This program simulates an evolving viral population where the epidemiology is described by SIRS dynamics and the molecular evolution is given by codons mutating according to the Kimura two-parameter model. This is described in more detail in here

This program uses the R-standalone library which is included in the R source files Note that it is not installed by default

> cd R-<version>
> ./configure

This step is system-dependent but problems can be inconsistent libaries This can be resolved by explicitly defining the architecture, i.e

> ./configure r_arch=x86_64 CC='gcc -arch x86_64' CXX='g++ -arch x86_64'
      F77='gfortran -arch x86_64' FC='gfortran x86_64'
      OBJC='gcc -arch x86_64' --with-x=no

Once the configuration step is performed, makefiles will be generated in all the sub-directories. For the standalone library, we don't need the top-level files

> cd src/nmath/standalone
> make

If the install occurs properly this should generate 'libRmath.a' The first lines in the Makefile should be modified to match the location of the R library.

Once the library installed properly, simEpiCodon can be compiled by typing 'make' in the directory containing the source code

To run the simulation type

> ./epiCodon -o <outfile> [options]