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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 |
| Reference manual: | eDNAjoint.pdf |
| Package source: | eDNAjoint_0.2.tar.gz |
| Windows binaries: | r-devel: eDNAjoint_0.2.zip, r-release: eDNAjoint_0.2.zip, r-oldrel: eDNAjoint_0.2.zip |
| macOS binaries: | r-release (arm64): eDNAjoint_0.2.tgz, r-oldrel (arm64): eDNAjoint_0.2.tgz, r-release (x86_64): eDNAjoint_0.2.tgz, r-oldrel (x86_64): eDNAjoint_0.2.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.