R: Estimates the complete clonal relative abundance distribution

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", 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 `data` column containing clone identifiers.
`copy` | name of the `data` column containing copy numbers for each sequence. If `copy=NULL` (the default), then clone abundance is determined by the number of sequences. If a `copy` column is specified, then clone abundances is determined by the sum of copy numbers within each clonal group.
`group` | name of the `data` column containing group identifiers. If `NULL` then no grouping is performed and the `GROUP` column of the output will contain the value `NA` for each row.
`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 `NULL` then no maximum is set.
`uniform` | if `TRUE` then uniformly resample each group to the same number of observations. If `FALSE` then allow each group to be resampled to its original size or, if specified, `max_size`.
`ci` | confidence interval to calculate; the value must be between 0 and 1.
`nboot` | number of bootstrap realizations to generate.
`progress` | if `TRUE` show a progress bar.

### Value

A AbundanceCurve object summarizing the abundances.

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

3. 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", nboot=100)

[Package alakazam version 0.3.0 Index]