Description Usage Arguments Details Value References Examples

Implements the master gene model in Marchani et al (2009)

1 2 | ```
MasterGene(mismatch, len, r = 0.013, plotFit = FALSE,
main = sprintf("n = %d", n))
``` |

`mismatch` |
A vector containing the number of mismatches. |

`len` |
A vector containing the length of each element. |

`r` |
Mutation rate (substitutions/(million year * site)) used in the calculation. |

`plotFit` |
Whether to plot the distribution fits. |

`main` |
The title for the plot. |

For the method implemented see References.

This function returns various parameter estimates described in Marchani et al (2009), containing the following fields. The unit for time is million years ago (mya):

`B` |
The constant insertion rate |

`q` |
The constant excision rate |

`lam` |
The population growth rate |

`R` |
The ratio of the number of elements in class j over class j+1, which is constant by assumption |

`age1` |
The age of the system under model 1 (lambda > 1) |

`age2` |
The age of the system under model 2 (an initial burst followed by stasis lambda = 1) |

Marchani, Elizabeth E., Jinchuan Xing, David J. Witherspoon, Lynn B. Jorde, and Alan R. Rogers. "Estimating the age of retrotransposon subfamilies using maximum likelihood." Genomics 94, no. 1 (2009): 78-82.

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