R/fish.R

In fukayak/occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding

#' Fish eDNA metabarcoding dataset
#'
#' A dataset of fish eDNA metabarcoding collected in the Kasumigaura watershed, Japan.
#'
#' @format An occumbData class object containing the sequence read count \code{y},
#'  a species covariate \code{mismatch}, and a site covariate \code{riverbank}.
#'  \code{mismatch} represents the total number of mismatched bases in the
#'  priming region of the forward and reverse primers for each species.
#'  \code{riverbank} indicates whether the riverbank at each site lacks aquatic
#'  and riparian vegetation.
#'  Sequence reads were obtained from three replicates (collected from the
#'  center of the river and near the left and right riverbanks)
#'  from 50 sites across the watershed, of which read counts from six samples were
#'  missing.
#'  The resulting sequence counts of 50 freshwater fish taxa were recorded.
#' @source K. Fukaya, N. I. Kondo, S. S. Matsuzaki, T. Kadoya (2021) Data from: Multispecies site occupancy modeling and study design for spatially replicated environmental DNA metabarcoding. Dryad Digital Repository. \doi{10.5061/dryad.3bk3j9kkm}
"fish"