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

Sys.which("gcc")
##            gcc 
## "/usr/bin/gcc"

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

library("mkin", quietly = TRUE)
SFO_SFO <- mkinmod(
  parent = mkinsub("SFO", "m1"),
  m1 = mkinsub("SFO"))
## 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   2.319    1.000     2.317    0.000
## 1 deSolve, not compiled            3  17.483    7.539    17.473    0.000
## 2      Eigenvalue based            3   2.857    1.232     2.852    0.003
##   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   4.102    1.000     4.100        0
## 1 deSolve, not compiled            3  37.059    9.034    37.041        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 0.9.47.5 on

## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 9 (stretch)
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor