Description Usage Arguments Details Value Note Author(s) References

This function calculates locus and pairwise confidence intervals for Weir & Cockerham's (1984) F_ST and F_IT. These statistics can also be calculated using the `divPart`

function, however, `fstOnly`

is designed to be more memory efficient for larger datasets (e.g. SNPs).

1 2 |

`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 |

`bs_locus` |
Specifies whether locus bootstrapped confidence intervals should be calculated. |

`bs_pairwise` |
Specified whether pairwise population bootstrapped confidence intervals should be calculated. |

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

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

Because `fstOnly`

is intended to maximise memory (RAM) efficiency, the function does not provide many of the plotting utilities that `divPart`

does.

`locus` |
A list object containing two matrices, F_ST and F_IT. These matrices contain actual, lower 95% confidence interval and upper 95% confidence interval per locus. Global values are also presented with their respective confidence intervals. |

`pairwise` |
A list object containing two matrices, F_ST and F_IT. These matrices contain actual, lower 95% confidence interval and upper 95% confidence interval per pairwise population comparison. |

This function has become obsolete following improvements to `fastDivPart`

and `diffCalc`

. The use of either of these two functions is recommended over `fstOnly`

. `fstOnly`

will be deprecated in future `diveRsity`

releases.

Kevin Keenan <kkeenan02@qub.ac.uk>

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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