2 from the FOCUS kinetics
-report, p. 287
-
-```{r}
-FOCUS_2006_L2 = data.frame(
- t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
- parent = c(96.1, 91.8, 41.4, 38.7,
- 19.3, 22.3, 4.6, 4.6,
- 2.6, 1.2, 0.3, 0.6))
-FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
-```
-
-Again, the SFO model is fitted and a summary is obtained.
-
-```{r}
-m.L2.SFO <- mkinfit(SFO, FOCUS_2006_L2_mkin, quiet=TRUE)
-summary(m.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 and the residuals.
-
-```{r fig.height = 8}
-par(mfrow = c(2, 1))
-plot(m.L2.SFO)
-mkinresplot(m.L2.SFO)
-```
-
-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
-day 5), and there is an underestimation beyond that point.
-
-We may add that it is difficult to judge the random nature of the residuals just
-from the three samplings at days 0, 1 and 3. Also, it is not clear _a
-priori_ why a consistent underestimation after the approximate DT90 should be
-irrelevant. However, this can be rationalised by the fact that the FOCUS fate
-models generally only implement SFO kinetics.
-
-For comparison, the FOMC model is fitted as well, and the chi^2 error level
-is checked.
-
-```{r fig.height = 8}
-m.L2.FOMC <- mkinfit(FOMC, FOCUS_2006_L2_mkin, quiet = TRUE)
-par(mfrow = c(2, 1))
-plot(m.L2.FOMC)
-mkinresplot(m.L2.FOMC)
-summary(m.L2.FOMC, data = FALSE)
-```
-
-The error level at which the chi^2 test passes is much lower in this case.
-Therefore, the FOMC model provides a better description of the data, as less
-experimental error has to be assumed in order to explain the data.
-
-Fitting the four parameter DFOP model further reduces the chi^2 error level.
-
-```{r fig.height = 5}
-m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.DFOP)
-```
-
-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
-parameters.
-
-```{r fig.height = 5}
-m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin,
- parms.ini = c(k1 = 1, k2 = 0.01, g = 0.8),
- quiet=TRUE)
-plot(m.L2.DFOP)
-summary(m.L2.DFOP, data = FALSE)
-```
-
-Here, the DFOP model is clearly the best-fit model for dataset L2 based on the
-chi^2 error level criterion. However, the failure to calculate the covariance
-matrix indicates that the parameter estimates correlate excessively. Therefore,
-the FOMC model may be preferred for this dataset.
-
-## Laboratory Data L3
-
-The following code defines example dataset L3 from the FOCUS kinetics report,
-p. 290.
-
-```{r}
-FOCUS_2006_L3 = data.frame(
- t = c(0, 3, 7, 14, 30, 60, 91, 120),
- parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
-FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
-```
-
-SFO model, summary and plot:
-
-```{r fig.height = 5}
-m.L3.SFO <- mkinfit(SFO, FOCUS_2006_L3_mkin, quiet = TRUE)
-plot(m.L3.SFO)
-summary(m.L3.SFO)
-```
-
-The chi^2 error level of 21% as well as the plot suggest that the model
-does not fit very well.
-
-The FOMC model performs better:
-
-```{r fig.height = 5}
-m.L3.FOMC <- mkinfit(FOMC, FOCUS_2006_L3_mkin, quiet = TRUE)
-plot(m.L3.FOMC)
-summary(m.L3.FOMC, data = FALSE)
-```
-
-The error level at which the chi^2 test passes is 7% in this case.
-
-Fitting the four parameter DFOP model further reduces the chi^2 error level
-considerably:
-
-```{r fig.height = 5}
-m.L3.DFOP <- mkinfit(DFOP, FOCUS_2006_L3_mkin, quiet = TRUE)
-plot(m.L3.DFOP)
-summary(m.L3.DFOP, data = FALSE)
-```
-
-Here, a look to the model plot, the confidence intervals of the parameters
-and the correlation matrix suggest that the parameter estimates are reliable, and
-the DFOP model can be used as the best-fit model based on the chi^2 error
-level criterion for laboratory data L3.
-
-## Laboratory Data L4
-
-The following code defines example dataset L4 from the FOCUS kinetics
-report, p. 293
-
-```{r}
-FOCUS_2006_L4 = data.frame(
- t = c(0, 3, 7, 14, 30, 60, 91, 120),
- parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
-FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
-```
-
-SFO model, summary and plot:
-
-```{r fig.height = 5}
-m.L4.SFO <- mkinfit(SFO, FOCUS_2006_L4_mkin, quiet = TRUE)
-plot(m.L4.SFO)
-summary(m.L4.SFO, data = FALSE)
-```
-
-The chi^2 error level of 3.3% as well as the plot suggest that the model
-fits very well.
-
-The FOMC model for comparison
-
-```{r fig.height = 5}
-m.L4.FOMC <- mkinfit(FOMC, FOCUS_2006_L4_mkin, quiet = TRUE)
-plot(m.L4.FOMC)
-summary(m.L4.FOMC, data = FALSE)
-```
-
-The error level at which the chi^2 test passes is slightly lower for the FOMC
-model. However, the difference appears negligible.
-
diff --git a/vignettes/FOCUS_L.md b/vignettes/FOCUS_L.md
deleted file mode 100644
index 6c43889..0000000
--- a/vignettes/FOCUS_L.md
+++ /dev/null
@@ -1,931 +0,0 @@
-<!--
-%\VignetteEngine{knitr::knitr}
-%\VignetteIndexEntry{Example evaluation of FOCUS Laboratory Data L1 to L3}
--->
-
-# Example evaluation of FOCUS Laboratory Data L1 to L3
-
-## Laboratory Data L1
-
-The following code defines example dataset L1 from the FOCUS kinetics
-report, p. 284
-
-
-```r
-library("mkin")
-```
-
-```
-## Loading required package: FME
-## Loading required package: deSolve
-## Loading required package: rootSolve
-## Loading required package: minpack.lm
-## Loading required package: MASS
-## Loading required package: coda
-## Loading required package: lattice
-```
-
-```r
-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, 72, 71.9, 50.3, 59.4, 47,
- 45.1, 27.7, 27.3, 10, 10.4, 2.9, 4))
-FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
-```
-
-
-The next step is to set up the models used for the kinetic analysis. Note that
-the model definitions contain the names of the observed variables in the data.
-In this case, there is only one variable called `parent`.
-
-
-```r
-SFO <- mkinmod(parent = list(type = "SFO"))
-FOMC <- mkinmod(parent = list(type = "FOMC"))
-DFOP <- mkinmod(parent = list(type = "DFOP"))
-```
-
-
-The three models cover the first assumption of simple first order (SFO),
-the case of declining rate constant over time (FOMC) and the case of two
-different phases of the kinetics (DFOP). For a more detailed discussion
-of the models, please see the FOCUS kinetics report.
-
-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.
-
-
-```r
-m.L1.SFO <- mkinfit(SFO, FOCUS_2006_L1_mkin, quiet = TRUE)
-summary(m.L1.SFO)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:54 2013
-## Date of summary: Sun Nov 17 15:02:54 2013
-##
-## Equations:
-## [1] d_parent = - k_parent_sink * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 100.0 state 100.000
-## k_parent_sink 0.1 deparm -2.303
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 92.50 1.3700 89.60 95.40
-## k_parent_sink -2.35 0.0406 -2.43 -2.26
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 92.5000 89.6000 95.400
-## k_parent_sink 0.0956 0.0877 0.104
-##
-## Residual standard error: 2.95 on 16 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 3.42 2 7
-## parent 3.42 2 7
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 7.25 24.1
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## parent_0 k_parent_sink
-## parent_0 1.000 0.625
-## k_parent_sink 0.625 1.000
-##
-## Data:
-## time variable observed predicted residual
-## 0 parent 88.3 92.47 -4.171
-## 0 parent 91.4 92.47 -1.071
-## 1 parent 85.6 84.04 1.561
-## 1 parent 84.5 84.04 0.461
-## 2 parent 78.9 76.38 2.524
-## 2 parent 77.6 76.38 1.224
-## 3 parent 72.0 69.41 2.588
-## 3 parent 71.9 69.41 2.488
-## 5 parent 50.3 57.33 -7.030
-## 5 parent 59.4 57.33 2.070
-## 7 parent 47.0 47.35 -0.352
-## 7 parent 45.1 47.35 -2.252
-## 14 parent 27.7 24.25 3.453
-## 14 parent 27.3 24.25 3.053
-## 21 parent 10.0 12.42 -2.416
-## 21 parent 10.4 12.42 -2.016
-## 30 parent 2.9 5.25 -2.351
-## 30 parent 4.0 5.25 -1.251
-```
-
-
-A plot of the fit is obtained with the plot function for mkinfit objects.
-
-
-```r
-plot(m.L1.SFO)
-```
-
-![plot of chunk unnamed-chunk-4](figure/unnamed-chunk-4.png)
-
-The residual plot can be easily obtained by
-
-
-```r
-mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
-```
-
-![plot of chunk unnamed-chunk-5](figure/unnamed-chunk-5.png)
-
-
-For comparison, the FOMC model is fitted as well, and the chi^2 error level
-is checked.
-
-
-```r
-m.L1.FOMC <- mkinfit(FOMC, FOCUS_2006_L1_mkin, quiet = TRUE)
-summary(m.L1.FOMC, data = FALSE)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:55 2013
-## Date of summary: Sun Nov 17 15:02:55 2013
-##
-## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 100 state 100.000
-## alpha 1 deparm 0.000
-## beta 10 deparm 2.303
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 92.5 NA NA NA
-## alpha 25.6 NA NA NA
-## beta 28.0 NA NA NA
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 9.25e+01 NA NA
-## alpha 1.35e+11 NA NA
-## beta 1.41e+12 NA NA
-##
-## Residual standard error: 3.05 on 15 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 3.62 3 6
-## parent 3.62 3 6
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 7.25 24.1
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## Could not estimate covariance matrix; singular system:
-```
-
-
-Due to the higher number of parameters, and the lower number of degrees of
-freedom of the fit, the chi^2 error level is actually higher for the FOMC
-model (3.6%) than for the SFO model (3.4%). Additionally, the covariance
-matrix can not be obtained, indicating overparameterisation of the model.
-As a consequence, no standard errors for transformed parameters nor
-confidence intervals for backtransformed parameters are available.
-
-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.
-
-Furthermore, 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 is a widely used standard package in this field.
-Therefore, the reason for the difference was not investigated further.
-
-## Laboratory Data L2
-
-The following code defines example dataset L2 from the FOCUS kinetics
-report, p. 287
-
-
-```r
-FOCUS_2006_L2 = data.frame(t = rep(c(0, 1, 3, 7, 14, 28), each = 2), parent = c(96.1,
- 91.8, 41.4, 38.7, 19.3, 22.3, 4.6, 4.6, 2.6, 1.2, 0.3, 0.6))
-FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
-```
-
-
-Again, the SFO model is fitted and a summary is obtained.
-
-
-```r
-m.L2.SFO <- mkinfit(SFO, FOCUS_2006_L2_mkin, quiet = TRUE)
-summary(m.L2.SFO)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:55 2013
-## Date of summary: Sun Nov 17 15:02:55 2013
-##
-## Equations:
-## [1] d_parent = - k_parent_sink * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 100.0 state 100.000
-## k_parent_sink 0.1 deparm -2.303
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 91.500 3.810 83.000 99.900
-## k_parent_sink -0.411 0.107 -0.651 -0.172
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 91.500 83.000 99.900
-## k_parent_sink 0.663 0.522 0.842
-##
-## Residual standard error: 5.51 on 10 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 14.4 2 4
-## parent 14.4 2 4
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 1.05 3.47
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## parent_0 k_parent_sink
-## parent_0 1.00 0.43
-## k_parent_sink 0.43 1.00
-##
-## Data:
-## time variable observed predicted residual
-## 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 -5.740
-## 1 parent 38.7 4.71e+01 -8.440
-## 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
-## 7 parent 4.6 8.83e-01 3.717
-## 14 parent 2.6 8.53e-03 2.591
-## 14 parent 1.2 8.53e-03 1.191
-## 28 parent 0.3 7.96e-07 0.300
-## 28 parent 0.6 7.96e-07 0.600
-```
-
-
-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 and the residuals.
-
-
-```r
-par(mfrow = c(2, 1))
-plot(m.L2.SFO)
-mkinresplot(m.L2.SFO)
-```
-
-![plot of chunk unnamed-chunk-9](figure/unnamed-chunk-9.png)
-
-
-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
-day 5), and there is an underestimation beyond that point.
-
-We may add that it is difficult to judge the random nature of the residuals just
-from the three samplings at days 0, 1 and 3. Also, it is not clear _a
-priori_ why a consistent underestimation after the approximate DT90 should be
-irrelevant. However, this can be rationalised by the fact that the FOCUS fate
-models generally only implement SFO kinetics.
-
-For comparison, the FOMC model is fitted as well, and the chi^2 error level
-is checked.
-
-
-```r
-m.L2.FOMC <- mkinfit(FOMC, FOCUS_2006_L2_mkin, quiet = TRUE)
-par(mfrow = c(2, 1))
-plot(m.L2.FOMC)
-mkinresplot(m.L2.FOMC)
-```
-
-![plot of chunk unnamed-chunk-10](figure/unnamed-chunk-10.png)
-
-```r
-summary(m.L2.FOMC, data = FALSE)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:56 2013
-## Date of summary: Sun Nov 17 15:02:56 2013
-##
-## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 100 state 100.000
-## alpha 1 deparm 0.000
-## beta 10 deparm 2.303
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 93.800 1.860 89.600 98.000
-## alpha 0.318 0.187 -0.104 0.740
-## beta 0.210 0.294 -0.456 0.876
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 93.80 89.600 98.0
-## alpha 1.37 0.901 2.1
-## beta 1.23 0.634 2.4
-##
-## Residual standard error: 2.63 on 9 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 6.2 3 3
-## parent 6.2 3 3
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 0.809 5.36
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## parent_0 alpha beta
-## parent_0 1.0000 -0.0955 -0.186
-## alpha -0.0955 1.0000 0.976
-## beta -0.1863 0.9757 1.000
-```
-
-
-The error level at which the chi^2 test passes is much lower in this case.
-Therefore, the FOMC model provides a better description of the data, as less
-experimental error has to be assumed in order to explain the data.
-
-Fitting the four parameter DFOP model further reduces the chi^2 error level.
-
-
-```r
-m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.DFOP)
-```
-
-![plot of chunk unnamed-chunk-11](figure/unnamed-chunk-11.png)
-
-
-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
-parameters.
-
-
-```r
-m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, parms.ini = c(k1 = 1, k2 = 0.01,
- g = 0.8), quiet = TRUE)
-plot(m.L2.DFOP)
-```
-
-![plot of chunk unnamed-chunk-12](figure/unnamed-chunk-12.png)
-
-```r
-summary(m.L2.DFOP, data = FALSE)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:57 2013
-## Date of summary: Sun Nov 17 15:02:57 2013
-##
-## Equations:
-## [1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 1e+02 state 100.0000
-## k1 1e+00 deparm 0.0000
-## k2 1e-02 deparm -4.6052
-## g 8e-01 deparm 0.9803
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 93.900 NA NA NA
-## k1 4.960 NA NA NA
-## k2 -1.090 NA NA NA
-## g -0.282 NA NA NA
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 93.900 NA NA
-## k1 142.000 NA NA
-## k2 0.337 NA NA
-## g 0.402 NA NA
-##
-## Residual standard error: 1.73 on 8 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 2.53 4 2
-## parent 2.53 4 2
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent NA NA
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## Could not estimate covariance matrix; singular system:
-```
-
-
-Here, the DFOP model is clearly the best-fit model for dataset L2 based on the
-chi^2 error level criterion. However, the failure to calculate the covariance
-matrix indicates that the parameter estimates correlate excessively. Therefore,
-the FOMC model may be preferred for this dataset.
-
-## Laboratory Data L3
-
-The following code defines example dataset L3 from the FOCUS kinetics report,
-p. 290.
-
-
-```r
-FOCUS_2006_L3 = data.frame(t = c(0, 3, 7, 14, 30, 60, 91, 120), parent = c(97.8,
- 60, 51, 43, 35, 22, 15, 12))
-FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
-```
-
-
-SFO model, summary and plot:
-
-
-```r
-m.L3.SFO <- mkinfit(SFO, FOCUS_2006_L3_mkin, quiet = TRUE)
-plot(m.L3.SFO)
-```
-
-![plot of chunk unnamed-chunk-14](figure/unnamed-chunk-14.png)
-
-```r
-summary(m.L3.SFO)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:57 2013
-## Date of summary: Sun Nov 17 15:02:57 2013
-##
-## Equations:
-## [1] d_parent = - k_parent_sink * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 100.0 state 100.000
-## k_parent_sink 0.1 deparm -2.303
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 74.90 8.460 54.20 95.60
-## k_parent_sink -3.68 0.326 -4.48 -2.88
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 74.9000 54.2000 95.6000
-## k_parent_sink 0.0253 0.0114 0.0561
-##
-## Residual standard error: 12.9 on 6 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 21.2 2 6
-## parent 21.2 2 6
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 27.4 91.1
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## parent_0 k_parent_sink
-## parent_0 1.000 0.548
-## k_parent_sink 0.548 1.000
-##
-## Data:
-## time variable observed predicted residual
-## 0 parent 97.8 74.87 22.9273
-## 3 parent 60.0 69.41 -9.4065
-## 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
-```
-
-
-The chi^2 error level of 21% as well as the plot suggest that the model
-does not fit very well.
-
-The FOMC model performs better:
-
-
-```r
-m.L3.FOMC <- mkinfit(FOMC, FOCUS_2006_L3_mkin, quiet = TRUE)
-plot(m.L3.FOMC)
-```
-
-![plot of chunk unnamed-chunk-15](figure/unnamed-chunk-15.png)
-
-```r
-summary(m.L3.FOMC, data = FALSE)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:57 2013
-## Date of summary: Sun Nov 17 15:02:57 2013
-##
-## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 100 state 100.000
-## alpha 1 deparm 0.000
-## beta 10 deparm 2.303
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 97.000 4.550 85.3 109.000
-## alpha -0.862 0.170 -1.3 -0.424
-## beta 0.619 0.474 -0.6 1.840
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 97.000 85.300 109.000
-## alpha 0.422 0.273 0.655
-## beta 1.860 0.549 6.290
-##
-## Residual standard error: 4.57 on 5 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 7.32 3 5
-## parent 7.32 3 5
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 7.73 431
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## parent_0 alpha beta
-## parent_0 1.000 -0.151 -0.427
-## alpha -0.151 1.000 0.911
-## beta -0.427 0.911 1.000
-```
-
-
-The error level at which the chi^2 test passes is 7% in this case.
-
-Fitting the four parameter DFOP model further reduces the chi^2 error level
-considerably:
-
-
-```r
-m.L3.DFOP <- mkinfit(DFOP, FOCUS_2006_L3_mkin, quiet = TRUE)
-plot(m.L3.DFOP)
-```
-
-![plot of chunk unnamed-chunk-16](figure/unnamed-chunk-16.png)
-
-```r
-summary(m.L3.DFOP, data = FALSE)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:58 2013
-## Date of summary: Sun Nov 17 15:02:58 2013
-##
-## Equations:
-## [1] d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 1e+02 state 100.000
-## k1 1e-01 deparm -2.303
-## k2 1e-02 deparm -4.605
-## g 5e-01 deparm 0.000
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 97.700 1.4400 93.800 102.0000
-## k1 -0.661 0.1330 -1.030 -0.2910
-## k2 -4.290 0.0590 -4.450 -4.1200
-## g -0.123 0.0512 -0.265 0.0193
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 97.7000 93.8000 102.0000
-## k1 0.5160 0.3560 0.7480
-## k2 0.0138 0.0117 0.0162
-## g 0.4570 0.4070 0.5070
-##
-## Residual standard error: 1.44 on 4 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 2.23 4 4
-## parent 2.23 4 4
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 7.46 123
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## parent_0 k1 k2 g
-## parent_0 1.0000 0.164 0.0131 0.425
-## k1 0.1640 1.000 0.4648 -0.553
-## k2 0.0131 0.465 1.0000 -0.663
-## g 0.4253 -0.553 -0.6631 1.000
-```
-
-
-Here, a look to the model plot, the confidence intervals of the parameters
-and the correlation matrix suggest that the parameter estimates are reliable, and
-the DFOP model can be used as the best-fit model based on the chi^2 error
-level criterion for laboratory data L3.
-
-## Laboratory Data L4
-
-The following code defines example dataset L4 from the FOCUS kinetics
-report, p. 293
-
-
-```r
-FOCUS_2006_L4 = data.frame(t = c(0, 3, 7, 14, 30, 60, 91, 120), parent = c(96.6,
- 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49))
-FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
-```
-
-
-SFO model, summary and plot:
-
-
-```r
-m.L4.SFO <- mkinfit(SFO, FOCUS_2006_L4_mkin, quiet = TRUE)
-plot(m.L4.SFO)
-```
-
-![plot of chunk unnamed-chunk-18](figure/unnamed-chunk-18.png)
-
-```r
-summary(m.L4.SFO, data = FALSE)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:58 2013
-## Date of summary: Sun Nov 17 15:02:58 2013
-##
-## Equations:
-## [1] d_parent = - k_parent_sink * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 100.0 state 100.000
-## k_parent_sink 0.1 deparm -2.303
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 96.40 1.95 91.70 101.00
-## k_parent_sink -5.03 0.08 -5.23 -4.83
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 96.40000 91.70000 1.01e+02
-## k_parent_sink 0.00654 0.00538 7.95e-03
-##
-## Residual standard error: 3.65 on 6 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 3.29 2 6
-## parent 3.29 2 6
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 106 352
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## parent_0 k_parent_sink
-## parent_0 1.000 0.587
-## k_parent_sink 0.587 1.000
-```
-
-
-The chi^2 error level of 3.3% as well as the plot suggest that the model
-fits very well.
-
-The FOMC model for comparison
-
-
-```r
-m.L4.FOMC <- mkinfit(FOMC, FOCUS_2006_L4_mkin, quiet = TRUE)
-plot(m.L4.FOMC)
-```
-
-![plot of chunk unnamed-chunk-19](figure/unnamed-chunk-19.png)
-
-```r
-summary(m.L4.FOMC, data = FALSE)
-```
-
-```
-## mkin version: 0.9.25
-## R version: 3.0.2
-## Date of fit: Sun Nov 17 15:02:59 2013
-## Date of summary: Sun Nov 17 15:02:59 2013
-##
-## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
-##
-## Method used for solution of differential equation system:
-## analytical
-##
-## Weighting: none
-##
-## Starting values for optimised parameters:
-## value type transformed
-## parent_0 100 state 100.000
-## alpha 1 deparm 0.000
-## beta 10 deparm 2.303
-##
-## Fixed parameter values:
-## None
-##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper
-## parent_0 99.100 1.680 94.80 103.000
-## alpha -0.351 0.372 -1.31 0.607
-## beta 4.170 0.564 2.73 5.620
-##
-## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 99.100 94.80 103.00
-## alpha 0.704 0.27 1.83
-## beta 65.000 15.30 277.00
-##
-## Residual standard error: 2.31 on 5 degrees of freedom
-##
-## Chi2 error levels in percent:
-## err.min n.optim df
-## All data 2.03 3 5
-## parent 2.03 3 5
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 109 1644
-##
-## Estimated formation fractions:
-## ff
-## parent_sink 1
-##
-## Parameter correlation:
-## parent_0 alpha beta
-## parent_0 1.000 -0.536 -0.608
-## alpha -0.536 1.000 0.991
-## beta -0.608 0.991 1.000
-```
-
-
-The error level at which the chi^2 test passes is slightly lower for the FOMC
-model. However, the difference appears negligible.
-
diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw
deleted file mode 100644
index b551007..0000000
--- a/vignettes/FOCUS_Z.Rnw
+++ /dev/null
@@ -1,310 +0,0 @@
-%\VignetteIndexEntry{Examples evaluation of FOCUS dataset Z}
-%\VignetteEngine{knitr::knitr}
-\documentclass[12pt,a4paper]{article}
-\usepackage{a4wide}
-\input{header}
-\hypersetup{
- pdftitle = {Example evaluation of FOCUS dataset Z},
- pdfsubject = {Manuscript},
- pdfauthor = {Johannes Ranke},
- colorlinks = {true},
- linkcolor = {blue},
- citecolor = {blue},
- urlcolor = {red},
- hyperindex = {true},
- linktocpage = {true},
-}
-
-\begin{document}
-
-<<include=FALSE>>=
-require(knitr)
-opts_chunk$set(engine='R', tidy=FALSE)
-@
-
-\title{Example evaluation of FOCUS dataset Z}
-\author{\textbf{Johannes Ranke} \\[0.5cm]
-%EndAName
-Wissenschaftlicher Berater\\
-Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm]
-and\\[0.5cm]
-University of Bremen\\
-}
-\maketitle
-
-\thispagestyle{empty} \setcounter{page}{0}
-
-\clearpage
-
-\tableofcontents
-
-\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation
-
-\section{The data}
-
-The following code defines the example dataset from Appendix 7 to the FOCUS kinetics
-report \citep{FOCUSkinetics2011}, p.350.
-
-<<FOCUS_2006_Z_data, echo=TRUE, eval=TRUE>>=
-require(mkin)
-LOD = 0.5
-FOCUS_2006_Z = data.frame(
- t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
- 42, 61, 96, 124),
- Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8,
- 2.9, 3.5, 5.3, 4.4, 1.2, 0.7),
- Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1,
- 1.6, 0.6, 0.5 * LOD, NA, NA, NA),
- Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5,
- 0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA),
- Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5,
- 25.2, 17.2, 4.8, 4.5, 2.8, 4.4))
-
-FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
-@
-
-\section{Parent compound and one metabolite}
-
-The next step is to set up the models used for the kinetic analysis. As the
-simultaneous fit of parent and the first metabolite is usually straightforward,
-Step 1 (SFO for parent only) is skipped here. We start with the model 2a,
-with formation and decline of metabolite Z1 and the pathway from parent
-directly to sink included (default in mkin).
-
-<<FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=4>>=
-Z.2a <- mkinmod(Z0 = list(type = "SFO", to = "Z1"),
- Z1 = list(type = "SFO"))
-m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot(m.Z.2a)
-summary(m.Z.2a, data = FALSE)
-@
-
-As obvious from the summary, the kinetic rate constant from parent compound Z to sink
-is negligible. Accordingly, the exact magnitude of the fitted parameter
-\texttt{log k\_Z\_sink} is ill-defined and the covariance matrix is not returned.
-This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify
-the model by removing the pathway to sink.
-
-A similar result can be obtained when formation fractions are used in the model
-formulation:
-
-<<FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=4>>=
-Z.2a.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1"),
- Z1 = list(type = "SFO"),
- use_of_ff = "max")
-
-m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot(m.Z.2a.ff)
-summary(m.Z.2a.ff, data = FALSE)
-@
-
-Here, the ilr transformed formation fraction fitted in the model takes a very
-large value, and the backtransformed formation fraction from parent Z to Z1 is
-practically unity. Again, the covariance matrix is not returned as the model is
-overparameterised.
-
-The simplified model is obtained by setting the list component \texttt{sink} to
-\texttt{FALSE}.
-
-<<FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=4>>=
-Z.3 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
- Z1 = list(type = "SFO"))
-m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot(m.Z.3)
-summary(m.Z.3, data = FALSE)
-@
-
-This model definition is not supported when formation fractions
-are used, but the formation fraction can be fixed to unity.
-
-<<FOCUS_2006_Z_fits_3.ff, echo=TRUE, fig.height=4>>=
-Z.3.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1"),
- Z1 = list(type = "SFO"), use_of_ff = "max")
-m.Z.3.ff <- mkinfit(Z.3.ff, FOCUS_2006_Z_mkin,
- parms.ini = c(f_Z0_to_Z1 = 1),
- fixed_parms = "f_Z0_to_Z1",
- quiet = TRUE)
-summary(m.Z.3.ff, data = FALSE)
-@
-
-\section{Including metabolites Z2 and Z3}
-
-As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as
-well in the next step. While this step appears questionable on the basis of the above results, it
-is followed here for the purpose of comparison. Also, in the FOCUS report, it is
-assumed that there is additional empirical evidence that Z1 quickly and exclusively
-hydrolyses to Z2.
-
-<<FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=4>>=
-Z.5 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
- Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
- Z2 = list(type = "SFO"))
-m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot(m.Z.5)
-summary(m.Z.5, data = FALSE)
-@
-
-Finally, metabolite Z3 is added to the model. The fit is accellerated
-by using the starting parameters from the previous fit.
-
-<<FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=4>>=
-Z.FOCUS <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
- Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
- Z2 = list(type = "SFO", to = "Z3"),
- Z3 = list(type = "SFO"))
-m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
- parms.ini = m.Z.5$bparms.ode,
- quiet = TRUE)
-plot(m.Z.FOCUS)
-summary(m.Z.FOCUS, data = FALSE)
-@
-
-This is the fit corresponding to the final result chosen in Appendix 7 of the
-FOCUS report. The residual plots can be obtained by
-
-<<FOCUS_2006_Z_residuals_6, echo=TRUE>>=
-par(mfrow = c(2, 2))
-mkinresplot(m.Z.FOCUS, "Z0", lpos = "bottomright")
-mkinresplot(m.Z.FOCUS, "Z1", lpos = "bottomright")
-mkinresplot(m.Z.FOCUS, "Z2", lpos = "bottomright")
-mkinresplot(m.Z.FOCUS, "Z3", lpos = "bottomright")
-@
-
-We can also investigate the confidence interval for the formation
-fraction from Z1 to Z2 by specifying the model using formation
-fractions, and fixing only the formation fraction from Z0 to Z1
-to unity.
-
-<<FOCUS_2006_Z_fits_6_ff, echo=TRUE, fig.height=4>>=
-Z.FOCUS.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1"),
- Z1 = list(type = "SFO", to = "Z2"),
- Z2 = list(type = "SFO", to = "Z3"),
- Z3 = list(type = "SFO"), use_of_ff = "max")
-m.Z.FOCUS.ff <- mkinfit(Z.FOCUS.ff, FOCUS_2006_Z_mkin,
- parms.ini = c(f_Z0_to_Z1 = 1),
- fixed_parms = c("f_Z0_to_Z1"), quiet = TRUE)
-plot(m.Z.FOCUS.ff)
-summary(m.Z.FOCUS.ff, data = FALSE)
-@
-
-\section{Using the SFORB model for parent and metabolites}
-
-As the FOCUS report states, there is a certain tailing of the time course of metabolite
-Z3. Also, the time course of the parent compound is not fitted very well using the
-SFO model, as residues at a certain low level remain.
-
-Therefore, an additional model is offered here, using the single first-order
-reversible binding (SFORB) model for metabolite Z3. As expected, the $\chi^2$
-error level is lower for metabolite Z3 using this model and the graphical
-fit for Z3 is improved. However, the covariance matrix is not returned.
-
-<<FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=4>>=
-Z.mkin.1 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE),
- Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
- Z2 = list(type = "SFO", to = "Z3"),
- Z3 = list(type = "SFORB"))
-m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin,
- parms.ini = c(k_Z0_Z1 = 0.5, k_Z1_Z2 = 0.3),
- quiet = TRUE)
-plot(m.Z.mkin.1)
-summary(m.Z.mkin.1, data = FALSE)
-@
-
-Therefore, a further stepwise model building is performed starting from the
-stage of parent and one metabolite, starting from the assumption that the model
-fit for the parent compound can be improved by using the SFORB model.
-
-<<FOCUS_2006_Z_fits_8, echo=TRUE, fig.height=4>>=
-Z.mkin.2 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE),
- Z1 = list(type = "SFO"))
-m.Z.mkin.2 <- mkinfit(Z.mkin.2, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot(m.Z.mkin.2)
-summary(m.Z.mkin.2, data = FALSE)
-@
-
-When metabolite Z2 is added, the additional sink for Z1 is turned off again,
-for the same reasons as in the original analysis.
-
-<<FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=4>>=
-Z.mkin.3 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE),
- Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
- Z2 = list(type = "SFO"))
-m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot(m.Z.mkin.3)
-summary(m.Z.mkin.3, data = FALSE)
-@
-
-This results in a much better representation of the behaviour of the parent
-compound Z0.
-
-Finally, Z3 is added as well. These models appear overparameterised (no
-covariance matrix returned) if the sink for Z1 is left in the models.
-
-<<FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=4>>=
-Z.mkin.4 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE),
- Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
- Z2 = list(type = "SFO", to = "Z3"),
- Z3 = list(type = "SFO"))
-m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
- parms.ini = c(k_Z1_Z2 = 0.05),
- quiet = TRUE)
-plot(m.Z.mkin.4)
-summary(m.Z.mkin.4, data = FALSE)
-@
-
-The error level of the fit, but especially of metabolite Z3, can be improved if
-the SFORB model is chosen for this metabolite, as this model is capable of
-representing the tailing of the metabolite decline phase.
-
-<<FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=4>>=
-Z.mkin.5 <- mkinmod(Z0 = list(type = "SFORB", to = "Z1", sink = FALSE),
- Z1 = list(type = "SFO", to = "Z2", sink = FALSE),
- Z2 = list(type = "SFO", to = "Z3"),
- Z3 = list(type = "SFORB"))
-m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
- parms.ini = m.Z.mkin.4$bparms.ode[1:5],
- quiet = TRUE)
-plot(m.Z.mkin.5)
-summary(m.Z.mkin.5, data = FALSE)$bpar
-@
-
-The summary view of the backtransformed parameters shows that we get no
-confidence intervals due to overparameterisation. As the optimized
-\texttt{k\_Z3\_bound\_free} is excessively small, it is reasonable to fix it to
-zero.
-
-<<FOCUS_2006_Z_fits_11a, echo=TRUE>>=
-m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
- parms.ini = c(m.Z.mkin.4$bparms.ode[1:5],
- k_Z3_bound_free = 0),
- fixed_parms = "k_Z3_bound_free",
- quiet = TRUE)
-summary(m.Z.mkin.5a, data = FALSE)$bpar
-@
-
-A graphical representation of the confidence intervals can finally be obtained.
-<<FOCUS_2006_Z_fits_11b, echo=TRUE>>=
-mkinparplot(m.Z.mkin.5a)
-@
-
-It is clear that nothing can be said about the degradation rate of Z3 towards
-the end of the experiment. However, this appears to be a feature of the data.
-
-<<FOCUS_2006_Z_residuals_11>>=
-par(mfrow = c(2, 2))
-mkinresplot(m.Z.mkin.5, "Z0", lpos = "bottomright")
-mkinresplot(m.Z.mkin.5, "Z1", lpos = "bottomright")
-mkinresplot(m.Z.mkin.5, "Z2", lpos = "bottomright")
-mkinresplot(m.Z.mkin.5, "Z3", lpos = "bottomright")
-@
-
-As expected, the residual plots are much more random than in the case of the
-all SFO model for which they were shown above. In conclusion, the model
-\texttt{Z.mkin.5} is proposed as the best-fit model for the dataset from
-Appendix 7 of the FOCUS report.
-
-\bibliographystyle{plainnat}
-\bibliography{references}
-
-\end{document}
-% vim: set foldmethod=syntax:
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diff --git a/vignettes/header.tex b/vignettes/header.tex
deleted file mode 100644
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--- a/vignettes/header.tex
+++ /dev/null
@@ -1,23 +0,0 @@
-\usepackage{booktabs}
-\usepackage{amsfonts}
-\usepackage{latexsym}
-\usepackage{amsmath}
-\usepackage{amssymb}
-\usepackage{graphicx}
-\usepackage{parskip}
-\usepackage[round]{natbib}
-\usepackage{amstext}
-\usepackage{hyperref}
-\usepackage[utf8]{inputenc}
-
-\newcommand{\Rpackage}[1]{{\normalfont\fontseries{b}\selectfont #1}}
-\newcommand{\Robject}[1]{\texttt{#1}}
-\newcommand{\Rclass}[1]{\textit{#1}}
-\newcommand{\Rcmd}[1]{\texttt{#1}}
-
-\newcommand{\RR}{\textsf{R}}
-
-\RequirePackage[T1]{fontenc}
-\RequirePackage{graphicx,ae,fancyvrb}
-\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
-\usepackage{relsize}
diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw
deleted file mode 100644
index 0ac114e..0000000
--- a/vignettes/mkin.Rnw
+++ /dev/null
@@ -1,74 +0,0 @@
-%\VignetteIndexEntry{Routines for fitting kinetic models with one or more state variables to chemical degradation data}
-%\VignetteEngine{knitr::knitr}
-\documentclass[12pt,a4paper]{article}
-\usepackage{a4wide}
-\input{header}
-\hypersetup{
- pdftitle = {mkin - Routines for fitting kinetic models with one or more state variables to chemical degradation data},
- pdfsubject = {Manuscript},
- pdfauthor = {Johannes Ranke},
- colorlinks = {true},
- linkcolor = {blue},
- citecolor = {blue},
- urlcolor = {red},
- linktocpage = {true},
-}
-
-\begin{document}
-
-<<include=FALSE>>=
-require(knitr)
-opts_chunk$set(engine='R', tidy=FALSE)
-@
-
-\title{mkin -\\
-Routines for fitting kinetic models with one or more state variables to
-chemical degradation data}
-\author{\textbf{Johannes Ranke} \\[0.5cm]
-%EndAName
-Wissenschaftlicher Berater\\
-Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm]
-and\\[0.5cm]
-University of Bremen\\
-}
-\maketitle
-
-\begin{abstract}
-In the regulatory evaluation of chemical substances like plant protection
-products (pesticides), biocides and other chemicals, degradation data play an
-important role. For the evaluation of pesticide degradation experiments,
-detailed guidance has been developed, based on nonlinear optimisation.
-The \RR{} add-on package \Rpackage{mkin} implements fitting some of the models
-recommended in this guidance from within R and calculates some statistical
-measures for data series within one or more compartments, for parent and
-metabolites.
-\end{abstract}
-
-
-\thispagestyle{empty} \setcounter{page}{0}
-
-\clearpage
-
-\tableofcontents
-
-\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation
-
-\section{Introduction}
-\label{intro}
-
-Many approaches are possible regarding the evaluation of chemical degradation
-data. The \Rpackage{kinfit} package \citep{pkg:kinfit} in \RR{}
-\citep{rcore2013} implements the approach recommended in the kinetics report
-provided by the FOrum for Co-ordination of pesticide fate models and their
-USe \citep{FOCUS2006, FOCUSkinetics2011} for simple data series for one parent
-compound in one compartment.
-
-The \Rpackage{mkin} package \citep{pkg:mkin} extends this approach to data series
-with metabolites and more than one compartment and includes the possibility
-for back reactions.
-
-\bibliographystyle{plainnat}
-\bibliography{references}
-
-\end{document}
-% vim: set foldmethod=syntax:
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
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index 42a44d6..0000000
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diff --git a/vignettes/references.bib b/vignettes/references.bib
deleted file mode 100644
index e069daf..0000000
--- a/vignettes/references.bib
+++ /dev/null
@@ -1,79 +0,0 @@
-% This file was originally created with JabRef 2.7b.
-% Encoding: ISO8859_1
-
-@BOOK{bates88,
- title = {Nonlinear regression and its applications},
- publisher = {Wiley-Interscience},
- year = {1988},
- author = {D. Bates and D. Watts}
-}
-
-@MANUAL{FOCUSkinetics2011,
- title = {Generic guidance for estimating persistence and degradation kinetics
- from environmental fate studies on pesticides in EU registration},
- author = {{FOCUS Work Group on Degradation Kinetics}},
- edition = {1.0},
- month = {November},
- year = {2011},
- file = {FOCUS kinetics 2011 Generic guidance:/home/ranke/dok/orgs/focus/FOCUSkineticsvc_1_0_Nov23.pdf:PDF},
- url = {http://focus.jrc.ec.europa.eu/dk}
-}
-
-@MANUAL{FOCUS2006,
- title = {Guidance Document on Estimating Persistence and Degradation Kinetics
- from Environmental Fate Studies on Pesticides in EU Registration.
- Report of the FOCUS Work Group on Degradation Kinetics},
- author = {{FOCUS Work Group on Degradation Kinetics}},
- year = {2006},
- note = {EC Document Reference Sanco/10058/2005 version 2.0},
- url = {http://focus.jrc.ec.europa.eu/dk}
-}
-
-@MANUAL{rcore2013,
- title = {\textsf{R}: A Language and Environment for Statistical Computing},
- author = {{R Development Core Team}},
- organization = {R Foundation for Statistical Computing},
- address = {Vienna, Austria},
- year = {2013},
- note = {{ISBN} 3-900051-07-0},
- url = {http://www.R-project.org}
-}
-
-@MANUAL{pkg:kinfit,
- title = {kinfit: {R}outines for fitting simple kinetic models to chemical
- degradation data},
- author = {Johannes Ranke},
- year = {2013},
- url = {http://CRAN.R-project.org/package=kinfit}
-}
-
-@MANUAL{pkg:mkin,
- title = {mkin: {R}outines for fitting kinetic models with one or more state
- variables to chemical degradation data},
- author = {Johannes Ranke},
- year = {2013},
- url = {http://CRAN.R-project.org/package/kinfit}
-}
-
-@INPROCEEDINGS{schaefer2007,
- author = {D. Sch\"{a}fer and M. Mikolasch and P. Rainbird and B. Harvey},
- title = {{KinGUI}: a new kinetic software tool for evaluations according to
- FOCUS degradation kinetics},
- booktitle = {Proceedings of the XIII Symposium Pesticide Chemistry},
- year = {2007},
- editor = {Del Re A. A. M. and Capri E. and Fragoulis G. and Trevisan M.},
- pages = {916--923},
- address = {Piacenza}
-}
-
-@ARTICLE{soetaert10,
- author = {Karline Soetaert and Thomas Petzoldt},
- title = {Inverse Modelling, Sensitivity and Monte Carlo Analysis in {R} Using
- Package {FME}},
- journal = {Journal of Statistical Software},
- year = {2010},
- volume = {33},
- pages = {1--28},
- number = {3},
- url = {http://www.jstatsoft.org/v33/i03/}
-}

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