calcCoverage {alakazam} | R Documentation |
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)
x |
numeric vector of abundance counts. |
r |
coverage order to calculate. |
The sample coverage of the given order r
.
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.
Used by alphaDiversity.
# 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"])