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 .

cuperdec

R package to generate 'Cumulative Percent Decay' curves, with optional filtering functions, for microbial taxonomic profiles.

Example of Cumulative Percent Decay curves

These curves aim to represent the level of 'endogenous' content of microbiome samples, such as ancient dental calculus, to help to identify samples with low levels of preservation that should be discarded for downstream analysis.

Installation

cuperdec is on CRAN. You can install the package with the usual command

install.packages("cuperdec")

To install the development version for testing, you can run the following

# install.packages("devtools")
devtools::install_github("jfy133/cuperdec")

Documentation

Please see vignettes/cuperdec-intro.Rmd.

Citation

If you use cuperdec, please use the following citation:

Fellows Yates, J. A. et al. (2021) ‘The evolution and changing ecology of the African hominid oral microbiome’, Proceedings of the National Academy of Sciences of the United States of America, 118(20), p. e2021655118. doi: 10.1073/pnas.2021655118.