Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and gear scaling coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
| Version: | 0.3.3 |
| Depends: | R (≥ 4.1) |
| Imports: | bayestestR,dplyr,ggplot2,lifecycle,loo, methods,Rcpp (≥0.12.0),RcppParallel (≥ 5.0.1),rlist,rstan (≥ 2.26.23),rstantools (≥ 2.3.1.1),tidyr,scales |
| LinkingTo: | BH (≥ 1.66.0),Rcpp (≥ 0.12.0),RcppEigen (≥ 0.3.3.3.0),RcppParallel (≥ 5.0.1),rstan (≥ 2.26.23),StanHeaders (≥2.26.22) |
| Suggests: | bayesplot,knitr,rmarkdown,testthat (≥ 3.0.0) |
| Published: | 2025-06-21 |
| DOI: | 10.32614/CRAN.package.eDNAjoint |
| Author: | Abigail G. Keller [aut, cre], Ryan P. Kelly [ctb], Chitra M. Saraswati [rev], Saras M. Windecker [rev] |
| Maintainer: | Abigail G. Keller <agkeller at berkeley.edu> |
| BugReports: | https://github.com/ropensci/eDNAjoint/issues |
| License: | GPL-3 |
| URL: | https://github.com/ropensci/eDNAjoint,https://docs.ropensci.org/eDNAjoint/ |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make |
| Materials: | README |
| CRAN checks: | eDNAjoint results |