R library to generate 'Cumulative Percent Decay' curves for microbial taxonomic profiles
R package to generate 'Cumulative Percent Decay' curves, with optional filtering functions, for microbial taxonomic profiles.
These curves aim to represent the level of 'endogenous' content of microbiome samples, such as ancient dental calculus, to help to identify samples with lowlevels of preservation that should be discarded for downstream analysis.
cuperdec is on CRAN. You can install the package with the usual command
To install the development version for testing, you can runthe following
Please see vignettes/cuperdec-intro.Rmd.
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.
Irina Velsko (@ivelsko), Zandra Fagerness (@ZandraFagernas), and Lena Semerau for testing and bug reports.