R/occCiteData.R

In occCite: Querying and Managing Large Biodiversity Occurrence Datasets

#' @title occCite Data Class
#'
#' @description A class for managing metadata associated with occCite
#' queries and data manipulation.
#'
#' @slot userQueryType A vector of type character specifying whether the
#' user made their original taxonomic query based on a vector of taxon names
#' or a phylogeny.
#'
#' @slot userSpecTaxonomy A vector of type character that presents a
#' list of taxonomic sources for cleaning taxonomy of queries. This can be
#' user-specified or default.
#'
#' @slot cleanedTaxonomy A data frame with containing input taxon names, the
#' closest match according to \code{\link{gnr_resolve}}, and a list of
#' taxonomic data sources that contain the matching name, generated
#' by \code{\link{studyTaxonList}}.
#'
#' @slot occSources A vector of class "character" containing a list of
#' occurrence data sources, generated when passing a \code{\link{occCiteData}}
#' object through \code{\link{occQuery}}.
#'
#' @slot occCiteSearchDate The date on which the occurrence search query
#' was conducted via occCite.
#'
#' @slot occResults The results of an \code{\link{occQuery}} search, stored
#' as a named list, each of the items named after a searched taxon and
#' containing a data frame with occurrence information.
#'
#' @importFrom methods new
#'
#' @export
occCiteData <- methods::setClass("occCiteData",
  slots = c(
    userQueryType = "vector",
    userSpecTaxonomy = "vector",
    cleanedTaxonomy = "data.frame",
    occSources = "vector",
    occCiteSearchDate = "character",
    occResults = "list"
  )
)