From 30f55769fe2f042c7753144051dd34eec3596adc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2016 16:48:21 +0100 Subject: Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE) Again with the jranke branch of jranke/pkgdown --- docs/articles/FOCUS_D.html | 37 +- docs/articles/FOCUS_D_cache/html/__packages | 2 + .../data_7c3240ac153a7639ee517a9110a0f103.RData | Bin 3175 -> 0 bytes .../html/data_7c3240ac153a7639ee517a9110a0f103.rdb | 0 .../html/data_7c3240ac153a7639ee517a9110a0f103.rdx | Bin 113 -> 0 bytes .../fit_33941ca5d01df032930f2f38dc298a59.RData | Bin 2735 -> 0 bytes .../html/fit_33941ca5d01df032930f2f38dc298a59.rdb | Bin 15588 -> 0 bytes .../html/fit_33941ca5d01df032930f2f38dc298a59.rdx | Bin 161 -> 0 bytes .../html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb | Bin 100337 -> 100468 bytes .../html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx | Bin 168 -> 169 bytes .../model_7de92bef541220dbe2d2832243e35870.RData | Bin 2927 -> 0 bytes .../model_7de92bef541220dbe2d2832243e35870.rdb | Bin 1776 -> 0 bytes .../model_7de92bef541220dbe2d2832243e35870.rdx | Bin 147 -> 0 bytes .../model_911bdb95adf8c19a8e50c4150b20f2fc.rdb | Bin 1778 -> 1777 bytes .../model_911bdb95adf8c19a8e50c4150b20f2fc.rdx | Bin 147 -> 147 bytes .../plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData | Bin 2756 -> 0 bytes .../plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb | 0 .../plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx | Bin 113 -> 0 bytes .../plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData | Bin 2786 -> 0 bytes .../html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb | 0 .../html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx | Bin 113 -> 0 bytes ...-chunk-2_2c30ef6f2fb33a606bda3c2882a070ab.RData | Bin 4629 -> 0 bytes ...ed-chunk-2_2c30ef6f2fb33a606bda3c2882a070ab.rdb | 0 ...ed-chunk-2_2c30ef6f2fb33a606bda3c2882a070ab.rdx | Bin 113 -> 0 bytes ...-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData | Bin 4624 -> 4627 bytes docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 38557 -> 95834 bytes .../FOCUS_D_files/figure-html/plot_2-1.png | Bin 6091 -> 14059 bytes docs/articles/FOCUS_L.html | 67 +- docs/articles/FOCUS_Z.aux | 26 - docs/articles/FOCUS_Z.bbl | 15 - docs/articles/FOCUS_Z.blg | 46 -- docs/articles/FOCUS_Z.log | 821 --------------------- docs/articles/FOCUS_Z.out | 4 - docs/articles/FOCUS_Z.tex | 566 -------------- docs/articles/FOCUS_Z.toc | 4 - ..._fits_10_ad34939f1c4da097e64c6add505f564d.RData | Bin 3289 -> 0 bytes ..._Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdb | Bin 25733 -> 0 bytes ..._Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdx | Bin 176 -> 0 bytes ..._fits_11_9a3c490a93568b80d56e768bd4d45f20.RData | Bin 3303 -> 0 bytes ..._Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdb | Bin 27314 -> 0 bytes ..._Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdx | Bin 176 -> 0 bytes ...fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.RData | Bin 3053 -> 0 bytes ...Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdb | Bin 25771 -> 0 bytes ...Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdx | Bin 170 -> 0 bytes ...fits_11b_659cb7280818c6f1fe7ac209dfe2b150.RData | Bin 2882 -> 0 bytes ...Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdb | 0 ...Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdx | Bin 113 -> 0 bytes ...ndpoints_63bd41a9e7a7db8d50672d1d2818a3de.RData | Bin 3141 -> 0 bytes ..._endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdb | 0 ..._endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdx | Bin 113 -> 0 bytes ...Z_fits_1_632387249aeb91d63b5958d33dba1ca2.RData | Bin 3562 -> 0 bytes ...6_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdb | Bin 16564 -> 0 bytes ...6_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdx | Bin 171 -> 0 bytes ...Z_fits_2_3ad73869115f92c555719677ea29ac80.RData | Bin 3567 -> 0 bytes ...6_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdb | Bin 16548 -> 0 bytes ...6_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdx | Bin 174 -> 0 bytes ...Z_fits_3_fc3af4746f8762d3e69b54efed402074.RData | Bin 3520 -> 0 bytes ...6_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdb | Bin 15981 -> 0 bytes ...6_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdx | Bin 169 -> 0 bytes ...Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.RData | Bin 3249 -> 0 bytes ...6_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdb | Bin 19433 -> 0 bytes ...6_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdx | Bin 170 -> 0 bytes ...Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.RData | Bin 3902 -> 0 bytes ...6_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdb | Bin 23550 -> 0 bytes ...6_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdx | Bin 175 -> 0 bytes ...Z_fits_7_8ed2205e23e7632fdcfd418445aca562.RData | Bin 3308 -> 0 bytes ...6_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdb | Bin 25240 -> 0 bytes ...6_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdx | Bin 176 -> 0 bytes ...Z_fits_9_c9d06bd14747fc380b2418122f60bd56.RData | Bin 3243 -> 0 bytes ...6_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdb | Bin 21191 -> 0 bytes ...6_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdx | Bin 176 -> 0 bytes docs/articles/cache/__packages | 6 - docs/articles/compiled_models.html | 57 +- .../figure-html/benchmark_FOMC_SFO-1.png | Bin 10757 -> 9843 bytes .../figure-html/benchmark_SFO_SFO-1.png | Bin 10610 -> 11615 bytes docs/articles/index.html | 29 +- docs/articles/mkin.R | 30 - docs/articles/mkin.html | 31 +- docs/articles/mkin_cache/html/__packages | 2 + ...-chunk-2_1255937aa4f0d68ff78163262b20b976.RData | Bin 3367 -> 0 bytes ...ed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb | Bin 20287 -> 0 bytes ...ed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx | Bin 225 -> 0 bytes ...ed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdb | Bin 105223 -> 105229 bytes ...ed-chunk-2_160d963eca06fe4baa61a0a422a1ea70.rdx | Bin 236 -> 236 bytes .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 45379 -> 112161 bytes 85 files changed, 148 insertions(+), 1595 deletions(-) delete mode 100644 docs/articles/FOCUS_D_cache/html/data_7c3240ac153a7639ee517a9110a0f103.RData delete mode 100644 docs/articles/FOCUS_D_cache/html/data_7c3240ac153a7639ee517a9110a0f103.rdb delete mode 100644 docs/articles/FOCUS_D_cache/html/data_7c3240ac153a7639ee517a9110a0f103.rdx delete mode 100644 docs/articles/FOCUS_D_cache/html/fit_33941ca5d01df032930f2f38dc298a59.RData delete mode 100644 docs/articles/FOCUS_D_cache/html/fit_33941ca5d01df032930f2f38dc298a59.rdb delete mode 100644 docs/articles/FOCUS_D_cache/html/fit_33941ca5d01df032930f2f38dc298a59.rdx delete mode 100644 docs/articles/FOCUS_D_cache/html/model_7de92bef541220dbe2d2832243e35870.RData delete mode 100644 docs/articles/FOCUS_D_cache/html/model_7de92bef541220dbe2d2832243e35870.rdb delete mode 100644 docs/articles/FOCUS_D_cache/html/model_7de92bef541220dbe2d2832243e35870.rdx delete mode 100644 docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData delete mode 100644 docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb delete mode 100644 docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx delete mode 100644 docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData delete mode 100644 docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb delete mode 100644 docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx delete mode 100644 docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_2c30ef6f2fb33a606bda3c2882a070ab.RData delete mode 100644 docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_2c30ef6f2fb33a606bda3c2882a070ab.rdb delete mode 100644 docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_2c30ef6f2fb33a606bda3c2882a070ab.rdx delete mode 100644 docs/articles/FOCUS_Z.aux delete mode 100644 docs/articles/FOCUS_Z.bbl delete mode 100644 docs/articles/FOCUS_Z.blg delete mode 100644 docs/articles/FOCUS_Z.log delete mode 100644 docs/articles/FOCUS_Z.out delete mode 100644 docs/articles/FOCUS_Z.tex delete mode 100644 docs/articles/FOCUS_Z.toc delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdx delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.RData delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdb delete mode 100644 docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdx delete mode 100644 docs/articles/cache/__packages delete mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData delete mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb delete mode 100644 docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 0ce7bd07..ad53126e 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -16,14 +16,27 @@ 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 15:22:03 2016 
-## Date of summary: Fri Nov 18 15:22:03 2016 
+## Date of fit:     Fri Nov 18 16:48:11 2016 
+## Date of summary: Fri Nov 18 16:48:11 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.09 s
+## Fitted with method Port using 37 model solutions performed in 0.085 s
 ## 
 ## Weighting: none
 ## 
@@ -156,8 +169,8 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 15:22:04 2016 
-## Date of summary: Fri Nov 18 15:22:04 2016 
+## Date of fit:     Fri Nov 18 16:48:12 2016 
+## Date of summary: Fri Nov 18 16:48:12 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -169,7 +182,7 @@ FOCUS_2006_L1_mkin <-  
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 15:22:05 2016 
-## Date of summary: Fri Nov 18 15:22:05 2016 
+## Date of fit:     Fri Nov 18 16:48:13 2016 
+## Date of summary: Fri Nov 18 16:48:13 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.19 s
+## Fitted with method Port using 81 model solutions performed in 0.196 s
 ## 
 ## Weighting: none
 ## 
@@ -323,8 +336,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 15:22:06 2016 
-## Date of summary: Fri Nov 18 15:22:06 2016 
+## Date of fit:     Fri Nov 18 16:48:14 2016 
+## Date of summary: Fri Nov 18 16:48:14 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -333,7 +346,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 15:22:07 2016 
-## Date of summary: Fri Nov 18 15:22:07 2016 
+## Date of fit:     Fri Nov 18 16:48:15 2016 
+## Date of summary: Fri Nov 18 16:48:15 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -422,7 +435,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 15:22:08 2016 
-## Date of summary: Fri Nov 18 15:22:08 2016 
+## Date of fit:     Fri Nov 18 16:48:15 2016 
+## Date of summary: Fri Nov 18 16:48:16 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.109 s
+## Fitted with method Port using 46 model solutions performed in 0.107 s
 ## 
 ## Weighting: none
 ## 
@@ -572,8 +585,8 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 15:22:08 2016 
-## Date of summary: Fri Nov 18 15:22:08 2016 
+## Date of fit:     Fri Nov 18 16:48:16 2016 
+## Date of summary: Fri Nov 18 16:48:16 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/FOCUS_Z.aux b/docs/articles/FOCUS_Z.aux
deleted file mode 100644
index f997f2d7..00000000
--- a/docs/articles/FOCUS_Z.aux
+++ /dev/null
@@ -1,26 +0,0 @@
-\relax 
-\providecommand\hyper@newdestlabel[2]{}
-\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
-\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
-\global\let\oldcontentsline\contentsline
-\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
-\global\let\oldnewlabel\newlabel
-\gdef\newlabel#1#2{\newlabelxx{#1}#2}
-\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
-\AtEndDocument{\ifx\hyper@anchor\@undefined
-\let\contentsline\oldcontentsline
-\let\newlabel\oldnewlabel
-\fi}
-\fi}
-\global\let\hyper@last\relax 
-\gdef\HyperFirstAtBeginDocument#1{#1}
-\providecommand\HyField@AuxAddToFields[1]{}
-\providecommand\HyField@AuxAddToCoFields[2]{}
-\citation{FOCUSkinetics2011}
-\@writefile{toc}{\contentsline {section}{\numberline {1}The data}{1}{section.1}}
-\@writefile{toc}{\contentsline {section}{\numberline {2}Parent compound and one metabolite}{2}{section.2}}
-\@writefile{toc}{\contentsline {section}{\numberline {3}Including metabolites Z2 and Z3}{8}{section.3}}
-\@writefile{toc}{\contentsline {section}{\numberline {4}Using the SFORB model for parent and metabolites}{12}{section.4}}
-\bibstyle{plainnat}
-\bibdata{references}
-\bibcite{FOCUSkinetics2011}{{1}{2011}{{FOCUS Work Group on Degradation Kinetics}}{{}}}
diff --git a/docs/articles/FOCUS_Z.bbl b/docs/articles/FOCUS_Z.bbl
deleted file mode 100644
index 451497c8..00000000
--- a/docs/articles/FOCUS_Z.bbl
+++ /dev/null
@@ -1,15 +0,0 @@
-\begin{thebibliography}{1}
-\providecommand{\natexlab}[1]{#1}
-\providecommand{\url}[1]{\texttt{#1}}
-\expandafter\ifx\csname urlstyle\endcsname\relax
-  \providecommand{\doi}[1]{doi: #1}\else
-  \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi
-
-\bibitem[{FOCUS Work Group on Degradation Kinetics}(2011)]{FOCUSkinetics2011}
-{FOCUS Work Group on Degradation Kinetics}.
-\newblock \emph{Generic guidance for estimating persistence and degradation
-  kinetics from environmental fate studies on pesticides in EU registration},
-  1.0 edition, November 2011.
-\newblock URL \url{http://focus.jrc.ec.europa.eu/dk}.
-
-\end{thebibliography}
diff --git a/docs/articles/FOCUS_Z.blg b/docs/articles/FOCUS_Z.blg
deleted file mode 100644
index 1da213fb..00000000
--- a/docs/articles/FOCUS_Z.blg
+++ /dev/null
@@ -1,46 +0,0 @@
-This is BibTeX, Version 0.99d (TeX Live 2015/dev/Debian)
-Capacity: max_strings=35307, hash_size=35307, hash_prime=30011
-The top-level auxiliary file: FOCUS_Z.aux
-The style file: plainnat.bst
-Database file #1: references.bib
-You've used 1 entry,
-            2773 wiz_defined-function locations,
-            599 strings with 5084 characters,
-and the built_in function-call counts, 324 in all, are:
-= -- 28
-> -- 10
-< -- 1
-+ -- 4
-- -- 3
-* -- 23
-:= -- 57
-add.period$ -- 3
-call.type$ -- 1
-change.case$ -- 4
-chr.to.int$ -- 1
-cite$ -- 2
-duplicate$ -- 17
-empty$ -- 26
-format.name$ -- 4
-if$ -- 59
-int.to.chr$ -- 1
-int.to.str$ -- 1
-missing$ -- 0
-newline$ -- 13
-num.names$ -- 4
-pop$ -- 6
-preamble$ -- 1
-purify$ -- 3
-quote$ -- 0
-skip$ -- 13
-stack$ -- 0
-substring$ -- 2
-swap$ -- 3
-text.length$ -- 0
-text.prefix$ -- 0
-top$ -- 0
-type$ -- 11
-warning$ -- 0
-while$ -- 3
-width$ -- 0
-write$ -- 20
diff --git a/docs/articles/FOCUS_Z.log b/docs/articles/FOCUS_Z.log
deleted file mode 100644
index c90bf27b..00000000
--- a/docs/articles/FOCUS_Z.log
+++ /dev/null
@@ -1,821 +0,0 @@
-This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex 2015.11.18)  24 OCT 2016 13:58
-entering extended mode
- restricted \write18 enabled.
- %&-line parsing enabled.
-**\nonstopmode \input ./FOCUS_Z.tex
-(./FOCUS_Z.tex (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
-Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
-(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo
-File: size12.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
-)
-\c@part=\count79
-\c@section=\count80
-\c@subsection=\count81
-\c@subsubsection=\count82
-\c@paragraph=\count83
-\c@subparagraph=\count84
-\c@figure=\count85
-\c@table=\count86
-\abovecaptionskip=\skip41
-\belowcaptionskip=\skip42
-\bibindent=\dimen102
-)
-(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
-Package: graphicx 2014/04/25 v1.0g Enhanced LaTeX Graphics (DPC,SPQR)
-
-(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty
-Package: keyval 2014/05/08 v1.15 key=value parser (DPC)
-\KV@toks@=\toks14
-)
-(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
-Package: graphics 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
-
-(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty
-Package: trig 1999/03/16 v1.09 sin cos tan (DPC)
-)
-(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg
-File: graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live
-)
-Package graphics Info: Driver file: pdftex.def on input line 91.
-
-(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
-File: pdftex.def 2011/05/27 v0.06d Graphics/color for pdfTeX
-
-(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty
-Package: infwarerr 2010/04/08 v1.3 Providing info/warning/error messages (HO)
-)
-(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty
-Package: ltxcmds 2011/11/09 v1.22 LaTeX kernel commands for general use (HO)
-)
-\Gread@gobject=\count87
-))
-\Gin@req@height=\dimen103
-\Gin@req@width=\dimen104
-)
-(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
-Package: color 2014/04/23 v1.1a Standard LaTeX Color (DPC)
-
-(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg
-File: color.cfg 2007/01/18 v1.5 color configuration of teTeX/TeXLive
-)
-Package color Info: Driver file: pdftex.def on input line 137.
-)
-(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty
-Package: framed 2011/10/22 v 0.96: framed or shaded text with page breaks
-\OuterFrameSep=\skip43
-\fb@frw=\dimen105
-\fb@frh=\dimen106
-\FrameRule=\dimen107
-\FrameSep=\dimen108
-)
-(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty
-Package: alltt 1997/06/16 v2.0g defines alltt environment
-)
-(/usr/share/texlive/texmf-dist/tex/latex/a4wide/a4wide.sty
-Package: a4wide 1994/08/30
-
-(/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty
-Package: a4 2004/04/15 v1.2g A4 based page layout
-)) (./header.tex
-(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty
-Package: booktabs 2005/04/14 v1.61803 publication quality tables
-\heavyrulewidth=\dimen109
-\lightrulewidth=\dimen110
-\cmidrulewidth=\dimen111
-\belowrulesep=\dimen112
-\belowbottomsep=\dimen113
-\aboverulesep=\dimen114
-\abovetopsep=\dimen115
-\cmidrulesep=\dimen116
-\cmidrulekern=\dimen117
-\defaultaddspace=\dimen118
-\@cmidla=\count88
-\@cmidlb=\count89
-\@aboverulesep=\dimen119
-\@belowrulesep=\dimen120
-\@thisruleclass=\count90
-\@lastruleclass=\count91
-\@thisrulewidth=\dimen121
-)
-(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty
-Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support
-\@emptytoks=\toks15
-\symAMSa=\mathgroup4
-\symAMSb=\mathgroup5
-LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
-(Font)                  U/euf/m/n --> U/euf/b/n on input line 106.
-)
-(/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty
-Package: latexsym 1998/08/17 v2.2e Standard LaTeX package (lasy symbols)
-\symlasy=\mathgroup6
-LaTeX Font Info:    Overwriting symbol font `lasy' in version `bold'
-(Font)                  U/lasy/m/n --> U/lasy/b/n on input line 47.
-)
-(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
-Package: amsmath 2013/01/14 v2.14 AMS math features
-\@mathmargin=\skip44
-
-For additional information on amsmath, use the `?' option.
-(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
-Package: amstext 2000/06/29 v2.01
-
-(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty
-File: amsgen.sty 1999/11/30 v2.0
-\@emptytoks=\toks16
-\ex@=\dimen122
-))
-(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty
-Package: amsbsy 1999/11/29 v1.2d
-\pmbraise@=\dimen123
-)
-(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty
-Package: amsopn 1999/12/14 v2.01 operator names
-)
-\inf@bad=\count92
-LaTeX Info: Redefining \frac on input line 210.
-\uproot@=\count93
-\leftroot@=\count94
-LaTeX Info: Redefining \overline on input line 306.
-\classnum@=\count95
-\DOTSCASE@=\count96
-LaTeX Info: Redefining \ldots on input line 378.
-LaTeX Info: Redefining \dots on input line 381.
-LaTeX Info: Redefining \cdots on input line 466.
-\Mathstrutbox@=\box26
-\strutbox@=\box27
-\big@size=\dimen124
-LaTeX Font Info:    Redeclaring font encoding OML on input line 566.
-LaTeX Font Info:    Redeclaring font encoding OMS on input line 567.
-\macc@depth=\count97
-\c@MaxMatrixCols=\count98
-\dotsspace@=\muskip10
-\c@parentequation=\count99
-\dspbrk@lvl=\count100
-\tag@help=\toks17
-\row@=\count101
-\column@=\count102
-\maxfields@=\count103
-\andhelp@=\toks18
-\eqnshift@=\dimen125
-\alignsep@=\dimen126
-\tagshift@=\dimen127
-\tagwidth@=\dimen128
-\totwidth@=\dimen129
-\lineht@=\dimen130
-\@envbody=\toks19
-\multlinegap=\skip45
-\multlinetaggap=\skip46
-\mathdisplay@stack=\toks20
-LaTeX Info: Redefining \[ on input line 2665.
-LaTeX Info: Redefining \] on input line 2666.
-)
-(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
-Package: amssymb 2013/01/14 v3.01 AMS font symbols
-)
-(/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty
-Package: parskip 2001/04/09 non-zero parskip adjustments
-)
-(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty
-Package: natbib 2010/09/13 8.31b (PWD, AO)
-\bibhang=\skip47
-\bibsep=\skip48
-LaTeX Info: Redefining \cite on input line 694.
-\c@NAT@ctr=\count104
-)
-(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
-Package: hyperref 2012/11/06 v6.83m Hypertext links for LaTeX
-
-(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
-Package: hobsub-hyperref 2012/05/28 v1.13 Bundle oberdiek, subset hyperref (HO)
-
-
-(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty
-Package: hobsub-generic 2012/05/28 v1.13 Bundle oberdiek, subset generic (HO)
-Package: hobsub 2012/05/28 v1.13 Construct package bundles (HO)
-Package hobsub Info: Skipping package `infwarerr' (already loaded).
-Package hobsub Info: Skipping package `ltxcmds' (already loaded).
-Package: ifluatex 2010/03/01 v1.3 Provides the ifluatex switch (HO)
-Package ifluatex Info: LuaTeX not detected.
-Package: ifvtex 2010/03/01 v1.5 Detect VTeX and its facilities (HO)
-Package ifvtex Info: VTeX not detected.
-Package: intcalc 2007/09/27 v1.1 Expandable calculations with integers (HO)
-Package: ifpdf 2011/01/30 v2.3 Provides the ifpdf switch (HO)
-Package ifpdf Info: pdfTeX in PDF mode is detected.
-Package: etexcmds 2011/02/16 v1.5 Avoid name clashes with e-TeX commands (HO)
-Package etexcmds Info: Could not find \expanded.
-(etexcmds)             That can mean that you are not using pdfTeX 1.50 or
-(etexcmds)             that some package has redefined \expanded.
-(etexcmds)             In the latter case, load this package earlier.
-Package: kvsetkeys 2012/04/25 v1.16 Key value parser (HO)
-Package: kvdefinekeys 2011/04/07 v1.3 Define keys (HO)
-Package: pdftexcmds 2011/11/29 v0.20 Utility functions of pdfTeX for LuaTeX (HO
-)
-Package pdftexcmds Info: LuaTeX not detected.
-Package pdftexcmds Info: \pdf@primitive is available.
-Package pdftexcmds Info: \pdf@ifprimitive is available.
-Package pdftexcmds Info: \pdfdraftmode found.
-Package: pdfescape 2011/11/25 v1.13 Implements pdfTeX's escape features (HO)
-Package: bigintcalc 2012/04/08 v1.3 Expandable calculations on big integers (HO
-)
-Package: bitset 2011/01/30 v1.1 Handle bit-vector datatype (HO)
-Package: uniquecounter 2011/01/30 v1.2 Provide unlimited unique counter (HO)
-)
-Package hobsub Info: Skipping package `hobsub' (already loaded).
-Package: letltxmacro 2010/09/02 v1.4 Let assignment for LaTeX macros (HO)
-Package: hopatch 2012/05/28 v1.2 Wrapper for package hooks (HO)
-Package: xcolor-patch 2011/01/30 xcolor patch
-Package: atveryend 2011/06/30 v1.8 Hooks at the very end of document (HO)
-Package atveryend Info: \enddocument detected (standard20110627).
-Package: atbegshi 2011/10/05 v1.16 At begin shipout hook (HO)
-Package: refcount 2011/10/16 v3.4 Data extraction from label references (HO)
-Package: hycolor 2011/01/30 v1.7 Color options for hyperref/bookmark (HO)
-)
-(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty
-Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
-)
-(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty
-Package: auxhook 2011/03/04 v1.3 Hooks for auxiliary files (HO)
-)
-(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
-Package: kvoptions 2011/06/30 v3.11 Key value format for package options (HO)
-)
-\@linkdim=\dimen131
-\Hy@linkcounter=\count105
-\Hy@pagecounter=\count106
-
-(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def
-File: pd1enc.def 2012/11/06 v6.83m Hyperref: PDFDocEncoding definition (HO)
-)
-\Hy@SavedSpaceFactor=\count107
-
-(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg
-File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
-)
-Package hyperref Info: Hyper figures OFF on input line 4443.
-Package hyperref Info: Link nesting OFF on input line 4448.
-Package hyperref Info: Hyper index ON on input line 4451.
-Package hyperref Info: Plain pages OFF on input line 4458.
-Package hyperref Info: Backreferencing OFF on input line 4463.
-Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
-Package hyperref Info: Bookmarks ON on input line 4688.
-\c@Hy@tempcnt=\count108
-
-(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty
-\Urlmuskip=\muskip11
-Package: url 2013/09/16  ver 3.4  Verb mode for urls, etc.
-)
-LaTeX Info: Redefining \url on input line 5041.
-\XeTeXLinkMargin=\dimen132
-\Fld@menulength=\count109
-\Field@Width=\dimen133
-\Fld@charsize=\dimen134
-Package hyperref Info: Hyper figures OFF on input line 6295.
-Package hyperref Info: Link nesting OFF on input line 6300.
-Package hyperref Info: Hyper index ON on input line 6303.
-Package hyperref Info: backreferencing OFF on input line 6310.
-Package hyperref Info: Link coloring OFF on input line 6315.
-Package hyperref Info: Link coloring with OCG OFF on input line 6320.
-Package hyperref Info: PDF/A mode OFF on input line 6325.
-LaTeX Info: Redefining \ref on input line 6365.
-LaTeX Info: Redefining \pageref on input line 6369.
-\Hy@abspage=\count110
-\c@Item=\count111
-\c@Hfootnote=\count112
-)
-
-Package hyperref Message: Driver (autodetected): hpdftex.
-
-(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
-File: hpdftex.def 2012/11/06 v6.83m Hyperref driver for pdfTeX
-\Fld@listcount=\count113
-\c@bookmark@seq@number=\count114
-
-(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty
-Package: rerunfilecheck 2011/04/15 v1.7 Rerun checks for auxiliary files (HO)
-Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
-82.
-)
-\Hy@SectionHShift=\skip49
-)
-(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
-Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
-
-(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def
-File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
-LaTeX Font Info:    Redeclaring font encoding T1 on input line 43.
-))
-(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
-Package: ae 2001/02/12 1.3 Almost European Computer Modern
-
-(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
-Package: fontenc 2005/09/27 v1.99g Standard LaTeX package
-
-(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def
-File: t1enc.def 2005/09/27 v1.99g Standard LaTeX file
-LaTeX Font Info:    Redeclaring font encoding T1 on input line 43.
-)
-LaTeX Font Info:    Try loading font information for T1+aer on input line 100.
-
-(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd
-File: t1aer.fd 1997/11/16 Font definitions for T1/aer.
-)))
-(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
-Package: fancyvrb 2008/02/07
-
-Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
-<2008/02/07> (tvz)
-\FV@CodeLineNo=\count115
-\FV@InFile=\read1
-\FV@TabBox=\box28
-\c@FancyVerbLine=\count116
-\FV@StepNumber=\count117
-\FV@OutFile=\write3
-)
-(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
-Package: upquote 2012/04/19 v1.3 upright-quote and grave-accent glyphs in verba
-tim
-
-(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
-Package: textcomp 2005/09/27 v1.99g Standard LaTeX package
-Package textcomp Info: Sub-encoding information:
-(textcomp)               5 = only ISO-Adobe without \textcurrency
-(textcomp)               4 = 5 + \texteuro
-(textcomp)               3 = 4 + \textohm
-(textcomp)               2 = 3 + \textestimated + \textcurrency
-(textcomp)               1 = TS1 - \textcircled - \t
-(textcomp)               0 = TS1 (full)
-(textcomp)             Font families with sub-encoding setting implement
-(textcomp)             only a restricted character set as indicated.
-(textcomp)             Family '?' is the default used for unknown fonts.
-(textcomp)             See the documentation for details.
-Package textcomp Info: Setting ? sub-encoding to TS1/1 on input line 71.
-
-(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
-File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
-)
-LaTeX Info: Redefining \oldstylenums on input line 266.
-Package textcomp Info: Setting cmr sub-encoding to TS1/0 on input line 281.
-Package textcomp Info: Setting cmss sub-encoding to TS1/0 on input line 282.
-Package textcomp Info: Setting cmtt sub-encoding to TS1/0 on input line 283.
-Package textcomp Info: Setting cmvtt sub-encoding to TS1/0 on input line 284.
-Package textcomp Info: Setting cmbr sub-encoding to TS1/0 on input line 285.
-Package textcomp Info: Setting cmtl sub-encoding to TS1/0 on input line 286.
-Package textcomp Info: Setting ccr sub-encoding to TS1/0 on input line 287.
-Package textcomp Info: Setting ptm sub-encoding to TS1/4 on input line 288.
-Package textcomp Info: Setting pcr sub-encoding to TS1/4 on input line 289.
-Package textcomp Info: Setting phv sub-encoding to TS1/4 on input line 290.
-Package textcomp Info: Setting ppl sub-encoding to TS1/3 on input line 291.
-Package textcomp Info: Setting pag sub-encoding to TS1/4 on input line 292.
-Package textcomp Info: Setting pbk sub-encoding to TS1/4 on input line 293.
-Package textcomp Info: Setting pnc sub-encoding to TS1/4 on input line 294.
-Package textcomp Info: Setting pzc sub-encoding to TS1/4 on input line 295.
-Package textcomp Info: Setting bch sub-encoding to TS1/4 on input line 296.
-Package textcomp Info: Setting put sub-encoding to TS1/5 on input line 297.
-Package textcomp Info: Setting uag sub-encoding to TS1/5 on input line 298.
-Package textcomp Info: Setting ugq sub-encoding to TS1/5 on input line 299.
-Package textcomp Info: Setting ul8 sub-encoding to TS1/4 on input line 300.
-Package textcomp Info: Setting ul9 sub-encoding to TS1/4 on input line 301.
-Package textcomp Info: Setting augie sub-encoding to TS1/5 on input line 302.
-Package textcomp Info: Setting dayrom sub-encoding to TS1/3 on input line 303.
-Package textcomp Info: Setting dayroms sub-encoding to TS1/3 on input line 304.
-
-Package textcomp Info: Setting pxr sub-encoding to TS1/0 on input line 305.
-Package textcomp Info: Setting pxss sub-encoding to TS1/0 on input line 306.
-Package textcomp Info: Setting pxtt sub-encoding to TS1/0 on input line 307.
-Package textcomp Info: Setting txr sub-encoding to TS1/0 on input line 308.
-Package textcomp Info: Setting txss sub-encoding to TS1/0 on input line 309.
-Package textcomp Info: Setting txtt sub-encoding to TS1/0 on input line 310.
-Package textcomp Info: Setting lmr sub-encoding to TS1/0 on input line 311.
-Package textcomp Info: Setting lmdh sub-encoding to TS1/0 on input line 312.
-Package textcomp Info: Setting lmss sub-encoding to TS1/0 on input line 313.
-Package textcomp Info: Setting lmssq sub-encoding to TS1/0 on input line 314.
-Package textcomp Info: Setting lmvtt sub-encoding to TS1/0 on input line 315.
-Package textcomp Info: Setting qhv sub-encoding to TS1/0 on input line 316.
-Package textcomp Info: Setting qag sub-encoding to TS1/0 on input line 317.
-Package textcomp Info: Setting qbk sub-encoding to TS1/0 on input line 318.
-Package textcomp Info: Setting qcr sub-encoding to TS1/0 on input line 319.
-Package textcomp Info: Setting qcs sub-encoding to TS1/0 on input line 320.
-Package textcomp Info: Setting qpl sub-encoding to TS1/0 on input line 321.
-Package textcomp Info: Setting qtm sub-encoding to TS1/0 on input line 322.
-Package textcomp Info: Setting qzc sub-encoding to TS1/0 on input line 323.
-Package textcomp Info: Setting qhvc sub-encoding to TS1/0 on input line 324.
-Package textcomp Info: Setting futs sub-encoding to TS1/4 on input line 325.
-Package textcomp Info: Setting futx sub-encoding to TS1/4 on input line 326.
-Package textcomp Info: Setting futj sub-encoding to TS1/4 on input line 327.
-Package textcomp Info: Setting hlh sub-encoding to TS1/3 on input line 328.
-Package textcomp Info: Setting hls sub-encoding to TS1/3 on input line 329.
-Package textcomp Info: Setting hlst sub-encoding to TS1/3 on input line 330.
-Package textcomp Info: Setting hlct sub-encoding to TS1/5 on input line 331.
-Package textcomp Info: Setting hlx sub-encoding to TS1/5 on input line 332.
-Package textcomp Info: Setting hlce sub-encoding to TS1/5 on input line 333.
-Package textcomp Info: Setting hlcn sub-encoding to TS1/5 on input line 334.
-Package textcomp Info: Setting hlcw sub-encoding to TS1/5 on input line 335.
-Package textcomp Info: Setting hlcf sub-encoding to TS1/5 on input line 336.
-Package textcomp Info: Setting pplx sub-encoding to TS1/3 on input line 337.
-Package textcomp Info: Setting pplj sub-encoding to TS1/3 on input line 338.
-Package textcomp Info: Setting ptmx sub-encoding to TS1/4 on input line 339.
-Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 340.
-)))
-(/usr/share/texlive/texmf-dist/tex/latex/relsize/relsize.sty
-Package: relsize 2013/03/29 ver 4.1
-)
-Package hyperref Info: Option `colorlinks' set `true' on input line 66.
-
-
-Package hyperref Warning: Option `hyperindex' has already been used,
-(hyperref)                setting the option has no effect on input line 66.
-
-Package hyperref Info: Option `linktocpage' set `true' on input line 66.
-(./FOCUS_Z.aux)
-\openout1 = `FOCUS_Z.aux'.
-
-LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 68.
-LaTeX Font Info:    ... okay on input line 68.
-LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 68.
-LaTeX Font Info:    ... okay on input line 68.
-LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 68.
-LaTeX Font Info:    ... okay on input line 68.
-LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 68.
-LaTeX Font Info:    ... okay on input line 68.
-LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 68.
-LaTeX Font Info:    ... okay on input line 68.
-LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 68.
-LaTeX Font Info:    ... okay on input line 68.
-LaTeX Font Info:    Checking defaults for PD1/pdf/m/n on input line 68.
-LaTeX Font Info:    ... okay on input line 68.
-LaTeX Font Info:    Checking defaults for TS1/cmr/m/n on input line 68.
-LaTeX Font Info:    Try loading font information for TS1+cmr on input line 68.
- (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd
-File: ts1cmr.fd 2014/09/29 v2.5h Standard LaTeX font definitions
-)
-LaTeX Font Info:    ... okay on input line 68.
-
-(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
-[Loading MPS to PDF converter (version 2006.09.02).]
-\scratchcounter=\count118
-\scratchdimen=\dimen135
-\scratchbox=\box29
-\nofMPsegments=\count119
-\nofMParguments=\count120
-\everyMPshowfont=\toks21
-\MPscratchCnt=\count121
-\MPscratchDim=\dimen136
-\MPnumerator=\count122
-\makeMPintoPDFobject=\count123
-\everyMPtoPDFconversion=\toks22
-) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
-Package: epstopdf-base 2010/02/09 v2.5 Base part for package epstopdf
-
-(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty
-Package: grfext 2010/08/19 v1.1 Manage graphics extensions (HO)
-)
-Package grfext Info: Graphics extension search list:
-(grfext)             [.png,.pdf,.jpg,.mps,.jpeg,.jbig2,.jb2,.PNG,.PDF,.JPG,.JPE
-G,.JBIG2,.JB2,.eps]
-(grfext)             \AppendGraphicsExtensions on input line 452.
-
-(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg
-File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv
-e
-))
-\AtBeginShipoutBox=\box30
-Package hyperref Info: Link coloring ON on input line 68.
-
-(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
-Package: nameref 2012/10/27 v2.43 Cross-referencing by name of section
-
-(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty
-Package: gettitlestring 2010/12/03 v1.4 Cleanup title references (HO)
-)
-\c@section@level=\count124
-)
-LaTeX Info: Redefining \ref on input line 68.
-LaTeX Info: Redefining \pageref on input line 68.
-LaTeX Info: Redefining \nameref on input line 68.
-
-(./FOCUS_Z.out) (./FOCUS_Z.out)
-\@outlinefile=\write4
-\openout4 = `FOCUS_Z.out'.
-
-LaTeX Font Info:    Try loading font information for U+msa on input line 81.
-
-(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd
-File: umsa.fd 2013/01/14 v3.01 AMS symbols A
-)
-LaTeX Font Info:    Try loading font information for U+msb on input line 81.
-
-(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd
-File: umsb.fd 2013/01/14 v3.01 AMS symbols B
-)
-LaTeX Font Info:    Try loading font information for U+lasy on input line 81.
-
-(/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd
-File: ulasy.fd 1998/08/17 v2.2e LaTeX symbol font definitions
-) [0
-
-{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./FOCUS_Z.toc)
-\tf@toc=\write5
-\openout5 = `FOCUS_Z.toc'.
-
-Package color Info: Redefining color shadecolor on input line 96.
-LaTeX Font Info:    Try loading font information for T1+aett on input line 97.
-
-(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd
-File: t1aett.fd 1997/11/16 Font definitions for T1/aett.
-)
-
-LaTeX Font Warning: Font shape `T1/aett/bx/n' undefined
-(Font)              using `T1/aett/m/n' instead on input line 98.
-
-[1
-
-]
-Package color Info: Redefining color shadecolor on input line 140.
-LaTeX Font Info:    Try loading font information for TS1+aett on input line 147
-.
- (/usr/share/R/share/texmf/tex/latex/ts1aett.fd
-File: ts1aett.fd 
-)
-LaTeX Font Info:    Try loading font information for TS1+cmtt on input line 147
-.
-
-(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd
-File: ts1cmtt.fd 2014/09/29 v2.5h Standard LaTeX font definitions
-)
-LaTeX Font Info:    Font shape `TS1/aett/m/n' in size <12> not available
-(Font)              Font shape `TS1/cmtt/m/n' tried instead on input line 147.
-
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 147--147
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 150--150
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-

-File: figure/FOCUS_2006_Z_fits_1-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_1-1.pdf used on input line 15
-5.
-(pdftex.def)             Requested size: 460.72124pt x 394.91241pt.
- [2] [3 <./figure/FOCUS_2006_Z_fits_1-1.pdf>]
-Package color Info: Redefining color shadecolor on input line 186.
-
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 194--194
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 197--197
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-

-File: figure/FOCUS_2006_Z_fits_2-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_2-1.pdf used on input line 20
-2.
-(pdftex.def)             Requested size: 460.72124pt x 394.91241pt.
- [4] [5 <./figure/FOCUS_2006_Z_fits_2-1.pdf>]
-Package color Info: Redefining color shadecolor on input line 237.
-
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 244--244
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 247--247
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-

-File: figure/FOCUS_2006_Z_fits_3-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_3-1.pdf used on input line 25
-2.
-(pdftex.def)             Requested size: 460.72124pt x 394.91241pt.
- [6] [7 <./figure/FOCUS_2006_Z_fits_3-1.pdf>]
-Package color Info: Redefining color shadecolor on input line 281.
-
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 289--289
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 292--292
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-

-File: figure/FOCUS_2006_Z_fits_5-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_5-1.pdf used on input line 29
-7.
-(pdftex.def)             Requested size: 460.72124pt x 460.73112pt.
- [8]
-Package color Info: Redefining color shadecolor on input line 306.
-
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 316--316
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 319--319
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-
-Underfull \vbox (badness 10000) detected at line 325
- []
-
-[9 <./figure/FOCUS_2006_Z_fits_5-1.pdf>]
-

-File: figure/FOCUS_2006_Z_fits_6-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_6-1.pdf used on input line 32
-6.
-(pdftex.def)             Requested size: 460.72124pt x 526.54988pt.
- [10]
-Underfull \vbox (badness 3229) detected at line 364
- []
-
-[11 <./figure/FOCUS_2006_Z_fits_6-1.pdf>]
-Package color Info: Redefining color shadecolor on input line 383.
-
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 392--392
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 395--395
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-[12] 

-File: figure/FOCUS_2006_Z_fits_7-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_7-1.pdf used on input line 40
-0.
-(pdftex.def)             Requested size: 460.72124pt x 526.54988pt.
- [13]
-Package color Info: Redefining color shadecolor on input line 415.
- [14 <./figure/FOCUS_2006_Z_fits_7-1.pdf>]
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 423--423
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 426--426
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-

-File: figure/FOCUS_2006_Z_fits_9-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_9-1.pdf used on input line 43
-1.
-(pdftex.def)             Requested size: 460.72124pt x 526.54988pt.
- [15]
-Package color Info: Redefining color shadecolor on input line 442.
- [16 <./figure/FOCUS_2006_Z_fits_9-1.pdf>]
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 451--451
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 454--454
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-

-File: figure/FOCUS_2006_Z_fits_10-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_10-1.pdf used on input line 4
-61.
-(pdftex.def)             Requested size: 460.72124pt x 526.54988pt.
- [17]
-Package color Info: Redefining color shadecolor on input line 470.
-
-Overfull \hbox (57.39793pt too wide) in paragraph at lines 479--479
-[]\T1/aett/bx/n/12 ## make[1]: warning: jobserver unavailable: using -j1.  Add 
-\TS1/cmtt/m/n/12 '\T1/aett/bx/n/12 +\TS1/cmtt/m/n/12 ' \T1/aett/bx/n/12 to pare
-nt make rule.[] 
- []
-
-
-Overfull \hbox (4.58922pt too wide) in paragraph at lines 482--482
-[]\T1/aett/m/it/12 ## Suc-cess-fully com-piled dif-fer-en-tial equa-tion model 
-from auto-generated C
- []
-
-
-Underfull \vbox (badness 3229) detected at line 488
- []
-
-[18 <./figure/FOCUS_2006_Z_fits_10-1.pdf>]
-

-File: figure/FOCUS_2006_Z_fits_11-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_11-1.pdf used on input line 4
-89.
-(pdftex.def)             Requested size: 460.72124pt x 526.54988pt.
- [19]
-Package color Info: Redefining color shadecolor on input line 499.
-
-Underfull \vbox (badness 3229) detected at line 508
- []
-
-[20 <./figure/FOCUS_2006_Z_fits_11-1.pdf>]
-

-File: figure/FOCUS_2006_Z_fits_11a-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_11a-1.pdf used on input line 
-509.
-(pdftex.def)             Requested size: 460.72124pt x 460.73112pt.
-Package color Info: Redefining color shadecolor on input line 521.
- [21 <./figure/FOCUS_2006_Z_fits_11a-1.pdf>] 

-File: figure/FOCUS_2006_Z_fits_11b-1.pdf Graphic file (type pdf)
-
-
-Package pdftex.def Info: figure/FOCUS_2006_Z_fits_11b-1.pdf used on input line 
-526.
-(pdftex.def)             Requested size: 460.72124pt x 460.73112pt.
-Package color Info: Redefining color shadecolor on input line 533.
- [22 <./figure/FOCUS_2006_Z_fits_11b-1.pdf>] (./FOCUS_Z.bbl)
-Package atveryend Info: Empty hook `BeforeClearDocument' on input line 565.
- [23]
-Package atveryend Info: Empty hook `AfterLastShipout' on input line 565.
- (./FOCUS_Z.aux)
-Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 565.
-Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 565.
-Package rerunfilecheck Info: File `FOCUS_Z.out' has not changed.
-(rerunfilecheck)             Checksum: B13DB9712199BAA629673E11D2FD6F47;261.
-
-
-LaTeX Font Warning: Some font shapes were not available, defaults substituted.
-
-Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 565.
- ) 
-Here is how much of TeX's memory you used:
- 7809 strings out of 494895
- 112616 string characters out of 6177381
- 189876 words of memory out of 5000000
- 10805 multiletter control sequences out of 15000+600000
- 43056 words of font info for 107 fonts, out of 8000000 for 9000
- 59 hyphenation exceptions out of 8191
- 31i,8n,28p,354b,380s stack positions out of 10000i,500n,10000p,200000b,80000s
- 
-Output written on FOCUS_Z.pdf (24 pages, 241995 bytes).
-PDF statistics:
- 281 PDF objects out of 1000 (max. 8388607)
- 218 compressed objects within 3 object streams
- 33 named destinations out of 1000 (max. 500000)
- 88 words of extra memory for PDF output out of 10000 (max. 10000000)
-
diff --git a/docs/articles/FOCUS_Z.out b/docs/articles/FOCUS_Z.out
deleted file mode 100644
index 61a86d0f..00000000
--- a/docs/articles/FOCUS_Z.out
+++ /dev/null
@@ -1,4 +0,0 @@
-\BOOKMARK [1][-]{section.1}{The data}{}% 1
-\BOOKMARK [1][-]{section.2}{Parent compound and one metabolite}{}% 2
-\BOOKMARK [1][-]{section.3}{Including metabolites Z2 and Z3}{}% 3
-\BOOKMARK [1][-]{section.4}{Using the SFORB model for parent and metabolites}{}% 4
diff --git a/docs/articles/FOCUS_Z.tex b/docs/articles/FOCUS_Z.tex
deleted file mode 100644
index f1886acd..00000000
--- a/docs/articles/FOCUS_Z.tex
+++ /dev/null
@@ -1,566 +0,0 @@
-%\VignetteIndexEntry{Example evaluation of FOCUS dataset Z}
-%\VignetteEngine{knitr::knitr}
-\documentclass[12pt,a4paper]{article}\usepackage[]{graphicx}\usepackage[]{color}
-%% maxwidth is the original width if it is less than linewidth
-%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
-\makeatletter
-\def\maxwidth{ %
-  \ifdim\Gin@nat@width>\linewidth
-    \linewidth
-  \else
-    \Gin@nat@width
-  \fi
-}
-\makeatother
-
-\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
-\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
-\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
-\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
-\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
-\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
-\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
-\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
-\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
-\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
-\let\hlipl\hlkwb
-
-\usepackage{framed}
-\makeatletter
-\newenvironment{kframe}{%
- \def\at@end@of@kframe{}%
- \ifinner\ifhmode%
-  \def\at@end@of@kframe{\end{minipage}}%
-  \begin{minipage}{\columnwidth}%
- \fi\fi%
- \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
- \colorbox{shadecolor}{##1}\hskip-\fboxsep
-     % There is no \\@totalrightmargin, so:
-     \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
- \MakeFramed {\advance\hsize-\width
-   \@totalleftmargin\z@ \linewidth\hsize
-   \@setminipage}}%
- {\par\unskip\endMakeFramed%
- \at@end@of@kframe}
-\makeatother
-
-\definecolor{shadecolor}{rgb}{.97, .97, .97}
-\definecolor{messagecolor}{rgb}{0, 0, 0}
-\definecolor{warningcolor}{rgb}{1, 0, 1}
-\definecolor{errorcolor}{rgb}{1, 0, 0}
-\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
-
-\usepackage{alltt}
-\usepackage{a4wide}
-\input{header}
-\hypersetup{  
-  pdftitle = {Example evaluation of FOCUS dataset Z},
-  pdfsubject = {Manuscript},
-  pdfauthor = {Johannes Ranke},
-  colorlinks = {true},
-  linkcolor = {blue},
-  citecolor = {blue},
-  urlcolor = {red},
-  hyperindex = {true},
-  linktocpage = {true},
-}
-\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
-\begin{document}
-
-
-
-\title{Example evaluation of FOCUS dataset Z}
-\author{\textbf{Johannes Ranke} \\[0.5cm]
-%EndAName
-Wissenschaftlicher Berater\\
-Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany\\[0.5cm]
-and\\[0.5cm]
-University of Bremen\\
-}
-\maketitle
-
-\thispagestyle{empty} \setcounter{page}{0}
-
-\clearpage
-
-\tableofcontents
-
-\textbf{Key words}: Kinetics, FOCUS, nonlinear optimisation
-
-\section{The data}
-
-The following code defines the example dataset from Appendix 7 to the FOCUS kinetics
-report \citep{FOCUSkinetics2011}, p.350.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{require}\hlstd{(mkin)}
-\end{alltt}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: mkin}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: minpack.lm}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: rootSolve}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: inline}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: methods}}
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Loading required package: parallel}}\begin{alltt}
-\hlstd{LOD} \hlkwb{=} \hlnum{0.5}
-\hlstd{FOCUS_2006_Z} \hlkwb{=} \hlkwd{data.frame}\hlstd{(}
-  \hlkwc{t} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{0.04}\hlstd{,} \hlnum{0.125}\hlstd{,} \hlnum{0.29}\hlstd{,} \hlnum{0.54}\hlstd{,} \hlnum{1}\hlstd{,} \hlnum{2}\hlstd{,} \hlnum{3}\hlstd{,} \hlnum{4}\hlstd{,} \hlnum{7}\hlstd{,} \hlnum{10}\hlstd{,} \hlnum{14}\hlstd{,} \hlnum{21}\hlstd{,}
-        \hlnum{42}\hlstd{,} \hlnum{61}\hlstd{,} \hlnum{96}\hlstd{,} \hlnum{124}\hlstd{),}
-  \hlkwc{Z0} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{100}\hlstd{,} \hlnum{81.7}\hlstd{,} \hlnum{70.4}\hlstd{,} \hlnum{51.1}\hlstd{,} \hlnum{41.2}\hlstd{,} \hlnum{6.6}\hlstd{,} \hlnum{4.6}\hlstd{,} \hlnum{3.9}\hlstd{,} \hlnum{4.6}\hlstd{,} \hlnum{4.3}\hlstd{,} \hlnum{6.8}\hlstd{,}
-         \hlnum{2.9}\hlstd{,} \hlnum{3.5}\hlstd{,} \hlnum{5.3}\hlstd{,} \hlnum{4.4}\hlstd{,} \hlnum{1.2}\hlstd{,} \hlnum{0.7}\hlstd{),}
-  \hlkwc{Z1} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{18.3}\hlstd{,} \hlnum{29.6}\hlstd{,} \hlnum{46.3}\hlstd{,} \hlnum{55.1}\hlstd{,} \hlnum{65.7}\hlstd{,} \hlnum{39.1}\hlstd{,} \hlnum{36}\hlstd{,} \hlnum{15.3}\hlstd{,} \hlnum{5.6}\hlstd{,} \hlnum{1.1}\hlstd{,}
-         \hlnum{1.6}\hlstd{,} \hlnum{0.6}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{),}
-  \hlkwc{Z2} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{2.6}\hlstd{,} \hlnum{3.8}\hlstd{,} \hlnum{15.3}\hlstd{,} \hlnum{37.2}\hlstd{,} \hlnum{31.7}\hlstd{,} \hlnum{35.6}\hlstd{,} \hlnum{14.5}\hlstd{,}
-         \hlnum{0.8}\hlstd{,} \hlnum{2.1}\hlstd{,} \hlnum{1.9}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{),}
-  \hlkwc{Z3} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{NA}\hlstd{,} \hlnum{0.5} \hlopt{*} \hlstd{LOD,} \hlnum{9.2}\hlstd{,} \hlnum{13.1}\hlstd{,} \hlnum{22.3}\hlstd{,} \hlnum{28.4}\hlstd{,} \hlnum{32.5}\hlstd{,}
-         \hlnum{25.2}\hlstd{,} \hlnum{17.2}\hlstd{,} \hlnum{4.8}\hlstd{,} \hlnum{4.5}\hlstd{,} \hlnum{2.8}\hlstd{,} \hlnum{4.4}\hlstd{))}
-
-\hlstd{FOCUS_2006_Z_mkin} \hlkwb{<-} \hlkwd{mkin_wide_to_long}\hlstd{(FOCUS_2006_Z)}
-\end{alltt}
-\end{kframe}
-\end{knitrout}
-
-\section{Parent compound and one metabolite}
-
-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, 
-with formation and decline of metabolite Z1 and the pathway from parent
-directly to sink included (default in mkin).
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.2a} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{),}
-                \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.2a} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.2a, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.2a)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_1-1} 
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.2a,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar}
-\end{alltt}
-\begin{verbatim}
-##               Estimate se_notrans      t value       Pr(>t)
-## Z0_0      9.701488e+01 3.55313691 2.730401e+01 1.679214e-21
-## k_Z0_sink 1.281376e-11 0.22689470 5.647447e-11 5.000000e-01
-## k_Z0_Z1   2.236006e+00 0.16507604 1.354531e+01 7.396594e-14
-## k_Z1_sink 4.821248e-01 0.06585369 7.321150e+00 3.552015e-08
-##                Lower       Upper
-## Z0_0      91.4058170 102.6239462
-## k_Z0_sink  0.0000000         Inf
-## k_Z0_Z1    1.8419826   2.7143172
-## k_Z1_sink  0.4005856   0.5802613
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-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 
-\texttt{log k\_Z0\_sink} is ill-defined and the covariance matrix is not
-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 
-formulation:
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.2a.ff} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{),}
-                   \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),}
-                   \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.2a.ff} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.2a.ff, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.2a.ff)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_2-1} 
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.2a.ff,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar}
-\end{alltt}
-\begin{verbatim}
-##              Estimate se_notrans   t value       Pr(>t)      Lower
-## Z0_0       97.0148812 3.55314944 27.303912 1.679369e-21 91.3287912
-## k_Z0        2.2360064 0.21684747 10.311425 3.661846e-11  1.8052909
-## k_Z1        0.4821248 0.06585372  7.321147 3.552045e-08  0.3996826
-## f_Z0_to_Z1  1.0000000 0.10147342  9.854798 9.707056e-11  0.0000000
-##                  Upper
-## Z0_0       102.7009713
-## k_Z0         2.7694843
-## k_Z1         0.5815722
-## f_Z0_to_Z1   1.0000000
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-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. 
-
-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.} 
-
-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 
-metabolite.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.3} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-               \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),} \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.3} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.3, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.3)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_3-1} 
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.3,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar}
-\end{alltt}
-\begin{verbatim}
-##        Estimate se_notrans  t value       Pr(>t)      Lower
-## Z0_0 97.0148815 2.68177093 36.17568 2.363587e-25 91.5215237
-## k_Z0  2.2360064 0.14686110 15.22531 2.246514e-15  1.9545310
-## k_Z1  0.4821248 0.04268712 11.29439 3.068581e-12  0.4021552
-##            Upper
-## Z0_0 102.5082392
-## k_Z0   2.5580177
-## k_Z1   0.5779966
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-As there is only one transformation product for Z0 and no pathway
-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 
-assumed that there is additional empirical evidence that Z1 quickly and exclusively
-hydrolyses to Z2. 
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.5} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-               \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-               \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),} \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.5} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.5, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.5)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_5-1} 
-
-\end{knitrout}
-
-Finally, metabolite Z3 is added to the model. We use the optimised
-differential equation parameter values from the previous fit in order to
-accelerate the optimization.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.FOCUS} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                   \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                   \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),}
-                   \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{),}
-                   \hlkwc{use_of_ff} \hlstd{=} \hlstr{"max"}\hlstd{)}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.FOCUS} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.FOCUS, FOCUS_2006_Z_mkin,}
-                     \hlkwc{parms.ini} \hlstd{= m.Z.5}\hlopt{$}\hlstd{bparms.ode,}
-                     \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.FOCUS)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_6-1} 
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.FOCUS,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{bpar}
-\end{alltt}
-\begin{verbatim}
-##               Estimate se_notrans   t value       Pr(>t)       Lower
-## Z0_0       96.83849566 2.05886133 47.034977 5.583742e-44 92.70517559
-## k_Z0        2.21540897 0.11813046 18.753919 7.744034e-25  1.99051134
-## k_Z1        0.47829896 0.02928763 16.331089 3.333376e-22  0.42297603
-## k_Z2        0.45161653 0.04421268 10.214638 3.110936e-14  0.37103495
-## k_Z3        0.05869343 0.01429485  4.105914 7.285393e-05  0.03599566
-## f_Z2_to_Z3  0.47150952 0.05705233  8.264510 2.809889e-11  0.36038193
-##                   Upper
-## Z0_0       100.97181573
-## k_Z0         2.46571661
-## k_Z1         0.54085782
-## k_Z2         0.54969886
-## k_Z3         0.09570371
-## f_Z2_to_Z3   0.58553462
-\end{verbatim}
-\begin{alltt}
-\hlkwd{endpoints}\hlstd{(m.Z.FOCUS)}
-\end{alltt}
-\begin{verbatim}
-## $ff
-##     Z2_Z3   Z2_sink 
-## 0.4715095 0.5284905 
-## 
-## $SFORB
-## logical(0)
-## 
-## $distimes
-##          DT50      DT90
-## Z0  0.3128755  1.039350
-## Z1  1.4491923  4.814113
-## Z2  1.5348136  5.098540
-## Z3 11.8096217 39.230714
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-This fit corresponds to the final result chosen in Appendix 7 of the FOCUS
-report. Confidence intervals returned by mkin are based on internally
-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 
-SFO model, as residues at a certain low level remain.
-
-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 
-fit for Z3 is improved. However, the covariance matrix is not returned.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.mkin.1} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                    \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                    \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),}
-                    \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.mkin.1} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.1, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.1)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_7-1} 
-\begin{kframe}\begin{alltt}
-\hlkwd{summary}\hlstd{(m.Z.mkin.1,} \hlkwc{data} \hlstd{=} \hlnum{FALSE}\hlstd{)}\hlopt{$}\hlstd{cov.unscaled}
-\end{alltt}
-\begin{verbatim}
-## NULL
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-Therefore, a further stepwise model building is performed starting from the
-stage of parent and two metabolites, starting from the assumption that the model
-fit for the parent compound can be improved by using the SFORB model.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.mkin.3} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                    \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                    \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.mkin.3} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.3, FOCUS_2006_Z_mkin,} \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.3)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_9-1} 
-
-\end{knitrout}
-
-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
-covariance matrix returned) if the sink for Z1 is left in the models.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.mkin.4} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                    \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                    \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),}
-                    \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.mkin.4} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.4, FOCUS_2006_Z_mkin,}
-                      \hlkwc{parms.ini} \hlstd{= m.Z.mkin.3}\hlopt{$}\hlstd{bparms.ode,}
-                      \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.4)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_10-1} 
-
-\end{knitrout}
-
-The error level of the fit, but especially of metabolite Z3, can be improved if
-the SFORB model is chosen for this metabolite, as this model is capable of
-representing the tailing of the metabolite decline phase.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{Z.mkin.5} \hlkwb{<-} \hlkwd{mkinmod}\hlstd{(}\hlkwc{Z0} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{,} \hlstr{"Z1"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                    \hlkwc{Z1} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z2"}\hlstd{,} \hlkwc{sink} \hlstd{=} \hlnum{FALSE}\hlstd{),}
-                    \hlkwc{Z2} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFO"}\hlstd{,} \hlstr{"Z3"}\hlstd{),}
-                    \hlkwc{Z3} \hlstd{=} \hlkwd{mkinsub}\hlstd{(}\hlstr{"SFORB"}\hlstd{))}
-\end{alltt}
-\begin{verbatim}
-## make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
-\end{verbatim}
-
-
-{\ttfamily\noindent\itshape\color{messagecolor}{\#\# Successfully compiled differential equation model from auto-generated C code.}}\begin{alltt}
-\hlstd{m.Z.mkin.5} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.5, FOCUS_2006_Z_mkin,}
-                      \hlkwc{parms.ini} \hlstd{= m.Z.mkin.4}\hlopt{$}\hlstd{bparms.ode[}\hlnum{1}\hlopt{:}\hlnum{4}\hlstd{],}
-                      \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.5)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11-1} 
-
-\end{knitrout}
-
-The summary view of the backtransformed parameters shows that we get no
-confidence intervals due to overparameterisation. As the optimized
-\texttt{k\_Z3\_bound\_free} is excessively small, it seems reasonable to fix it to
-zero. 
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlstd{m.Z.mkin.5a} \hlkwb{<-} \hlkwd{mkinfit}\hlstd{(Z.mkin.5, FOCUS_2006_Z_mkin,}
-                       \hlkwc{parms.ini} \hlstd{=} \hlkwd{c}\hlstd{(m.Z.mkin.5}\hlopt{$}\hlstd{bparms.ode[}\hlnum{1}\hlopt{:}\hlnum{7}\hlstd{],}
-                                     \hlkwc{k_Z3_bound_free} \hlstd{=} \hlnum{0}\hlstd{),}
-                       \hlkwc{fixed_parms} \hlstd{=} \hlstr{"k_Z3_bound_free"}\hlstd{,}
-                       \hlkwc{quiet} \hlstd{=} \hlnum{TRUE}\hlstd{)}
-\hlkwd{plot_sep}\hlstd{(m.Z.mkin.5a)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11a-1} 
-
-\end{knitrout}
-
-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.
-
-A graphical representation of the confidence intervals can finally be obtained.
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{mkinparplot}\hlstd{(m.Z.mkin.5a)}
-\end{alltt}
-\end{kframe}
-\includegraphics[width=\maxwidth]{figure/FOCUS_2006_Z_fits_11b-1} 
-
-\end{knitrout}
-
-The endpoints obtained with this model are
-
-\begin{knitrout}
-\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
-\begin{alltt}
-\hlkwd{endpoints}\hlstd{(m.Z.mkin.5a)}
-\end{alltt}
-\begin{verbatim}
-## $ff
-##   Z0_free_Z1        Z1_Z2      Z2_sink   Z2_Z3_free Z3_free_sink 
-##    1.0000000    1.0000000    0.4634431    0.5365569    1.0000000 
-## 
-## $SFORB
-##       Z0_b1       Z0_b2       Z3_b1       Z3_b2 
-## 2.447138640 0.007512589 0.080007099 0.000000000 
-## 
-## $distimes
-##         DT50     DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2
-## Z0 0.3042972 1.184811   0.283248   92.26476         NA         NA
-## Z1 1.5147787 5.031986         NA         NA         NA         NA
-## Z2 1.6413857 5.452565         NA         NA         NA         NA
-## Z3        NA       NA         NA         NA   8.663571        Inf
-\end{verbatim}
-\end{kframe}
-\end{knitrout}
-
-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.
-
-\bibliographystyle{plainnat}
-\bibliography{references}
-
-\end{document}
-% vim: set foldmethod=syntax:
diff --git a/docs/articles/FOCUS_Z.toc b/docs/articles/FOCUS_Z.toc
deleted file mode 100644
index ebb3b24a..00000000
--- a/docs/articles/FOCUS_Z.toc
+++ /dev/null
@@ -1,4 +0,0 @@
-\contentsline {section}{\numberline {1}The data}{1}{section.1}
-\contentsline {section}{\numberline {2}Parent compound and one metabolite}{2}{section.2}
-\contentsline {section}{\numberline {3}Including metabolites Z2 and Z3}{8}{section.3}
-\contentsline {section}{\numberline {4}Using the SFORB model for parent and metabolites}{12}{section.4}
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.RData b/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.RData
deleted file mode 100644
index 53e2a7d5..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdb
deleted file mode 100644
index a6cdae6f..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdx
deleted file mode 100644
index a07dfb62..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_10_ad34939f1c4da097e64c6add505f564d.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.RData b/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.RData
deleted file mode 100644
index 7fe16ba7..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdb
deleted file mode 100644
index 1a64b007..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdx
deleted file mode 100644
index 86d9cf65..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11_9a3c490a93568b80d56e768bd4d45f20.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.RData b/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.RData
deleted file mode 100644
index bc15e9f0..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdb
deleted file mode 100644
index b4d0ea88..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdx
deleted file mode 100644
index 78c9c03f..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11a_de0f5d38d53d39ab3bf4487eaf6f6bfe.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.RData b/docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.RData
deleted file mode 100644
index 87f2545c..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdb
deleted file mode 100644
index e69de29b..00000000
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdx
deleted file mode 100644
index 4a053a44..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11b_659cb7280818c6f1fe7ac209dfe2b150.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.RData b/docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.RData
deleted file mode 100644
index 711d340c..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdb
deleted file mode 100644
index e69de29b..00000000
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdx
deleted file mode 100644
index 4a053a44..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_11b_endpoints_63bd41a9e7a7db8d50672d1d2818a3de.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.RData b/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.RData
deleted file mode 100644
index d6860a12..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdb
deleted file mode 100644
index 48ee604b..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdx
deleted file mode 100644
index 61edd6ba..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_1_632387249aeb91d63b5958d33dba1ca2.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.RData b/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.RData
deleted file mode 100644
index 080fead7..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdb
deleted file mode 100644
index 72cacd80..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdx
deleted file mode 100644
index a0b9c984..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_2_3ad73869115f92c555719677ea29ac80.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.RData b/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.RData
deleted file mode 100644
index 44eac630..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdb
deleted file mode 100644
index 65b5dcc0..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdx
deleted file mode 100644
index a5b74eb7..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_3_fc3af4746f8762d3e69b54efed402074.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.RData b/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.RData
deleted file mode 100644
index 219b64bc..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdb
deleted file mode 100644
index dfea644d..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdx
deleted file mode 100644
index 428269a0..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_5_03ef5522bde971daafe1f7a8305fecc2.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.RData b/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.RData
deleted file mode 100644
index 1ac664a9..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdb
deleted file mode 100644
index b729b5e3..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdx
deleted file mode 100644
index a5554fc3..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_6_cf2ea2b55b5bd1a719a397d1d14a9b1f.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.RData b/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.RData
deleted file mode 100644
index 79d8608a..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdb
deleted file mode 100644
index a355ffa6..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdx
deleted file mode 100644
index cd8fe227..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_7_8ed2205e23e7632fdcfd418445aca562.rdx and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.RData b/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.RData
deleted file mode 100644
index 4866d4d9..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.RData and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdb b/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdb
deleted file mode 100644
index c1b8b1c1..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdb and /dev/null differ
diff --git a/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdx b/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdx
deleted file mode 100644
index 747c01e0..00000000
Binary files a/docs/articles/cache/FOCUS_2006_Z_fits_9_c9d06bd14747fc380b2418122f60bd56.rdx and /dev/null differ
diff --git a/docs/articles/cache/__packages b/docs/articles/cache/__packages
deleted file mode 100644
index 72bad839..00000000
--- a/docs/articles/cache/__packages
+++ /dev/null
@@ -1,6 +0,0 @@
-base
-knitr
-minpack.lm
-rootSolve
-inline
-mkin
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index ce149bc5..31340867 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -16,14 +16,27 @@
     
     

 
## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6341.1795 6363.5977 6373.7748 6386.0158 6390.0724
-##       Eigenvalue based  907.1699  908.8498  921.8335  910.5297  929.1653
-##      deSolve, compiled  747.5311  752.3718  754.2086  757.2125  757.5474
+##  deSolve, not compiled 6559.0772 6574.0500 6642.0659 6589.0229 6683.5603
+##       Eigenvalue based  921.0723  931.1284  940.3973  941.1845  950.0598
+##      deSolve, compiled  736.6534  741.6706  756.3600  746.6878  766.2132
 ##        max neval cld
-##  6394.1290     3   c
-##   947.8008     3  b 
-##   757.8823     3 a

+##  6778.0978     3   c
+##   958.9351     3  b 
+##   785.7386     3 a

 
autoplot(mb.1)

 

-
We see that using the compiled model is by a factor of 8.4 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

+
We see that using the compiled model is by a factor of 8.8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

 
rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]

 
##                         median
-## deSolve, not compiled 8.433585
-## Eigenvalue based      1.202476
+## deSolve, not compiled 8.824334
+## Eigenvalue based      1.260479
 ## deSolve, compiled     1.000000

 
 

@@ -113,19 +126,19 @@ smb.1["median"]/smb
smb.2 <- summary(mb.2)
 print(mb.2)

 
## Unit: seconds
-##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.214250 13.248908 13.384577 13.283565 13.469740
-##      deSolve, compiled  1.303868  1.307484  1.332879  1.311099  1.347384
+##                   expr       min        lq      mean   median        uq
+##  deSolve, not compiled 13.587184 13.616178 13.673277 13.64517 13.716324
+##      deSolve, compiled  1.307508  1.317114  1.337594  1.32672  1.352637
 ##        max neval cld
-##  13.655915     3   b
-##   1.383669     3  a

+##  13.787476     3   b
+##   1.378553     3  a

 
smb.2["median"]/smb.2["deSolve, compiled", "median"]

 
##   median
 ## 1     NA
 ## 2     NA

 
autoplot(mb.2)

 

-
Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!

+
Here we get a performance benefit of a factor of 10.3 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.44.9000 on

 
## R version 3.3.2 (2016-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index 53b631b1..b7fda1ed 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png differ
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index 6d78194f..bacdb814 100644
Binary files a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png and b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png differ
diff --git a/docs/articles/index.html b/docs/articles/index.html
index cd6a7bea..de2a8a61 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -49,13 +49,28 @@
     
   
diff --git a/docs/articles/mkin.R b/docs/articles/mkin.R
index 67dc3623..fc39bfda 100644
--- a/docs/articles/mkin.R
+++ b/docs/articles/mkin.R
@@ -2,33 +2,3 @@
 require(knitr)
 opts_chunk$set(engine='R', tidy=FALSE)
 
-## ---- echo = TRUE, cache = TRUE, fig = TRUE, fig.width = 8, fig.height = 7----
-library(mkin)
-# Define the kinetic model
-m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
-                         M1 = mkinsub("SFO", "M2"),
-                         M2 = mkinsub("SFO"),
-                         use_of_ff = "max", quiet = TRUE)
-
-
-# Produce model predictions using some arbitrary parameters
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-d_SFO_SFO_SFO <- mkinpredict(m_SFO_SFO_SFO,
-  c(k_parent = 0.03,
-    f_parent_to_M1 = 0.5, k_M1 = log(2)/100,
-    f_M1_to_M2 = 0.9, k_M2 = log(2)/50),
-  c(parent = 100, M1 = 0, M2 = 0),
-  sampling_times)
-
-# Generate a dataset by adding normally distributed errors with
-# standard deviation 3, for two replicates at each sampling time
-d_SFO_SFO_SFO_err <- add_err(d_SFO_SFO_SFO, reps = 2,
-                             sdfunc = function(x) 3,
-                             n = 1, seed = 123456789 )
-
-# Fit the model to the dataset
-f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE)
-
-# Plot the results separately for parent and metabolites
-plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright"))
-
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 8134287b..49c0389b 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -1,5 +1,5 @@
 
-mkin - Kinetic evaluation of chemical degradation data • mkinIntroduction to mkin • mkin
@@ -16,14 +16,27 @@