Fourteen years of R/qtl: Just barely sustainable

TL;DR

This paper reviews fourteen years of development and maintenance challenges of R/qtl, an essential R package for genetic mapping, emphasizing its sustainability driven by the chief developer’s ongoing research needs.

Contribution

It provides a comprehensive overview of the software's evolution, development challenges, and the importance of personal research motivation in maintaining scientific software.

Findings

R/qtl has undergone 38 releases since 2001.

The latest version includes 35k lines of R code and 24k lines of C code.

Maintenance success is linked to its role in the chief developer's research.

Abstract

R/qtl is an R package for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits) in experimental crosses. Its development began in 2000. There have been 38 software releases since 2001. The latest release contains 35k lines of R code and 24k lines of C code, plus 15k lines of code for the documentation. Challenges in the development and maintenance of the software are discussed. A key to the success of R/qtl is that it remains a central tool for the chief developer's own research work, and so its maintenance is of selfish importance.