From fff36cb5f60626d8dbfe97514226e0a46bb938f6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 5 May 2014 15:02:34 +0200 Subject: Update of vignettes --- vignettes/FOCUS_Z.Rnw | 24 +++++++++++++++++++++--- vignettes/FOCUS_Z.pdf | Bin 189030 -> 211848 bytes vignettes/figure/FOCUS_2006_Z_fits_1.pdf | Bin 5670 -> 5670 bytes vignettes/figure/FOCUS_2006_Z_fits_10.pdf | Bin 7587 -> 7587 bytes vignettes/figure/FOCUS_2006_Z_fits_11.pdf | Bin 7598 -> 7598 bytes vignettes/figure/FOCUS_2006_Z_fits_11b.pdf | Bin 5008 -> 5008 bytes vignettes/figure/FOCUS_2006_Z_fits_2.pdf | Bin 5670 -> 5670 bytes vignettes/figure/FOCUS_2006_Z_fits_3.pdf | Bin 5670 -> 5670 bytes vignettes/figure/FOCUS_2006_Z_fits_5.pdf | Bin 6155 -> 6155 bytes vignettes/figure/FOCUS_2006_Z_fits_6.pdf | Bin 6966 -> 6966 bytes vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf | Bin 0 -> 6937 bytes vignettes/figure/FOCUS_2006_Z_fits_7.pdf | Bin 6967 -> 6967 bytes vignettes/figure/FOCUS_2006_Z_fits_8.pdf | Bin 6158 -> 6158 bytes vignettes/figure/FOCUS_2006_Z_fits_9.pdf | Bin 6785 -> 6785 bytes vignettes/figure/FOCUS_2006_Z_residuals_11.pdf | Bin 5940 -> 5940 bytes vignettes/figure/FOCUS_2006_Z_residuals_6.pdf | Bin 5959 -> 5959 bytes vignettes/mkin.Rnw | 4 ++-- vignettes/mkin.pdf | Bin 125145 -> 124442 bytes 18 files changed, 23 insertions(+), 5 deletions(-) create mode 100644 vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf 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$set(engine='R', tidy=FALSE) \title{Example evaluation of FOCUS dataset Z} \author{\textbf{Johannes Ranke} \\[0.5cm] %EndAName -Eurofins Regulatory AG\\ -Weidenweg 15, CH--4310 Rheinfelden, Switzerland\\[0.5cm] +Wissenschaftlicher Berater\\ +Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm] and\\[0.5cm] University of Bremen\\ } @@ -170,6 +170,23 @@ mkinresplot(m.Z.FOCUS, "Z2", lpos = "bottomright") mkinresplot(m.Z.FOCUS, "Z3", lpos = "bottomright") @ +We can also investigate the confidence interval for the formation +fraction from Z1 to Z2 by specifying the model using formation +fractions, and fixing only the formation fraction from Z0 to Z1 +to unity. + +<>= +Z.FOCUS.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1"), + Z1 = list(type = "SFO", to = "Z2"), + Z2 = list(type = "SFO", to = "Z3"), + Z3 = list(type = "SFO"), use_of_ff = "max") +m.Z.FOCUS.ff <- mkinfit(Z.FOCUS.ff, FOCUS_2006_Z_mkin, + parms.ini = c(f_Z0_to_Z1 = 1), + fixed_parms = c("f_Z0_to_Z1"), quiet = TRUE) +plot(m.Z.FOCUS.ff) +summary(m.Z.FOCUS.ff, data = FALSE) +@ + \section{Using the SFORB model for parent and metabolites} As the FOCUS report states, there is a certain tailing of the time course of metabolite @@ -255,7 +272,8 @@ The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized \texttt{k\_Z3\_bound\_free} is excessively small, it is reasonable to fix it to zero. -<>= + +<>= m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.4$bparms.ode[1:5], k_Z3_bound_free = 0), diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf index e29de6c..9183333 100644 Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf index 346b9f2..abc94d3 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf index 26d2ec0..1e95815 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf index 577677b..889d48d 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf index 57880f1..7d04f02 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf index 8b6fd71..3b723cb 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf index 9d04fed..3b723cb 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf index cf9e2ff..aa58cc7 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf index 3c157dd..cc95d50 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf new file mode 100644 index 0000000..cec4ea0 Binary files /dev/null and b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf index b50959b..34f2a2f 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf index 21985bd..664c810 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf index 970aabd..ac2d70d 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf and b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf index f69ffd9..254671d 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf and b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf differ diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf index 22f62bc..3454b05 100644 Binary files a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf and b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf differ 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 index 6849fb4..42a44d6 100644 Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ -- cgit v1.2.1