alphaDiversity {alakazam}R Documentation

Calculate clonal alpha diversity

Description

alphaDiversity takes in a data.frame or AbundanceCurve and computes diversity scores (D) over an interval of diversity orders (q).

Usage

alphaDiversity(data, min_q = 0, max_q = 4, step_q = 0.1, ci = 0.95, ...)

Arguments

data

data.frame with Change-O style columns containing clonal assignments or a AbundanceCurve generate by estimateAbundance object containing a previously calculated bootstrap distributions of clonal abundance.

min_q

minimum value of q.

max_q

maximum value of q.

step_q

value by which to increment q.

ci

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

...

additional arguments to pass to estimateAbundance. Additional arguments are ignored if a AbundanceCurve is provided as input.

Details

Clonal diversity is calculated using the generalized diversity index (Hill numbers) proposed by Hill (Hill, 1973). See calcDiversity for further details.

To generate a smooth curve, D is calculated for each value of q from min_q to max_q incremented by step_q. When uniform=TRUE variability in total sequence counts across unique values in the group column is corrected by repeated resampling from the estimated complete clonal distribution to a common number of sequences. The complete clonal abundance distribution that is resampled from is inferred by using the Chao1 estimator to infer the number of unseen clones, followed by applying the relative abundance correction and unseen clone frequencies described in Chao et al, 2015.

The diversity index (D) for each group is the mean value of over all resampling realizations. Confidence intervals are derived using the standard deviation of the resampling realizations, as described in Chao et al, 2015.

Significance of the difference in diversity index (D) between groups is tested by constructing a bootstrap delta distribution for each pair of unique values in the group column. The bootstrap delta distribution is built by subtracting the diversity index Da in group a from the corresponding value Db in group b, for all bootstrap realizations, yielding a distribution of nboot total deltas; where group a is the group with the greater mean D. The p-value for hypothesis Da != Db is the value of P(0) from the empirical cumulative distribution function of the bootstrap delta distribution, multiplied by 2 for the two-tailed correction.

Note, this method may inflate statistical significance when clone sizes are uniformly small, such as when most clones sizes are 1, sample size is small, and max_n is near the total count of the smallest data group. Use caution when interpreting the results in such cases.

Value

A DiversityCurve object summarizing the diversity scores.

References

  1. Hill M. Diversity and evenness: a unifying notation and its consequences. Ecology. 1973 54(2):427-32.

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

  3. 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.

  4. 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 calcDiversity for the basic calculation and DiversityCurve for the return object. See plotDiversityCurve for plotting the return object.

Examples

# Group by sample identifier in two steps
abund <- estimateAbundance(ExampleDb, group="sample_id", nboot=100)
div <- alphaDiversity(abund, step_q=1, max_q=10)
plotDiversityCurve(div, legend_title="Sample")
                   
# Grouping by isotype rather than sample identifier in one step
div <- alphaDiversity(ExampleDb, group="c_call", min_n=40, step_q=1, max_q=10, 
                      nboot=100)
plotDiversityCurve(div, legend_title="Isotype")


[Package alakazam version 1.1.0 Index]