calcCoverage - Calculate sample coverage
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.
calcCoverage(x, r = 1)
- numeric vector of abundance counts.
- coverage order to calculate.
The sample coverage of the given order
- 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.
# 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"])
Used by alphaDiversity.