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

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.

### See Also

Used by alphaDiversity.

### Examples

```
# Calculate clone sizes
clones <- countClones(ExampleDb, groups="sample_id")
# Calculate 1first order coverage for a single sample
calcCoverage(clones$seq_count[clones$sample_id == "+7d"])
```

[Package

*alakazam*version 1.3.0 Index]