occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding

R-CMD-check CRAN status

occumb is an R package that provides functionalities to apply the multispecies site occupancy modeling for environmental DNA (eDNA) metabarcoding easily.

This package allows the users to fit the model with a fully Bayesian approach, using the conventional formulas in R. It enables the analysis of the detectability of species in different stages of the workflow of eDNA metabarcoding and inference of species site occupancy while accounting for false negatives. It also provides the functionality for a model-based inference to assist the optimization of the study design.

See the package vignette to learn how to use the package and the original paper for details of the model and inference.

Installation

You need first install JAGS following the instructions on the JAGS homepage.

You can then install the latest stable version of the package from CRAN:

install.packages("occumb")

or the GitHub repository:

remotes::install_github("fukayak/occumb", ref = "main")

Contact information

Questions and bug reports can be emailed to Keiichi Fukaya (fukaya.keiichi@nies.go.jp).

Credits

The development of occumb would not be possible without, among others, Martyn Plummer’s JAGS and Ken Kellner’s jagsUI R package, because the main functionality of occumb for model fitting via Markov chain Monte Carlo (MCMC) rely on these libraries. Taku Kadoya encouraged the author to develop the package. Koji Makiyama, Shinya Uryu, and Kentaro Matsuura contributed to the development of package testing. Mito Ikemoto and Kentaro Uehira provided valuable feedback through a package trial and a documentation review. Funding was provided by Japan Society for the Promotion of Science (KAKENHI, Nos 20K06102 and 23H02240).