Update of vignettes

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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