Package: cuperdec 1.1.0.9000

cuperdec: Cumulative Percent Decay Curve Generator

Calculates and visualises cumulative percent 'decay' curves, which are typically calculated from metagenomic taxonomic profiles. These can be used to estimate the level of expected 'endogenous' taxa at different abundance levels retrieved from metagenomic samples, when comparing to samples of known sampling site or source. Method described in Fellows Yates, J. A. et. al. (2021) Proceedings of the National Academy of Sciences USA <doi:10.1073/pnas.2021655118>.

Authors:James A. Fellows Yates [aut, cre]

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cuperdec.pdf |cuperdec.html
cuperdec/json (API)
NEWS

# Install 'cuperdec' in R:
install.packages('cuperdec', repos = c('https://jfy133.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jfy133/cuperdec/issues

Datasets:

On CRAN:

4.43 score 3 stars 18 scripts 189 downloads 8 exports 46 dependencies

Last updated 2 years agofrom:b06243e629. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:adaptive_burnin_filtercalculate_curvehard_burnin_filterload_databaseload_mapload_taxa_tableplot_cuperdecsimple_filter

Dependencies:bitbit64clicliprcolorspacecpp11crayondplyrfansifarvergenericsggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangscalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

Introduction to cuperdec

Rendered fromcuperdec-intro.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2021-09-12
Started: 2020-05-20