R/bridgeTreeData.R

In hannahlowens/BridgeTree: Tools for Building and Managing Data for Comparative Phylogenetics of Ecological Niches

#' @title bridgeTree Data Class
#'
#' @description A class for managing metadata associated with bridgeTree 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 userSpecTaxonomicSources 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 dataframe with containing input taxon names, the closeset match according to \code{\link{gnr_resolve}}, and a list of taxonomic datasources 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{bridgeTreeData}} object through \code{\link{taxaQuery}}.
#'
#' @slot occNLimit The limit of occurrence records to return for each species when executing \code{\link{occ}} through \code{\link{taxaQuery}}.
#'
#' @slot occurrenceSearchDate The date on which the occurrence search query was conducted.
#'
#' @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 dataframe with occurrence information.
#'
#' @export

bridgeTreeData <- setClass("bridgeTreeData",
                           slots = c(userQueryType = "vector",
                                     userSpecTaxonomicSources = "vector",
                                     cleanedTaxonomy = "data.frame",
                                     occSources = "vector",
                                     occurrenceSearchDate = "vector",
                                     occResults = "list")
                            );