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| author | Johannes Ranke <jranke@uni-bremen.de> | 2014-05-05 15:02:34 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2014-05-05 15:02:34 +0200 |
| commit | fff36cb5f60626d8dbfe97514226e0a46bb938f6 (patch) | |
| tree | 54f1858f44d45f5ff0bc21fc6a8f96f0f38dd592 /vignettes/FOCUS_Z.Rnw | |
| parent | fe88194f688a758b4a89b4502244038ddf6c549d (diff) | |
Update of vignettes
Diffstat (limited to 'vignettes/FOCUS_Z.Rnw')
| -rw-r--r-- | vignettes/FOCUS_Z.Rnw | 24 |
1 files changed, 21 insertions, 3 deletions
diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw index 694c5eea..279f09b1 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), |