Low-level generation of compiled models

As it is unclear if and when ccSolve will be published on CRAN,
the generation, compilation and use of the C version of the
system of differential equations was developed for mkin, inspired and
guided by the code from the ccSolve package. Many thanks again to
Karline Soetaert for all of her work on this and other R packages.

Now all model types, including the Hockey-Stick model for the parent
compund and the IORE model for parent and/or metabolites can be compiled.

2 files changed, 6 insertions, 8 deletions

diff --git a/vignettes/FOCUS_D.Rmd b/vignettes/FOCUS_D.Rmd
index 902d3d24..8ae73c16 100644
--- a/vignettes/FOCUS_D.Rmd
+++ b/vignettes/FOCUS_D.Rmd
@@ -27,7 +27,7 @@ kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics
 

 The call to mkinmod returns a degradation model. The differential equations represented in 

 R code can be found in the character vector `$diffs` of the `mkinmod` object. If

-the `ccSolve` package is installed and functional, the differential equation model

+the gcc compiler is installed and functional, the differential equation model

 will be compiled from auto-generated C code.

 

 

diff --git a/vignettes/compiled_models.Rmd b/vignettes/compiled_models.Rmd
index bac284c5..5d83cf3a 100644
--- a/vignettes/compiled_models.Rmd
+++ b/vignettes/compiled_models.Rmd
@@ -15,16 +15,14 @@ output:
 ```{r, include = FALSE}

 library(knitr)

 opts_chunk$set(tidy = FALSE, cache = TRUE)

-if (!require("ccSolve")) 

-  message("Please install the ccSolve package for this vignette to produce sensible output")

-

 ```

 

 # Benchmark for a model that can also be solved with Eigenvalues

 

 This evaluation is taken from the example section of mkinfit. When using an mkin version

-greater than 0.9-36 and the ccSolve package is installed and functional, you will get a

-message that the model is being compiled when defining a model using mkinmod.

+equal to or greater than 0.9-36 and a compiler (gcc) is installed, you will see

+a message that the model is being compiled from autogenerated C code when

+defining a model using mkinmod.

 

 ```{r create_SFO_SFO}

 library("mkin")

@@ -83,5 +81,5 @@ smb.2["median"]/smb.2["deSolve, compiled", "median"]
 

 ```

 

-Here we get a performance benefit of more than a factor of 8 using the version

-of the differential equation model compiled from C code using the ccSolve package!

+Here we get a performance benefit of more than a factor of 10 using the version

+of the differential equation model compiled from C code using the inline package!