The R Journal: accepted article

This article will be copy edited and may be changed before publication.

flan: An R Package for Inference on Mutation Models.
Adrien Mazoyer, Rémy Drouilhet, Stéphane Despréaux and Bernard Ycart

Abstract This paper describes flan, a package providing tools for fluctuation analysis of mutant cell counts. It includes functions dedicated to the distribution of final numbers of mutant cells. Parametric estimation and hypothesis testing are also implemented, enabling inference on different sorts of data with several possible methods. An overview of the subject is proposed. The general form of mutation models is described, including the classical models as particular cases. Estimating from a model, when the data have been generated by another, induces different possible biases, which are identified and discussed. The three estimation methods available in the package are described, and their mean squared errors are compared. Finally, implementation is discussed, and a few examples of usage on real data sets are given.

Received: 2016-09-12; online 2017-05-18
CRAN packages: flan, Rcpp, ggplot2, RcppGSL, polynom, RcppArmadillo, lbfgsb3 , CRAN Task Views implied by cited CRAN packages: NumericalMathematics, Graphics, HighPerformanceComputing, Optimization, Phylogenetics

CC BY 4.0
This article is licensed under a Creative Commons Attribution 4.0 International license.

  author = {Adrien Mazoyer and Rémy Drouilhet and Stéphane Despréaux and
          Bernard Ycart},
  title = {{flan: An R Package for Inference on Mutation Models.}},
  year = {2017},
  journal = {{The R Journal}},
  url = {}