The file evaluate-profiles.R has the R code that appears in the paper:

Maindonald, J.H. and Wilson, S.R. 2004. Evaluation of genetic and
environmental interactions. RECOMB satellite workshop, February 2004.

The file toy-npl.txt has the toy data that can be used to try out
the function.

The file read-npl.R has R code for processing output from
Genehunter into a form similar to toy-npl.txt