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.
Chao Deng, Timothy Daley, and Andrew D. Smith
Maintainer: Chao Deng <firstname.lastname@example.org>
Baker, G. A., & Graves-Morris, P. (1996). Pade approximants (Encyclopedia of Mathematics and its Applications vol 59).
Boneh, S., Boneh, A., & Caron, R. J. (1998). Estimating the prediction function and the number of unseen species in sampling with replacement. Journal of the American Statistical Association, 93(441), 372-379.
Chao, A., & Shen, T. J. (2004). Nonparametric prediction in species sampling. Journal of agricultural, biological, and environmental statistics, 9(3), 253-269.
Cohen Jr, A. C. (1960). Estimating the parameters of a modified Poisson distribution. Journal of the American Statistical Association, 55(289), 139-143.
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.
Efron, B., & Thisted, R. (1976). Estimating the number of unseen species: How many words did Shakespeare know?. Biometrika, 63(3), 435-447.
Efron, B. (1979). Bootstrap methods: another look at the jackknife. The annals of Statistics, 1-26.
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.
Good, I. J., & Toulmin, G. H. (1956). The number of new species, and the increase in population coverage, when a sample is increased. Biometrika, 43(1-2), 45-63.
Heck Jr, K. L., van Belle, G., & Simberloff, D. (1975). Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology, 1459-1461.
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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.