Include output in README, use mkinsub() in example code

14 files changed, 435 insertions, 32 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index bcd8f585..528d800a 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,5 +1,6 @@
 GNUmakefile
 NEWS.md
+README.Rmd
 gmkin_screenshot.png
 ^inst/web$
 out$
@@ -8,6 +9,7 @@ bbl$
 blg$
 aux$
 log$
+figure/*
 vignettes/.build.timestamp
 vignettes/figure
 vignettes/mkin.tex
diff --git a/.gitignore b/.gitignore
index d76ec9eb..fe72b773 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 NEWS
+README.html
 inst/web*
 vignettes/*.aux
 vignettes/*.bbl
diff --git a/GNUmakefile b/GNUmakefile
index 613c124c..a6b31f3b 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -28,12 +28,15 @@ pkgfiles = NEWS \
 	   TODO \
 	   vignettes/*
 
-all: NEWS check clean
+all: check clean
 
 # convert markdown to R's NEWS format (from knitr package)
 NEWS: NEWS.md
 	sed -e 's/^-/ -/' -e 's/^## *//' -e 's/^#/\t\t/' <NEWS.md | fmt -80 >NEWS
 
+README.md: README.Rmd
+	"$(RBIN)/Rscript" -e 'require(knitr); knit("README.Rmd")'
+
 $(TGZ): $(pkgfiles)
 	cd ..;\
 		"$(RBIN)/R" CMD build $(PKGSRC)
diff --git a/README.Rmd b/README.Rmd
new file mode 100644
index 00000000..a4723052
--- /dev/null
+++ b/README.Rmd
@@ -0,0 +1,212 @@
+# mkin
+
+The R package **mkin** provides calculation routines for the analysis of
+chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as
+needed for modelling the formation and decline of transformation products, or
+if several compartments are involved.
+
+## Installation
+
+You can install the latest released version from 
+[CRAN](http://cran.r-project.org/package=mkin) from within R:
+
+```{r, eval = FALSE}
+install.packages("mkin")
+```
+
+If looking for the latest features, you can install directly from 
+[github](http://github.com/jranke/mkin), e.g.  using the `devtools` package.
+Using `quick = TRUE` skips docs, multiple-architecture builds, demos, and
+vignettes, to make installation as fast and painless as possible.
+
+```{r, eval = FALSE}
+require(devtools)
+install_github("jranke/mkin", quick = TRUE)
+```
+
+## Background
+
+In the regulatory evaluation of chemical substances like plant protection
+products (pesticides), biocides and other chemicals, degradation data play an
+important role. For the evaluation of pesticide degradation experiments, 
+detailed guidance and helpful tools have been developed as detailed in
+'Credits and historical remarks' below.
+
+## Usage
+
+The simplest usage example that I can think of, using model shorthand notation
+(available since mkin 0.9-32) and a built-in dataset is
+
+```{r}
+library(mkin)
+fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
+plot(fit, show_residuals = TRUE) 
+```
+
+```{r, eval = FALSE}
+# Output not shown in this README to avoid distraction
+summary(fit)
+```
+
+A still very simple usage example including the definition of the same data in R
+code would be
+
+```{r}
+example_data = data.frame(
+  name = rep("parent", 9),
+  time = c(0, 1, 3, 7, 14, 28, 63, 91, 119),
+  value = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6)
+)
+fit2 <- mkinfit("FOMC", example_data, quiet = TRUE)
+plot(fit2, show_residuals = TRUE) 
+```
+
+A fairly complex usage example using another built-in dataset:
+
+```{r echo = FALSE}
+# Somehow knitr does not find the signature() function
+require(methods)
+```
+
+```{r}
+data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
+
+model <- mkinmod(
+  parent = mkinsub("SFO", c("A1", "B1", "C1"), sink = FALSE),
+  A1 = mkinsub("SFO", "A2"),
+  B1 = mkinsub("SFO"),
+  C1 = mkinsub("SFO"),
+  A2 = mkinsub("SFO"), use_of_ff = "max")
+
+fit3 <- mkinfit(model, data, method.modFit = "Port")
+
+plot(fit3, show_residuals = TRUE) 
+#summary(fit3) # Commented out to avoid distraction from README content
+mkinparplot(fit3)
+```
+
+For more examples and to see results, have a look at the examples provided in the
+[`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
+documentation or the package vignettes referenced from the 
+[mkin package documentation page](http://kinfit.r-forge.r-project.org/mkin_static/index.html)
+
+## Features
+
+* Highly flexible model specification using
+  [`mkinmod`](http://kinfit.r-forge.r-project.org/mkin_static/mkinmod.html),
+  including equilibrium reactions and using the single first-order 
+  reversible binding (SFORB) model, which will automatically create
+  two latent state variables for the observed variable.
+* Model solution (forward modelling) in the function
+  [`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html) 
+  is performed either using the analytical solution for the case of 
+  parent only degradation, an eigenvalue based solution if only simple
+  first-order (SFO) or SFORB kinetics are used in the model, or
+  using a numeric solver from the `deSolve` package (default is `lsoda`).
+  These have decreasing efficiency, and are automatically chosen 
+  by default. 
+* As of mkin 0.9-36, model solution for models with more than one observed
+  variable is based on the
+  [`ccSolve`](https://github.com/karlines/ccSolve) package, if installed.
+  This is even faster than eigenvalue based solution, at least in the example
+  shown in the [vignette `compiled_models`](http://rawgit.com/jranke/mkin/master/vignettes/compiled_models.html)
+* Model optimisation with 
+  [`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
+  internally using the `modFit` function from the `FME` package,
+  but using the Port routine `nlminb` per default.
+* By default, kinetic rate constants and kinetic formation fractions are
+  transformed internally using
+  [`transform_odeparms`](http://kinfit.r-forge.r-project.org/mkin_static/transform_odeparms.html)
+  so their estimators can more reasonably be expected to follow
+  a normal distribution. This has the side effect that no constraints
+  are needed in the optimisation. Thanks to René Lehmann for the nice
+  cooperation on this, especially the isometric logration transformation
+  that is now used for the formation fractions.
+* A side effect of this is that when parameter estimates are backtransformed
+  to match the model definition, confidence intervals calculated from
+  standard errors are also backtransformed to the correct scale, and will
+  not include meaningless values like negative rate constants or 
+  formation fractions adding up to more than 1, which can not occur in 
+  a single experiment with a single defined radiolabel position.
+* Summary and plotting functions. The `summary` of an `mkinfit` object is in
+  fact a full report that should give enough information to be able to
+  approximately reproduce the fit with other tools.
+* The chi-squared error level as defined in the FOCUS kinetics guidance
+  (see below) is calculated for each observed variable.
+* I recently added iteratively reweighted least squares in a similar way
+  it is done in KinGUII and CAKE (see below). Simply add the argument
+  `reweight = "obs"` to your call to `mkinfit` and a separate variance 
+  componenent for each of the observed variables will be optimised
+  in a second stage after the primary optimisation algorithm has converged.
+* When a metabolite decline phase is not described well by SFO kinetics, 
+  either IORE kinetics or SFORB kinetics can be used for the metabolite, 
+  adding one respectively two parameters to the system.
+
+## GUI
+
+There is a graphical user interface that I consider useful for real work. Please
+refer to its [documentation page](http://kinfit.r-forge.r-project.org/gmkin_static)
+for installation instructions and a manual.
+  
+## News
+
+Yes, there is a ![Changelog](NEWS.md).
+
+## Credits and historical remarks
+
+`mkin` would not be possible without the underlying software stack consisting
+of R and the packages [deSolve](http://cran.r-project.org/package=deSolve),
+[minpack.lm](http://cran.r-project.org/package=minpack.lm) and
+[FME](http://cran.r-project.org/package=FME), to say the least.
+
+It could not have been written without me being introduced to regulatory fate
+modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories
+Ltd (formerly RCC Ltd). `mkin` greatly profits from and largely follows
+the work done by the 
+[FOCUS Degradation Kinetics Workgroup](http://focus.jrc.ec.europa.eu/dk),
+as detailed in their guidance document from 2006, slightly updated in 2011.
+
+Also, it was inspired by the first version of KinGUI developed by
+BayerCropScience, which is based on the MatLab runtime environment.
+
+The companion package 
+[kinfit](http://kinfit.r-forge.r-project.org/kinfit_static/index.html) was 
+[started in 2008](https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2) and 
+[first published](http://cran.r-project.org/src/contrib/Archive/kinfit/) on
+CRAN on 01 May 2010.
+
+The first `mkin` code was 
+[published on 11 May 2010](https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8) and the 
+[first CRAN version](http://cran.r-project.org/src/contrib/Archive/mkin)
+on 18 May 2010.
+
+In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named 
+KinGUII whose R code is based on `mkin`, but which added, amongst other
+refinements, a closed source graphical user interface (GUI), iteratively
+reweighted least squares (IRLS) optimisation of the variance for each of the
+observed variables, and Markov Chain Monte Carlo (MCMC) simulation
+functionality, similar to what is available e.g. in the `FME` package.
+
+Somewhat in parallel, Syngenta has sponsored the development of an `mkin` and
+KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is
+more limited in the model formulation, but puts more weight on usability.
+CAKE is available for download from the [CAKE
+website](http://projects.tessella.com/cake), where you can also
+find a zip archive of the R scripts derived from `mkin`, published under the GPL
+license.
+
+Finally, there is 
+[KineticEval](http://github.com/zhenglei-gao/KineticEval), which contains 
+a further development of the scripts used for KinGUII, so the different tools
+will hopefully be able to learn from each other in the future as well.
+
+
+## Development
+
+Contributions are welcome! Your 
+[mkin fork](https://help.github.com/articles/fork-a-repo) is just a mouse click
+away... The master branch on github should always be in good shape, I implement 
+new features in separate branches now. If you prefer subversion, project
+members for the 
+[r-forge project](http://r-forge.r-project.org/R/?group_id=615) are welcome as well.
+Generally, the source code of the latest CRAN version should be available there.
diff --git a/README.md b/README.md
index ca256f92..454b0cd6 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,8 @@ if several compartments are involved.
 You can install the latest released version from 
 [CRAN](http://cran.r-project.org/package=mkin) from within R:
 
-```{r}
+
+```r
 install.packages("mkin")
 ```
 
@@ -19,7 +20,8 @@ If looking for the latest features, you can install directly from
 Using `quick = TRUE` skips docs, multiple-architecture builds, demos, and
 vignettes, to make installation as fast and painless as possible.
 
-```{r}
+
+```r
 require(devtools)
 install_github("jranke/mkin", quick = TRUE)
 ```
@@ -37,29 +39,54 @@ detailed guidance and helpful tools have been developed as detailed in
 The simplest usage example that I can think of, using model shorthand notation
 (available since mkin 0.9-32) and a built-in dataset is
 
-```{r}
+
+```r
 library(mkin)
-fit <- mkinfit("SFO", FOCUS_2006_C)
+```
+
+```
+## Loading required package: minpack.lm
+## Loading required package: rootSolve
+```
+
+```r
+fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
 plot(fit, show_residuals = TRUE) 
+```
+
+![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-1.png) 
+
+
+```r
+# Output not shown in this README to avoid distraction
 summary(fit)
 ```
 
 A still very simple usage example including the definition of the same data in R
 code would be
 
-```{r}
+
+```r
 example_data = data.frame(
   name = rep("parent", 9),
   time = c(0, 1, 3, 7, 14, 28, 63, 91, 119),
   value = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6)
 )
-fit2 <- mkinfit("FOMC", example_data)
+fit2 <- mkinfit("FOMC", example_data, quiet = TRUE)
 plot(fit2, show_residuals = TRUE) 
 ```
 
+![plot of chunk unnamed-chunk-5](figure/unnamed-chunk-5-1.png) 
+
 A fairly complex usage example using another built-in dataset:
 
-```{r}
+
+```
+## Loading required package: methods
+```
+
+
+```r
 data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
 
 model <- mkinmod(
@@ -68,14 +95,153 @@ model <- mkinmod(
   B1 = mkinsub("SFO"),
   C1 = mkinsub("SFO"),
   A2 = mkinsub("SFO"), use_of_ff = "max")
+```
 
+```
+## Compiling differential equation model from auto-generated C code...
+```
+
+```r
 fit3 <- mkinfit(model, data, method.modFit = "Port")
+```
 
+```
+## Model cost at call  1 :  2511.655 
+## Model cost at call  2 :  2511.655 
+## Model cost at call  11 :  1436.639 
+## Model cost at call  12 :  1436.638 
+## Model cost at call  13 :  1436.566 
+## Model cost at call  21 :  643.6583 
+## Model cost at call  22 :  643.6583 
+## Model cost at call  23 :  643.6582 
+## Model cost at call  29 :  643.6576 
+## Model cost at call  31 :  454.0244 
+## Model cost at call  32 :  454.0241 
+## Model cost at call  34 :  454.0229 
+## Model cost at call  43 :  378.1144 
+## Model cost at call  45 :  378.1143 
+## Model cost at call  53 :  357.245 
+## Model cost at call  55 :  357.2449 
+## Model cost at call  56 :  357.2447 
+## Model cost at call  63 :  354.3415 
+## Model cost at call  64 :  354.3415 
+## Model cost at call  65 :  354.3413 
+## Model cost at call  73 :  332.49 
+## Model cost at call  74 :  332.49 
+## Model cost at call  81 :  332.4899 
+## Model cost at call  83 :  315.2962 
+## Model cost at call  84 :  306.3085 
+## Model cost at call  86 :  306.3084 
+## Model cost at call  87 :  306.3084 
+## Model cost at call  92 :  306.3083 
+## Model cost at call  94 :  290.6377 
+## Model cost at call  96 :  290.6375 
+## Model cost at call  98 :  290.6375 
+## Model cost at call  101 :  290.6371 
+## Model cost at call  105 :  269.09 
+## Model cost at call  107 :  269.0899 
+## Model cost at call  115 :  259.7551 
+## Model cost at call  120 :  259.7549 
+## Model cost at call  123 :  259.7547 
+## Model cost at call  126 :  253.7973 
+## Model cost at call  128 :  253.7972 
+## Model cost at call  137 :  251.7358 
+## Model cost at call  139 :  251.7358 
+## Model cost at call  147 :  250.7394 
+## Model cost at call  149 :  250.7393 
+## Model cost at call  157 :  249.1148 
+## Model cost at call  159 :  249.1148 
+## Model cost at call  167 :  246.8768 
+## Model cost at call  169 :  246.8768 
+## Model cost at call  177 :  244.9758 
+## Model cost at call  179 :  244.9758 
+## Model cost at call  187 :  243.2914 
+## Model cost at call  189 :  243.2914 
+## Model cost at call  190 :  243.2914 
+## Model cost at call  194 :  243.2914 
+## Model cost at call  199 :  242.9202 
+## Model cost at call  201 :  242.9202 
+## Model cost at call  202 :  242.9202 
+## Model cost at call  209 :  242.7695 
+## Model cost at call  211 :  242.7695 
+## Model cost at call  216 :  242.7695 
+## Model cost at call  219 :  242.5771 
+## Model cost at call  221 :  242.5771 
+## Model cost at call  229 :  242.4402 
+## Model cost at call  231 :  242.4402 
+## Model cost at call  239 :  242.1878 
+## Model cost at call  241 :  242.1878 
+## Model cost at call  249 :  242.0553 
+## Model cost at call  251 :  242.0553 
+## Model cost at call  256 :  242.0553 
+## Model cost at call  259 :  241.8761 
+## Model cost at call  260 :  241.7412 
+## Model cost at call  261 :  241.6954 
+## Model cost at call  264 :  241.6954 
+## Model cost at call  275 :  241.5982 
+## Model cost at call  277 :  241.5982 
+## Model cost at call  285 :  241.5459 
+## Model cost at call  287 :  241.5459 
+## Model cost at call  295 :  241.4837 
+## Model cost at call  297 :  241.4837 
+## Model cost at call  305 :  241.3882 
+## Model cost at call  306 :  241.3161 
+## Model cost at call  307 :  241.2315 
+## Model cost at call  309 :  241.2315 
+## Model cost at call  314 :  241.2315 
+## Model cost at call  317 :  240.9738 
+## Model cost at call  322 :  240.9738 
+## Model cost at call  327 :  240.8244 
+## Model cost at call  329 :  240.8244 
+## Model cost at call  337 :  240.7005 
+## Model cost at call  339 :  240.7005 
+## Model cost at call  342 :  240.7005 
+## Model cost at call  347 :  240.629 
+## Model cost at call  350 :  240.629 
+## Model cost at call  357 :  240.6193 
+## Model cost at call  358 :  240.6193 
+## Model cost at call  364 :  240.6193 
+## Model cost at call  367 :  240.6193 
+## Model cost at call  369 :  240.5873 
+## Model cost at call  374 :  240.5873 
+## Model cost at call  380 :  240.578 
+## Model cost at call  382 :  240.578 
+## Model cost at call  390 :  240.5723 
+## Model cost at call  393 :  240.5723 
+## Model cost at call  403 :  240.569 
+## Model cost at call  404 :  240.569 
+## Model cost at call  413 :  240.569 
+## Model cost at call  415 :  240.5688 
+## Model cost at call  416 :  240.5688 
+## Model cost at call  417 :  240.5688 
+## Model cost at call  431 :  240.5686 
+## Model cost at call  432 :  240.5686 
+## Model cost at call  434 :  240.5686 
+## Model cost at call  443 :  240.5686 
+## Model cost at call  444 :  240.5686 
+## Model cost at call  447 :  240.5686 
+## Model cost at call  449 :  240.5686 
+## Model cost at call  450 :  240.5686 
+## Model cost at call  466 :  240.5686 
+## Model cost at call  470 :  240.5686 
+## Model cost at call  485 :  240.5686 
+## Model cost at call  509 :  240.5686 
+## Optimisation by method Port successfully terminated.
+```
+
+```r
 plot(fit3, show_residuals = TRUE) 
-summary(fit3)
+```
+
+![plot of chunk unnamed-chunk-7](figure/unnamed-chunk-7-1.png) 
+
+```r
+#summary(fit3) # Commented out to avoid distraction from README content
 mkinparplot(fit3)
 ```
 
+![plot of chunk unnamed-chunk-7](figure/unnamed-chunk-7-2.png) 
+
 For more examples and to see results, have a look at the examples provided in the
 [`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
 documentation or the package vignettes referenced from the 
diff --git a/figure/unnamed-chunk-3-1.png b/figure/unnamed-chunk-3-1.png
new file mode 100644
index 00000000..c74f9dcc
--- /dev/null
+++ b/figure/unnamed-chunk-3-1.png
diff --git a/figure/unnamed-chunk-5-1.png b/figure/unnamed-chunk-5-1.png
new file mode 100644
index 00000000..331cd54e
--- /dev/null
+++ b/figure/unnamed-chunk-5-1.png
diff --git a/figure/unnamed-chunk-6-1.png b/figure/unnamed-chunk-6-1.png
new file mode 100644
index 00000000..e1feaf07
--- /dev/null
+++ b/figure/unnamed-chunk-6-1.png
diff --git a/figure/unnamed-chunk-6-2.png b/figure/unnamed-chunk-6-2.png
new file mode 100644
index 00000000..b4058df9
--- /dev/null
+++ b/figure/unnamed-chunk-6-2.png
diff --git a/figure/unnamed-chunk-7-1.png b/figure/unnamed-chunk-7-1.png
new file mode 100644
index 00000000..e1feaf07
--- /dev/null
+++ b/figure/unnamed-chunk-7-1.png
diff --git a/figure/unnamed-chunk-7-2.png b/figure/unnamed-chunk-7-2.png
new file mode 100644
index 00000000..b4058df9
--- /dev/null
+++ b/figure/unnamed-chunk-7-2.png
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 2d8d3726..93df5be1 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -237,36 +237,36 @@ fit <- mkinfit("FOMC", FOCUS_2006_C)
 summary(fit)
 
 # One parent compound, one metabolite, both single first order.
+# Use mkinsub for convenience in model formulation. Pathway to sink included per default.
 SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
 # Fit the model to the FOCUS example dataset D using defaults
-system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, 
-                           solution_type = "eigen"))
+print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, 
+                           solution_type = "eigen")))
 coef(fit)
 endpoints(fit)
 \dontrun{
-system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, 
-                           solution_type = "deSolve"))
+# deSolve is slower when ccSolve is not installed and set up
+print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, 
+                           solution_type = "deSolve")))
 coef(fit.deSolve)
 endpoints(fit.deSolve)
 }
 
 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC
 \dontrun{
-FOMC <- mkinmod(parent = list(type = "FOMC"))
 FOMC_SFO <- mkinmod(
-  parent = list(type = "FOMC", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
+  parent = mkinsub("FOMC", "m1"),
+  m1 = mkinsub("SFO"))
 # Fit the model to the FOCUS example dataset D using defaults
 fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D)
 # Use starting parameters from parent only FOMC fit
-fit.FOMC = mkinfit(FOMC, FOCUS_2006_D, plot=TRUE)
+fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)
 fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, 
   parms.ini = fit.FOMC$bparms.ode, plot=TRUE)
 
 # Use stepwise fitting, using optimised parameters from parent only fit, SFORB
-SFORB <- mkinmod(parent = list(type = "SFORB"))
 SFORB_SFO <- mkinmod(
   parent = list(type = "SFORB", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
@@ -274,14 +274,14 @@ SFORB_SFO <- mkinmod(
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D)
 fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve")
 # Use starting parameters from parent only SFORB fit (not really needed in this case)
-fit.SFORB = mkinfit(SFORB, FOCUS_2006_D)
+fit.SFORB = mkinfit("SFORB", FOCUS_2006_D)
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)
 }
 
 \dontrun{
 # Weighted fits, including IRLS
-SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                      m1 = list(type = "SFO"), use_of_ff = "max")
+SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
+                      m1 = mkinsub("SFO"), use_of_ff = "max")
 f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)
 summary(f.noweight)
 f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs")
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 4de4c98a..f6a8fe5d 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -77,12 +77,30 @@ mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
   Johannes Ranke

 }

 \examples{

-# Specify the SFO model

+# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)

 SFO <- mkinmod(parent = list(type = "SFO"))

 

 # One parent compound, one metabolite, both single first order.

 SFO_SFO <- mkinmod(

+  parent = mkinsub("SFO", "m1"),

+  m1 = mkinsub("SFO"))

+

+# The above model used to be specified like this, before the advent of mkinsub()

+SFO_SFO <- mkinmod(

   parent = list(type = "SFO", to = "m1"),

   m1 = list(type = "SFO"))

+

+# If we have several parallel metabolites 

+# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)

+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),

+                           M1 = mkinsub("SFO"),

+                           M2 = mkinsub("SFO"),

+                           use_of_ff = "max", quiet = TRUE)

+

+\dontrun{

+fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 

+                          synthetic_data_for_UBA_2014[[12]]$data,

+                          quiet = TRUE)

+}

 }

 \keyword{ models }

diff --git a/tests/testthat/test_synthetic_data_for_UBA_2014.R b/tests/testthat/test_synthetic_data_for_UBA_2014.R
index 25f841b1..ea762353 100644
--- a/tests/testthat/test_synthetic_data_for_UBA_2014.R
+++ b/tests/testthat/test_synthetic_data_for_UBA_2014.R
@@ -19,14 +19,15 @@
 context("Results for synthetic data established in expertise for UBA (Ranke 2014)")
 
 
-m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
-                           M1 = list(type = "SFO", to = "M2"),
-                           M2 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE)
-
-
-m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2")),
-                            M1 = list(type = "SFO"),
-                            M2 = list(type = "SFO"), use_of_ff = "max", quiet = TRUE)
+m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+                           M1 = mkinsub("SFO", "M2"),
+                           M2 = mkinsub("SFO"),
+                           use_of_ff = "max", quiet = TRUE)
+
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+                           M1 = mkinsub("SFO"),
+                           M2 = mkinsub("SFO"),
+                           use_of_ff = "max", quiet = TRUE)
 
 fit_SFO_lin_a <- mkinfit(m_synth_SFO_lin, 
                          synthetic_data_for_UBA_2014[[1]]$data,