chschan / simepicodon

Simulating viral molecular evolution with SIRS epidemiology

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

Install

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

Usage

To run the simulation type

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