To cite msr in publications use:

Samuel Gerber, Kristin Potter (2012). Data Analysis with the Morse-Smale Complex: The msr Package for R. Journal of Statistical Software, 50(2), 1-22. URL http://www.jstatsoft.org/v50/i02/.

Corresponding BibTeX entry:

  @Article{,
    title = {Data Analysis with the Morse-Smale Complex: The {msr}
      Package for {R}},
    author = {Samuel Gerber and Kristin Potter},
    journal = {Journal of Statistical Software},
    year = {2012},
    volume = {50},
    number = {2},
    pages = {1--22},
    url = {http://www.jstatsoft.org/v50/i02/},
  }