R: Calculate sample coverage

calcCoverage {alakazam} | R Documentation

## Calculate sample coverage

### Description

`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.

### Usage

    calcCoverage(x, r = 1)

### Arguments

`x` | numeric vector of abundance counts.
`r` | coverage order to calculate.

### Value

The sample coverage of the given order `r`.

### References

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

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

### See Also

Used by alphaDiversity.

### Examples

    # Calculate clone sizes
    clones <- countClones(ExampleDb, groups="SAMPLE")

    # Calculate 1first order coverage for a single sample
    calcCoverage(clones$SEQ_COUNT[clones$SAMPLE == "+7d"])

[Package alakazam version 0.3.0 Index]