This repository contains the source for the paper Broman KW (2012) Genotype probabilities at intermediate generations in the construction of recombinant inbred lines. Genetics 190:403-412

This is a complex and quite theoretical paper with lots of complicated algebraic results.

The Calculations directory contains all of the primary results. For each of various different situations, I have plain text files (e.g., this one), there are simple-to-parse versions of the algebraic expressions plus a perl script that converts them into Maxima code, R code, and LaTeX code. The Maxima and R versions are used to check the results, symbolically and numerically. The LaTeX versions are ultimately incorporated into the paper.

The Perl directory contains scripts that create the LaTeX tables in the paper.

The files preCCprob_notab.tex and preCCprob_supp_notab.tex contain the primary manuscript. The tables get added to create the final latex files preCCprob.tex and preCCprob_supp.tex.