Description Usage Arguments Details Value Author(s) References Examples

Function to generate the rarefaction data from a given sample

1 2 | ```
divsubsamples(mainsamp, nrf, minrarefac=1,
maxrarefac=length(format.input(mainsamp)), NResamples=1000)
``` |

`mainsamp` |
the main sample, either as a 2-column data.frame (species ID, count of species), or a vector of species IDs. |

`nrf` |
difference between lengths of successive rarefaction datapoints. |

`minrarefac` |
minimum rarefaction data x-axis value. Default is 1. |

`maxrarefac` |
maximum rarefaction data x-axis value. Default is length of the sample |

`NResamples` |
number of resamples used to calculate the rarefaction data. |

This function produces a vector of subsamples diversity values with subsample lengths evenly distributed between a specified minimum and maximum number. The curvature of the rarefaction curve can be obtained with the function `Curvature`

.

a list of class *divsubsamples* containing resampling results (i.e. the diversity data). This includes the following:

`RarefacXAxis ` |
vector of x-axis rarefaction data |

`RarefacYAxis ` |
vector of y-axis rarefaction data |

`div_sd ` |
vector of y-axis rarefaction data standard deviations |

`NResamples ` |
number of sampling iterations used to calculate sample means of each subsample diversity |

Daniel Laydon, Aaron Sim, Charles Bangham, Becca Asquith

Laydon, D., Melamed, A., Sim, A., Gillet, N. A., Sim, K., Darko, S., Kroll, S., Douek, D. C., Price, D., Bangham, C. R. M., Asquith, B., Quantification of HTLV-1 clonality and TCR diversity, PLOS Comput. Biol. 2014

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
require(DivE)
data(Bact1)
dss_1 <- divsubsamples(Bact1, nrf=2, minrarefac=1, maxrarefac=100,
NResamples=10)
dss_2 <- divsubsamples(Bact1, nrf=20, minrarefac=1, maxrarefac=100,
NResamples=10)
# Default NResamples=1000; low value of NResamples=10 is a set for quick evaluation
dss_1
dss_2
summary(dss_1)
dss_1$div_sd
dss_1$NResamples
Curvature(dss_1)
``` |

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