Description Details Author(s) References

The functionality of this package is to predict *r*-species
accumulaiton curves. The method is based on a nonparametric empirical Bayes approach
with rational function approximation. The estimator is
excellent in accuracy for both large values of *r* and long-range
extrapolations, which are essential to large-scale applications. Some
examples are predicting the molecular complexity of sequencing
libraries, estimating the minimum sufficient sequencing depths for
whole-exome sequencing experiments and optimizing depths for single-cell
whole-genome sequencing experiments.

main functions:

preseqR.rSAC

preseqR.rSAC.bootstrap

preseqR.optimal.sequencing

preseqR.rSAC.sequencing.rmdup

preseqR.sample.cov

preseqR.sample.cov.bootstrap

Chao Deng, Timothy Daley, and Andrew D. Smith

Maintainer: Chao Deng <chaodeng@usc.edu>

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Chao, A., & Shen, T. J. (2004). Nonparametric prediction in species sampling. Journal of agricultural, biological, and environmental statistics, 9(3), 253-269.

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Daley, T., & Smith, A. D. (2013). Predicting the molecular complexity of sequencing libraries. Nature methods, 10(4), 325-327.

Deng C, Daley T & Smith AD (2015). Applications of species accumulation curves in large-scale biological data analysis. Quantitative Biology, 3(3), 135-144. URL http://dx.doi.org/10.1007/s40484-015-0049-7.

Deng, C., Daley, T., Calabrese, P., Ren, J., & Smith, A.D. (2016). Estimating the number of species to attain sufficient representation in a random sample. arXiv preprint arXiv:1607.02804v3.

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Efron, B., & Tibshirani, R. J. (1994). An introduction to the bootstrap. CRC press.

Fisher, R. A., Corbet, A. S., and Williams, C. B. ,1943, The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population, Journal of Animal Ecology, 12, 42-58.

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Kalinin V (1965). Functionals related to the poisson distribution and statistical structure of a text. Articles on Mathematical Statistics and the Theory of Probability pp. 202-220.

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