R/eDNAjoint-package.R

In eDNAjoint: Joint Modeling of Traditional and Environmental DNA Survey Data in a Bayesian Framework

#' The 'eDNAjoint' package.
#'
#' @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.
#'
#' @docType package
#' @name eDNAjoint-package
#' @aliases eDNAjoint
#' @useDynLib eDNAjoint, .registration = TRUE
#' @import methods
#' @import Rcpp
#' @importFrom rstan sampling
#' @importFrom rstantools rstan_config
#' @importFrom RcppParallel RcppParallelLibs
#'
#' @references
#' Stan Development Team (NA). RStan: the R interface to Stan.
#'   https://mc-stan.org
#'
## usethis namespace: start
#' @importFrom lifecycle deprecated
## usethis namespace: end
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