preseqR

Predicting Species Accumulation Curves

v4.0.0 · Jun 27, 2018 · GPL-3

Description

Originally as an R version of Preseq <doi:10.1038/nmeth.2375>, the package has extended its functionality to predict the r-species accumulation curve (r-SAC), which is the number of species represented at least r times as a function of the sampling effort. When r = 1, the curve is known as the species accumulation curve, or the library complexity curve in high-throughput genomic sequencing. The package includes both parametric and nonparametric methods, as described by Deng C, et al. (2018) <arXiv:1607.02804v3>.

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CRAN Check Status

2 NOTE

12 OK

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	38.7s
r-devel-linux-x86_64-debian-gcc	NOTE	28.1s
r-devel-linux-x86_64-fedora-clang	OK	57.9s
r-devel-linux-x86_64-fedora-gcc	OK	56.1s
r-devel-macos-arm64	OK	13s
r-devel-windows-x86_64	OK	71s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	OK	28s
r-oldrel-windows-x86_64	OK	72s
r-patched-linux-x86_64	OK	34.2s
r-release-linux-x86_64	OK	33.4s
r-release-macos-arm64	OK
r-release-macos-x86_64	OK	32s
r-release-windows-x86_64	OK	72s

Check details (14 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Chao Deng <chaodeng@usc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chao",
                      family = "Deng",
                      role = c("aut", "cre"),
                      email = "chaodeng@usc.edu"),
               person(given = "Timothy",
                      family = "Daley",
                      role = "aut"),
               person(given = c("Andrew", "D."),
                      family = "Smith",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field contains
  Deng C, et al. (2018) <arXiv:1607.02804v3>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘bbc.rSAC.Rd’:
    \keyword{ estimator, r-SAC, nonparametric }
  File ‘cs.rSAC.Rd’:
    \keyword{ estimator, r-SAC, nonparametric }
  File ‘ds.rSAC.Rd’:
    \keyword{ estimator, r-SAC, RFA, nonparametric}
  File ‘ds.rSAC.bootsrap.Rd’:
    \keyword{ estimator, r-SAC, RFA, bootstrap, nonpar [TRUNCATED]
  File ‘fisher.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric }
  File ‘kmer.frac.curve.Rd’:
    \keyword{k-mer, sample coverage, high-throughput,  [TRUNCATED]
  File ‘kmer.frac.curve.bootstrap.Rd’:
    \keyword{k-mer, sample coverage, bootstrap, high-t [TRUNCATED]
  File ‘preseqR.interpolate.rSAC.Rd’:
    \keyword{ interpolation, r-SAC}
  File ‘preseqR.optimal.sequencing.Rd’:
    \keyword{WGS, high-throughput, benefit-cost ratio} [TRUNCATED]
  File ‘preseqR.rSAC.Rd’:
    \keyword{ estimator, r-SAC, RFA, ZTNB, best practi [TRUNCATED]
  File ‘preseqR.rSAC.bootstrap.Rd’:
    \keyword{ estimator, r-SAC, bootstrap, best practi [TRUNCATED]
  File ‘preseqR.rSAC.sequencing.rmdup.Rd’:
    \keyword{r-SAC, duplicates, WES, WGS, high-through [TRUNCATED]
  File ‘preseqR.sample.cov.Rd’:
    \keyword{ estimator, RFA, sample coverage}
  File ‘preseqR.sample.cov.bootstrap.Rd’:
    \keyword{ estimator, RFA, bootstrap, sample covera [TRUNCATED]
  File ‘preseqR.simu.hist.Rd’:
    \keyword{ simulation, sampling, mixture of Poisson [TRUNCATED]
  File ‘preseqR.ztnb.em.Rd’:
    \keyword{ negative binomial, EM}
  File ‘ztnb.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric, negative b [TRUNCATED]
  File ‘ztp.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric, Poisson}

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Chao Deng <chaodeng@usc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chao",
                      family = "Deng",
                      role = c("aut", "cre"),
                      email = "chaodeng@usc.edu"),
               person(given = "Timothy",
                      family = "Daley",
                      role = "aut"),
               person(given = c("Andrew", "D."),
                      family = "Smith",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Description field contains
  Deng C, et al. (2018) <arXiv:1607.02804v3>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘bbc.rSAC.Rd’:
    \keyword{ estimator, r-SAC, nonparametric }
  File ‘cs.rSAC.Rd’:
    \keyword{ estimator, r-SAC, nonparametric }
  File ‘ds.rSAC.Rd’:
    \keyword{ estimator, r-SAC, RFA, nonparametric}
  File ‘ds.rSAC.bootsrap.Rd’:
    \keyword{ estimator, r-SAC, RFA, bootstrap, nonpar [TRUNCATED]
  File ‘fisher.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric }
  File ‘kmer.frac.curve.Rd’:
    \keyword{k-mer, sample coverage, high-throughput,  [TRUNCATED]
  File ‘kmer.frac.curve.bootstrap.Rd’:
    \keyword{k-mer, sample coverage, bootstrap, high-t [TRUNCATED]
  File ‘preseqR.interpolate.rSAC.Rd’:
    \keyword{ interpolation, r-SAC}
  File ‘preseqR.optimal.sequencing.Rd’:
    \keyword{WGS, high-throughput, benefit-cost ratio} [TRUNCATED]
  File ‘preseqR.rSAC.Rd’:
    \keyword{ estimator, r-SAC, RFA, ZTNB, best practi [TRUNCATED]
  File ‘preseqR.rSAC.bootstrap.Rd’:
    \keyword{ estimator, r-SAC, bootstrap, best practi [TRUNCATED]
  File ‘preseqR.rSAC.sequencing.rmdup.Rd’:
    \keyword{r-SAC, duplicates, WES, WGS, high-through [TRUNCATED]
  File ‘preseqR.sample.cov.Rd’:
    \keyword{ estimator, RFA, sample coverage}
  File ‘preseqR.sample.cov.bootstrap.Rd’:
    \keyword{ estimator, RFA, bootstrap, sample covera [TRUNCATED]
  File ‘preseqR.simu.hist.Rd’:
    \keyword{ simulation, sampling, mixture of Poisson [TRUNCATED]
  File ‘preseqR.ztnb.em.Rd’:
    \keyword{ negative binomial, EM}
  File ‘ztnb.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric, negative b [TRUNCATED]
  File ‘ztp.rSAC.Rd’:
    \keyword{ estimator, r-SAC, parametric, Poisson}

OK r-devel-linux-x86_64-fedora-clang

OK r-devel-linux-x86_64-fedora-gcc

OK r-devel-macos-arm64

OK r-devel-windows-x86_64

OK r-oldrel-macos-arm64

OK r-oldrel-macos-x86_64

OK r-oldrel-windows-x86_64

OK r-patched-linux-x86_64

OK r-release-linux-x86_64

OK r-release-macos-arm64

OK r-release-macos-x86_64

OK r-release-windows-x86_64

Check History

NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Chao Deng <chaodeng@usc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chao",
                      family = "Deng",
                      role = c("aut", "cre"),
                      email = "chaodeng@usc.edu"),
               person(given = "Timothy",
                      family = "Daley",
                      role = "aut"),
               person(given = c("Andrew", "D."),
                      family = "Smith",

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Chao Deng <chaodeng@usc.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Chao",
                      family = "Deng",
                      role = c("aut", "cre"),
                      email = "chaodeng@usc.edu"),
               person(given = "Timothy",
                      family = "Daley",
                      role = "aut"),
               person(given = c("Andrew", "D."),
                      family = "Smith",

Dependency Network

Version History

new 4.0.0 Mar 9, 2026