Remove trailing whitespace, clean headers

Also ignore test.R in the top level directory, as it is not meant to
be public

1 files changed, 33 insertions, 33 deletions

diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw
index 5a66db24..5abda0e1 100644
--- a/vignettes/FOCUS_Z.Rnw
+++ b/vignettes/FOCUS_Z.Rnw
@@ -3,7 +3,7 @@
 \documentclass[12pt,a4paper]{article}
 \usepackage{a4wide}
 \input{header}
-\hypersetup{  
+\hypersetup{
   pdftitle = {Example evaluation of FOCUS dataset Z},
   pdfsubject = {Manuscript},
   pdfauthor = {Johannes Ranke},
@@ -50,15 +50,15 @@ report \citep{FOCUSkinetics2011}, p.350.
 require(mkin)
 LOD = 0.5
 FOCUS_2006_Z = data.frame(
-  t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21, 
+  t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
         42, 61, 96, 124),
-  Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8, 
+  Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8,
          2.9, 3.5, 5.3, 4.4, 1.2, 0.7),
-  Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1, 
+  Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1,
          1.6, 0.6, 0.5 * LOD, NA, NA, NA),
-  Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5, 
+  Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5,
          0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA),
-  Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5, 
+  Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5,
          25.2, 17.2, 4.8, 4.5, 2.8, 4.4))
 
 FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
@@ -66,9 +66,9 @@ FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
 
 \section{Parent compound and one metabolite}
 
-The next step is to set up the models used for the kinetic analysis. As the 
+The next step is to set up the models used for the kinetic analysis. As the
 simultaneous fit of parent and the first metabolite is usually straightforward,
-Step 1 (SFO for parent only) is skipped here. We start with the model 2a, 
+Step 1 (SFO for parent only) is skipped here. We start with the model 2a,
 with formation and decline of metabolite Z1 and the pathway from parent
 directly to sink included (default in mkin).
 
@@ -80,15 +80,15 @@ plot_sep(m.Z.2a)
 summary(m.Z.2a, data = FALSE)$bpar
 @
 
-As obvious from the parameter summary (the \texttt{bpar} component of the 
+As obvious from the parameter summary (the \texttt{bpar} component of the
 summary), the kinetic rate constant from parent compound Z to sink
-is negligible. Accordingly, the exact magnitude of the fitted parameter 
+is negligible. Accordingly, the exact magnitude of the fitted parameter
 \texttt{log k\_Z0\_sink} is ill-defined and the covariance matrix is not
-returned (not shown, would be visible in the complete summary). 
+returned (not shown, would be visible in the complete summary).
 This suggests, in agreement with the analysis in the FOCUS kinetics report, to
 simplify the model by removing the pathway to sink.
 
-A similar result can be obtained when formation fractions are used in the model 
+A similar result can be obtained when formation fractions are used in the model
 formulation:
 
 <<FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6>>=
@@ -104,16 +104,16 @@ summary(m.Z.2a.ff, data = FALSE)$bpar
 Here, the ilr transformed formation fraction fitted in the model takes a very
 large value, and the backtransformed formation fraction from parent Z to Z1 is
 practically unity. Again, the covariance matrix is not returned as the model is
-overparameterised. 
+overparameterised.
 
 The simplified model is obtained by setting the list component \texttt{sink} to
 \texttt{FALSE}.\footnote{If the model formulation without formation fractions
 is used, the same effect can be obtained by fixing the parameter \texttt{k\_Z\_sink}
-to a value of zero.} 
+to a value of zero.}
 
 In the following, we use the parameterisation with formation fractions in order
-to be able to compare with the results in the FOCUS guidance, and as it 
-makes it easier to use parameters obtained in a previous fit when adding a further 
+to be able to compare with the results in the FOCUS guidance, and as it
+makes it easier to use parameters obtained in a previous fit when adding a further
 metabolite.
 
 <<FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6>>=
@@ -130,10 +130,10 @@ to sink, the formation fraction is internally fixed to unity.
 \section{Including metabolites Z2 and Z3}
 
 As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as
-well in the next step. While this step appears questionable on the basis of the above results, it 
-is followed here for the purpose of comparison. Also, in the FOCUS report, it is 
+well in the next step. While this step appears questionable on the basis of the above results, it
+is followed here for the purpose of comparison. Also, in the FOCUS report, it is
 assumed that there is additional empirical evidence that Z1 quickly and exclusively
-hydrolyses to Z2. 
+hydrolyses to Z2.
 
 <<FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7>>=
 Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
@@ -151,9 +151,9 @@ accelerate the optimization.
 Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                    Z2 = mkinsub("SFO", "Z3"),
-                   Z3 = mkinsub("SFO"), 
+                   Z3 = mkinsub("SFO"),
                    use_of_ff = "max")
-m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, 
+m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
                      parms.ini = m.Z.5$bparms.ode,
                      quiet = TRUE)
 plot_sep(m.Z.FOCUS)
@@ -167,13 +167,13 @@ transformed parameters, however.
 
 \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 
-Z3. Also, the time course of the parent compound is not fitted very well using the 
+As the FOCUS report states, there is a certain tailing of the time course of metabolite
+Z3. Also, the time course of the parent compound is not fitted very well using the
 SFO model, as residues at a certain low level remain.
 
-Therefore, an additional model is offered here, using the single first-order 
+Therefore, an additional model is offered here, using the single first-order
 reversible binding (SFORB) model for metabolite Z3. As expected, the $\chi^2$
-error level is lower for metabolite Z3 using this model and the graphical 
+error level is lower for metabolite Z3 using this model and the graphical
 fit for Z3 is improved. However, the covariance matrix is not returned.
 
 <<FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8>>=
@@ -198,7 +198,7 @@ m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.mkin.3)
 @
 
-This results in a much better representation of the behaviour of the parent 
+This results in a much better representation of the behaviour of the parent
 compound Z0.
 
 Finally, Z3 is added as well. These models appear overparameterised (no
@@ -209,7 +209,7 @@ Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                     Z2 = mkinsub("SFO", "Z3"),
                     Z3 = mkinsub("SFO"))
-m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, 
+m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
                       parms.ini = m.Z.mkin.3$bparms.ode,
                       quiet = TRUE)
 plot_sep(m.Z.mkin.4)
@@ -224,7 +224,7 @@ Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                     Z2 = mkinsub("SFO", "Z3"),
                     Z3 = mkinsub("SFORB"))
-m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, 
+m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
                       parms.ini = m.Z.mkin.4$bparms.ode[1:4],
                       quiet = TRUE)
 plot_sep(m.Z.mkin.5)
@@ -233,10 +233,10 @@ plot_sep(m.Z.mkin.5)
 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 seems reasonable to fix it to
-zero. 
+zero.
 
 <<FOCUS_2006_Z_fits_11a, echo=TRUE>>=
-m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, 
+m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
                        parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
                                      k_Z3_bound_free = 0),
                        fixed_parms = "k_Z3_bound_free",
@@ -244,7 +244,7 @@ m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
 plot_sep(m.Z.mkin.5a)
 @
 
-As expected, the residual plots for Z0 and Z3 are more random than in the case of the 
+As expected, the residual plots for Z0 and Z3 are more random than in the case of the
 all SFO model for which they were shown above. In conclusion, the model
 \texttt{Z.mkin.5a} is proposed as the best-fit model for the dataset from
 Appendix 7 of the FOCUS report.
@@ -261,8 +261,8 @@ The endpoints obtained with this model are
 endpoints(m.Z.mkin.5a)
 @
 
-It is clear the degradation rate of Z3 towards the end of the experiment 
-is very low as DT50\_Z3\_b2 (the second Eigenvalue of the system of two differential 
+It is clear the degradation rate of Z3 towards the end of the experiment
+is very low as DT50\_Z3\_b2 (the second Eigenvalue of the system of two differential
 equations representing the SFORB system for Z3, corresponding to the slower rate
 constant of the DFOP model) is reported to be infinity.  However, this appears
 to be a feature of the data.