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authorJohannes Ranke <jranke@uni-bremen.de>2014-05-05 15:02:34 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2014-05-05 15:02:34 +0200
commitfff36cb5f60626d8dbfe97514226e0a46bb938f6 (patch)
tree54f1858f44d45f5ff0bc21fc6a8f96f0f38dd592 /vignettes
parentfe88194f688a758b4a89b4502244038ddf6c549d (diff)
Update of vignettes
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/FOCUS_Z.Rnw24
-rw-r--r--vignettes/FOCUS_Z.pdfbin189030 -> 211848 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_1.pdfbin5670 -> 5670 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_10.pdfbin7587 -> 7587 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_11.pdfbin7598 -> 7598 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_11b.pdfbin5008 -> 5008 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_2.pdfbin5670 -> 5670 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_3.pdfbin5670 -> 5670 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_5.pdfbin6155 -> 6155 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_6.pdfbin6966 -> 6966 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdfbin0 -> 6937 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_7.pdfbin6967 -> 6967 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_8.pdfbin6158 -> 6158 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_fits_9.pdfbin6785 -> 6785 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_residuals_11.pdfbin5940 -> 5940 bytes
-rw-r--r--vignettes/figure/FOCUS_2006_Z_residuals_6.pdfbin5959 -> 5959 bytes
-rw-r--r--vignettes/mkin.Rnw4
-rw-r--r--vignettes/mkin.pdfbin125145 -> 124442 bytes
18 files changed, 23 insertions, 5 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),
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index e29de6ca..9183333f 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
index 346b9f27..abc94d33 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_1.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
index 26d2ec09..1e95815d 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_10.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
index 577677bf..889d48d9 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_11.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
index 57880f13..7d04f022 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_11b.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
index 8b6fd715..3b723cb7 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_2.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
index 9d04fed7..3b723cb7 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_3.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
index cf9e2ffb..aa58cc7c 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_5.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
index 3c157dd3..cc95d502 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_6.pdf
Binary files 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 00000000..cec4ea0c
--- /dev/null
+++ b/vignettes/figure/FOCUS_2006_Z_fits_6_ff.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
index b50959bd..34f2a2f6 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_7.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
index 21985bd3..664c8105 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_8.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
index 970aabd3..ac2d70dc 100644
--- a/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_fits_9.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
index f69ffd9f..254671d1 100644
--- a/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_residuals_11.pdf
Binary files differ
diff --git a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
index 22f62bcb..3454b059 100644
--- a/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
+++ b/vignettes/figure/FOCUS_2006_Z_residuals_6.pdf
Binary files differ
diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw
index 398b5418..0ac114ed 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 6849fb48..42a44d64 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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