rtk: Rarefaction Tool Kit

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Allows normalization of very large abundance tables, from metagenomics applications or other sources, to an equal depth. Additionally diversity measures, such as richness, Shannon diversity, chao1, chao2 and others are calculated on the fly. The results may be plotted using the provided plotting functions.

Author
Paul Saary, Falk Hildebrand
Date of publication
2016-08-10 10:06:58
Maintainer
Paul Saary <rtk@paulsaary.de>
License
GPL (>= 2)
Version
0.2.2

View on CRAN

Man pages

collectors.curve
collectors.curve
get.diversity
get.diversity
plot.rarefaction
Plot rarfeaction results
rtk
Rarefy tables
rtk-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("rtk")}

Files in this package

rtk
rtk/tests
rtk/tests/testthat.R
rtk/tests/testthat
rtk/tests/testthat/test_rare.R
rtk/src
rtk/src/Makevars
rtk/src/Rwrapper.cpp
rtk/src/ClStr2Mat.cpp
rtk/src/Matrix.cpp
rtk/src/Math.h
rtk/src/Matrix.h
rtk/src/RRare.h
rtk/src/ClStr2Mat.h
rtk/src/RRare.cpp
rtk/src/IO.cpp
rtk/src/Makevars.win
rtk/src/RcppExports.cpp
rtk/src/Math.cpp
rtk/src/Rwrapper.h
rtk/src/IO.h
rtk/NAMESPACE
rtk/R
rtk/R/rarefaction.R
rtk/R/rarefaction.plots.R
rtk/R/RcppExports.R
rtk/R/collectorscurve.R
rtk/README.md
rtk/MD5
rtk/build
rtk/build/partial.rdb
rtk/DESCRIPTION
rtk/man
rtk/man/collectors.curve.Rd
rtk/man/rtk-package.Rd
rtk/man/rtk.Rd
rtk/man/plot.rarefaction.Rd
rtk/man/get.diversity.Rd