diff options
Diffstat (limited to 'vignettes')
18 files changed, 23 insertions, 5 deletions
diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw index 694c5ee..279f09b 100644 --- a/vignettes/FOCUS_Z.Rnw +++ b/vignettes/FOCUS_Z.Rnw @@ -25,8 +25,8 @@ opts_chunk$set(engine='R', tidy=FALSE) \title{Example evaluation of FOCUS dataset Z} \author{\textbf{Johannes Ranke} \\[0.5cm] %EndAName -Eurofins Regulatory AG\\ -Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm] +Wissenschaftlicher Berater\\ +Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm] and\\[0.5cm] University of Bremen\\ } @@ -170,6 +170,23 @@ mkinresplot(m.Z.FOCUS, "Z2", lpos = "bottomright") mkinresplot(m.Z.FOCUS, "Z3", lpos = "bottomright") @ +We can also investigate the confidence interval for the formation +fraction from Z1 to Z2 by specifying the model using formation +fractions, and fixing only the formation fraction from Z0 to Z1 +to unity. + +<<FOCUS_2006_Z_fits_6_ff, echo=TRUE, fig.height=4>>= +Z.FOCUS.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1"), + Z1 = list(type = "SFO", to = "Z2"), + Z2 = list(type = "SFO", to = "Z3"), + Z3 = list(type = "SFO"), use_of_ff = "max") +m.Z.FOCUS.ff <- mkinfit(Z.FOCUS.ff, FOCUS_2006_Z_mkin, + parms.ini = c(f_Z0_to_Z1 = 1), + fixed_parms = c("f_Z0_to_Z1"), quiet = TRUE) +plot(m.Z.FOCUS.ff) +summary(m.Z.FOCUS.ff, data = FALSE) +@ + \section{Using the SFORB model for parent and metabolites} As the FOCUS report states, there is a certain tailing of the time course of metabolite @@ -255,7 +272,8 @@ The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized \texttt{k\_Z3\_bound\_free} is excessively small, it is reasonable to fix it to zero. -<<FOCUS_2006_Z_fits_11a, echo=TRUE, fig.height=4>>= + +<<FOCUS_2006_Z_fits_11a, echo=TRUE>>= m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.4$bparms.ode[1:5], k_Z3_bound_free = 0), diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex e29de6c..9183333 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf Binary files differindex 346b9f2..abc94d3 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf Binary files differindex 26d2ec0..1e95815 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf Binary files differindex 577677b..889d48d 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf Binary files differindex 57880f1..7d04f02 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf Binary files differindex 8b6fd71..3b723cb 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf Binary files differindex 9d04fed..3b723cb 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf Binary files differindex cf9e2ff..aa58cc7 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf Binary files differindex 3c157dd..cc95d50 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf Binary files differnew file mode 100644 index 0000000..cec4ea0 --- /dev/null +++ b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf Binary files differindex b50959b..34f2a2f 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf Binary files differindex 21985bd..664c810 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf Binary files differindex 970aabd..ac2d70d 100644 --- a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf +++ b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf Binary files differindex f69ffd9..254671d 100644 --- a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf +++ b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf Binary files differindex 22f62bc..3454b05 100644 --- a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf +++ b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw index 398b541..0ac114e 100644 --- a/vignettes/mkin.Rnw +++ b/vignettes/mkin.Rnw @@ -26,8 +26,8 @@ Routines for fitting kinetic models with one or more state variables to chemical degradation data} \author{\textbf{Johannes Ranke} \\[0.5cm] %EndAName -Eurofins Regulatory AG\\ -Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm] +Wissenschaftlicher Berater\\ +Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm] and\\[0.5cm] University of Bremen\\ } diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex 6849fb4..42a44d6 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |