preseqR: Predicting the Number of Species in a Random Sample
Version 3.1.0

The relation between the number of species and the number of individuals in a random sample is a classic problem back to Fisher (1943) . We generalize this problem to estimate the number of species represented at least r times in a random sample. In particular when r=1, it becomes the classic problem. We use a mixture of Poisson processes to model sampling procedures and apply a nonparametric empirical Bayes approach to obtain an estimator. For more information on preseqR, see Deng C, Daley T and Smith AD (2015) and Deng C and Smith AD (2016) .

AuthorChao Deng, Timothy Daley and Andrew D. Smith
Date of publication2017-05-21 23:25:35 UTC
MaintainerChao Deng <chaodeng@usc.edu>
LicenseGPL-3
Version3.1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("preseqR")

Getting started

README.md

Popular man pages

chao.mincount: Estimating the expected number of species represented r or...
FisherButterflyHist: Fisher's butterfly data
preseqR.interpolate.mincount: Interpolating the number of species represented r or more...
preseqR.package: An R package for estimating the number of species represented...
preseqR.simu.hist: Simulating a histogram
preseqR.ztnb.em: Fitting a zero-truncated negative binomial distribution
ShakespeareWordHist: Shakespeare's word type frequencies
See all...

All man pages Function index File listing

Man pages

boneh.mincount: Estimating the expected number of species represented r or...
chao.mincount: Estimating the expected number of species represented r or...
Dickens: Dickens' vocabulary
ds.mincount: Estimating the expected number of species represented r or...
ds.mincount.bootstrap: Estimating the number of species represented r or more times
FisherButterflyHist: Fisher's butterfly data
preseqR.interpolate.mincount: Interpolating the number of species represented r or more...
preseqR.nonreplace.sampling: Sampling without replacement
preseqR.package: An R package for estimating the number of species represented...
preseqR.simu.hist: Simulating a histogram
preseqR.ztnb.em: Fitting a zero-truncated negative binomial distribution
ShakespeareWordHist: Shakespeare's word type frequencies
Twitter: Social network
ztnb.mincount: Estimating the expected number of species represented r or...
ztpois.mincount: Estimating the expected number of species represented r or...

Functions

Dickens Man page
FisherButterflyHist Man page
ShakespeareWordHist Man page
Twitter Man page
boneh.mincount Man page Source code
cfa2rf Source code
chao.mincount Man page Source code
checking.hist Source code
checking.matrix.det Source code
ds.mincount Man page Source code
ds.mincount.bootstrap Man page Source code
general.ds.mincount Source code
generating.ps Source code
get.expectation Source code
kmer.frac Source code
kmer.frac.bootstrap Source code
kmer.frac.curve Source code
lchoose Source code
nb.fitting Source code
nb.loglikelihood Source code
nb.mincount Source code
nonreplace.sampling Source code
pois.mincount Source code
preseqR Man page
preseqR-package Man page
preseqR.depthseq Source code
preseqR.interpolate.mincount Man page Source code
preseqR.nonreplace.sampling Man page Source code
preseqR.simu.hist Man page Source code
preseqR.simu.interpolate Source code
preseqR.ztnb.em Man page Source code
ps2cfa Source code
rf2rfa Source code
zerotruncated.dnbinom Source code
zerotruncated.minus.log.likelihood Source code
ztnb.mincount Man page Source code
ztpois.mincount Man page Source code

Files

inst
inst/CITATION
NAMESPACE
data
data/Twitter.txt.gz
data/ShakespeareWordHist.txt.gz
data/FisherButterflyHist.txt.gz
data/Dickens.txt.gz
R
R/rational_function.R
R/exome.R
R/simulation.R
R/mincount.R
R/tools.R
R/ztnb.R
R/kmer.R
R/compared_methods.R
README.md
MD5
DESCRIPTION
man
man/ds.mincount.Rd
man/Dickens.Rd
man/preseqR.ztnb.em.Rd
man/chao.mincount.Rd
man/boneh.mincount.Rd
man/preseqR.package.Rd
man/ds.mincount.bootstrap.Rd
man/FisherButterflyHist.Rd
man/preseqR.interpolate.mincount.Rd
man/preseqR.nonreplace.sampling.Rd
man/preseqR.simu.hist.Rd
man/ztnb.mincount.Rd
man/Twitter.Rd
man/ztpois.mincount.Rd
man/ShakespeareWordHist.Rd
preseqR documentation built on May 23, 2017, 9:09 a.m.

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