Model that can also be solved with Eigenvalues

This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The mkinmod() function checks for presence of the gcc compiler using

##            gcc 
## "/usr/bin/gcc"

First, we build a simple degradation model for a parent compound with one metabolite.

## Successfully compiled differential equation model from auto-generated C code.

We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.

## Lade nötiges Paket: rbenchmark
##                    test replications elapsed relative user.self sys.self
## 3     deSolve, compiled            3   2.302    1.000     2.301        0
## 1 deSolve, not compiled            3  17.754    7.712    17.743        0
## 2      Eigenvalue based            3   2.840    1.234     2.838        0
##   user.child sys.child
## 3          0         0
## 1          0         0
## 2          0         0

We see that using the compiled model is by a factor of around 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.

Model that can not be solved with Eigenvalues

This evaluation is also taken from the example section of mkinfit.

## Successfully compiled differential equation model from auto-generated C code.
##                    test replications elapsed relative user.self sys.self
## 2     deSolve, compiled            3   4.116    1.000     4.114        0
## 1 deSolve, not compiled            3  37.902    9.208    37.884        0
##   user.child sys.child
## 2          0         0
## 1          0         0

Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!

This vignette was built with mkin 0.9.47.6 on

## R version 3.5.1 (2018-07-02)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 9 (stretch)
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor