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 low levels of preservation that should be discarded for downstream analysis.
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")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 Fagernäs (@ZandraFagernas), and Lena Semerau for testing and bug reports.