DESCRIPTION

Package: eDNAjoint
Title: Joint Modeling of Traditional and Environmental DNA Survey Data in a Bayesian Framework
Version: 0.2
Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
Authors@R: 
    c(person("Abigail G.", "Keller", role = c("aut", "cre"), email="agkeller@berkeley.edu"),
    person("Ryan P.", "Kelly", role = "ctb", email="rpkelly@uw.edu"),
    person("Chitra M.", "Saraswati", role = "rev"),
    person("Saras M.", "Windecker", role = "rev"))
Description: 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 catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
License: GPL-3
URL: https://github.com/ropensci/eDNAjoint, https://docs.ropensci.org/eDNAjoint/
BugReports: https://github.com/ropensci/eDNAjoint/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE, roclets = c ("namespace", "rd", "srr::srr_stats_roclet"))
RoxygenNote: 7.3.1
Biarch: true
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)
SystemRequirements: GNU make
LazyData: true
Suggests: 
    bayesplot,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3