Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://bookdown.org/abigailkeller/eDNAjoint_vignette/>). 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 catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
| Version: |
0.2 |
| Depends: |
R (≥ 3.4.0) |
| Imports: |
bayestestR, dplyr, ggplot2, lifecycle, loo, magrittr, 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: |
2024-10-08 |
| 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 NEWS |
| CRAN checks: |
eDNAjoint results |