alakazam (version 0.2.2)

calcCoverage: 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 rarefyDiversity.

Examples

# Load example data
file <- system.file("extdata", "ExampleDb.gz", package="alakazam")
df <- readChangeoDb(file)

# Calculate clone sizes
clones <- countClones(df, groups="SAMPLE")
# Calculate 1st order coverage for a single sample
calcCoverage(clones$SEQ_COUNT[clones$SAMPLE == "RL01"])