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'))

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

Datasets:

cuperdec_database_ex - Example isolation source database input for cuperdec
cuperdec_metadata_ex - Example metadata file input for cuperdec
cuperdec_taxatable_ex - Example taxon table input for cuperdec

On CRAN:

4.43 score 3 stars 18 scripts 173 downloads 8 exports 46 dependencies

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

Target	Result	Date
Doc / Vignettes	OK	Oct 13 2024
R-4.5-win	OK	Oct 13 2024
R-4.5-linux	OK	Oct 13 2024
R-4.4-win	OK	Oct 13 2024
R-4.4-mac	OK	Oct 13 2024
R-4.3-win	OK	Oct 13 2024
R-4.3-mac	OK	Oct 13 2024

Exports:adaptive_burnin_filter calculate_curve hard_burnin_filter load_database load_map load_taxa_table plot_cuperdec simple_filter

Dependencies:bit bit64 cli clipr colorspace cpp11 crayon dplyr fansi farver generics ggplot2 glue gtable hms isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig prettyunits progress purrr R6 RColorBrewer readr rlang scales stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr

Introduction to cuperdec

James A. Fellows Yates

Rendered fromcuperdec-intro.Rmdusingknitr::rmarkdownon Oct 13 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate adaptive burn-in retain/discard list	adaptive_burnin_filter
Calculate cumulative decay percent curve	calculate_curve
Example isolation source database input for cuperdec	cuperdec_database_ex
Example metadata file input for cuperdec	cuperdec_metadata_ex
Example taxon table input for cuperdec	cuperdec_taxatable_ex
Calculate hard burn-in retain/discard list	hard_burnin_filter
Load database	load_database
Load metadata table	load_map
Load OTU table	load_taxa_table
Plot cumulative percent decay curves	plot_cuperdec
Apply simple percentage filter	simple_filter