Description Usage Arguments Details Value Author(s) References Examples

`fastDivPart`

is identical to the `divPart`

function in regards to what it calculates. The difference with this function is the speed with which it processes pairwise calculations. By using more efficient programming techniques, `fastDivPart`

can execute commands up to 20X faster than `divPart`

.

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`infile` |
Specifying the name of the |

`outfile` |
Allows users to specify a prefix for an output folder. Name must a character string enclosed in either “” or ''. |

`gp` |
Specifies the digit format of the |

`pairwise` |
A logical argument indicating whether standard pairwise diversity statistics should be calculated and returned as a diagonal matrix. |

`fst` |
A Logical argument indicating whether Weir & Cockerham's 1984 F-statistics should be calculated. NOTE - Calculating these statistics adds significant time to analysis when carrying out pairwise comparisons. |

`bs_locus` |
Gives users the option to bootstrap locus statistics. Results will be written to |

`bs_pairwise` |
Gives users the option to bootstrap statistics across all loci for each pairwise population comparison. Results will be written to a |

`boots` |
Determines the number of bootstrap iterations to be carried out. The default value is |

`plot` |
Optional interactive |

`para` |
A logical input, indicating whether your analysis should be run in parallel mode or sequentially. |

All results will be written to a user defined folder ("working\_directory/outfile"). The format of outputs will vary depending on the availability of the package `'xlsx'`

in the users local package library. If `'xlsx'`

is available, results will be written to an Excel workbook. If `'xlsx'`

is not available, results will be written to `.txt`

files.
Multi-locus estimates of Weir and Cockerham's theta are calculated as per Weir and Cockerham, 1984.

`standard` |
A matrix containing identical data to the |

`estimate` |
A matrix containing identical data to the |

`pairwise` |
A group of six matrices containing population pairwise statistics. This object is identical to that written as 'pairwise-stats' in the |

`bs_locus` |
A list containing six matrices of locus values for |

`bs_pairwise` |
A list containing three-four matrices (depending on whether Weir & Cockerham's Fst is calculated) of pairwise values for |

Kevin Keenan <kkeenan02@qub.ac.uk>

Dragulescu, A.D., “xlsx: Read, write, formal Excel 2007 and Excel 97/2000/xp/2003 files”, R package version 0.4.2, url:http://CRAN.R-project.org/package=xlsx, (2012).

Guile, D.P., Shepherd, L.A., Sucheston, L., Bruno, A., and Manly, K.F., “sendplot: Tool for sending interactive plots with tool-tip content.”, R package version 3.8.10, url: http://CRAN.R-project.org/package=sendplot, (2012).

Hedrick, P., “A standardized genetic differentiation measure,” Evolution, vol. 59, no. 8, pp. 1633-1638, (2005).

Jost, L., “G ST and its relatives do not measure differentiation,” Molec- ular Ecology, vol. 17, no. 18, pp. 4015-4026, (2008).

Manly, F.J., “Randomization, bootstrap and Monte Carlo methods in biology”, Chapman and Hall, London, 1997.

Nei, M. and Chesser, R., “Estimation of fixation indices and gene diver- sities,” Ann. Hum. Genet, vol. 47, no. Pt 3, pp. 253-259, (1983).

R Development Core Team (2011). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.

Revolution Analytics (2012). doParallel: Foreach parallel adaptor for the parallel package. R package version 1.0.1. http://CRAN.R-project.org/package=doParallel

Revolution Analytics (2012). foreach: Foreach looping construct for R. R package version 1.4.0. http://CRAN.R-project.org/package=foreach

Rousset, F., “genepop'007: a complete re-implementation of the genepop software for Windows and Linux.,” Molecular ecology resources, vol. 8, no. 1, pp. 103-6, (2008).

Weir, B.S. & Cockerham, C.C., Estimating F-Statistics, for the Analysis of Population Structure, Evolution, vol. 38, No. 6, pp. 1358-1370 (1984).

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