R/goby_data.R

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

#' goby_data
#' @srrstats {G5.1} data that is exported and is available for the the user can
#'   confirm tests and run examples
#'
#' Tidewater goby (Eucyclogobius newberryi) data from eDNA and traditional
#' (seine) surveys collected from 39 locations in California. Data can be used
#' to demonstrate functions in the R package eDNAjoint. Data is retrieved from
#' Schmelzle and Kinziger, 2016.
#'
#' @title goby_data
#' @docType data
#' @keywords data
#' @format A list with four matrices representing eDNA sampling data (pcr_n
#'   and pcr_k), seine sampling data (count), and site-level covariate data
#' (site_cov).
#' \describe{
#'   \item{pcr_n}{Total number of eDNA qPCR replicates at each site (row) and
#'     eDNA sample replicate (column). Data includes 39 total sites and a
#'     maximum of 22 eDNA sample replicates. NA indicates that fewer eDNA
#'     samples were collected than the maximum at a site.}
#'   \item{pcr_k}{Total number of positive eDNA qPCR detections at each site
#'     (row) and eDNA sample replicate (column). Data includes 39 total sites
#'     and a maximum of 22 eDNA sample replicates. NA indicates that fewer eDNA
#'     samples were collected than the maximum at a site.}
#'   \item{count}{Count of goby individuals in seine samples at each site (row)
#'     and seine sample replicate (column). Data includes 39 total sites and a
#'     maximum of 22 seine replicates. NA indicates that fewer seine samples
#'     were collected than the maximum at a site.}
#'   \item{site_cov}{Data representing site-level covariates at each site (row).
#'     Data includes mean salinity at a site ('Salinity'), mean time to filter
#'     eDNA samples ('Filter_time'), density of other fish species
#'     ('Other_fishes'), size of habitat ('Hab_size'), and presence of
#'     vegetation ('Veg'). All non-integer covariate data is standardized.}
#'}
#' @source \url{https://datadryad.org/dataset/doi:10.5061/dryad.6rs23}
#' @references Schmelzle, M.C. and Kinziger, A.P. (2016). Using occupancy
#'   modelling to compare environmental DNA to traditional field methods for
#'   regional-scale monitoring of an endangered aquatic species. Molecular
#'   Ecology Resources. 16(4): 895-908.
"goby_data"