estimateAbundance {alakazam} | R Documentation |

## Estimates the complete clonal relative abundance distribution

### Description

`estimateAbundance`

estimates the complete clonal relative abundance distribution
and confidence intervals on clone sizes using bootstrapping.

### Usage

```
estimateAbundance(
data,
clone = "clone_id",
copy = NULL,
group = NULL,
min_n = 30,
max_n = NULL,
uniform = TRUE,
ci = 0.95,
nboot = 200,
progress = FALSE
)
```

### Arguments

`data` |
data.frame with Change-O style columns containing clonal assignments. |

`clone` |
name of the |

`copy` |
name of the |

`group` |
name of the |

`min_n` |
minimum number of observations to sample. A group with less observations than the minimum is excluded. |

`max_n` |
maximum number of observations to sample. If |

`uniform` |
if |

`ci` |
confidence interval to calculate; the value must be between 0 and 1. |

`nboot` |
number of bootstrap realizations to generate. |

`progress` |
if |

### Value

A AbundanceCurve object summarizing the abundances.

### References

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

Chao A, et al. Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies. Ecol Monogr. 2014 84:45-67.

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

### See Also

See plotAbundanceCurve for plotting of the abundance distribution. See alphaDiversity for a similar application to clonal diversity.

### Examples

```
abund <- estimateAbundance(ExampleDb, group="sample_id", nboot=100)
```

*alakazam*version 1.3.0 Index]