Description Usage Arguments Value References See Also Examples

`calcCoverage`

calculates the sample coverage estimate, a measure of sample
completeness, for varying orders using the method of Chao et al, 2015, falling back
to the Chao1 method in the first order case.

1 | ```
calcCoverage(x, r = 1)
``` |

`x` |
numeric vector of abundance counts. |

`r` |
coverage order to calculate. |

The sample coverage of the given order `r`

.

Chao A. Nonparametric Estimation of the Number of Classes in a Population. Scand J Stat. 1984 11, 265270.

Chao A, et al. Unveiling the species-rank abundance distribution by generalizing the Good-Turing sample coverage theory. Ecology. 2015 96, 11891201.

Used by rarefyDiversity.

1 2 3 4 5 | ```
# Calculate clone sizes
clones <- countClones(ExampleDb, groups="SAMPLE")
# Calculate 1first order coverage for a single sample
calcCoverage(clones$SEQ_COUNT[clones$SAMPLE == "+7d"])
``` |

alakazam documentation built on April 1, 2018, 11:58 a.m.

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