R/taxa.R

In neotoma2: Working with the Neotoma Paleoecology Database

utils::globalVariables(c("context", "sites"))

#' @import dplyr
#' @export
#' @title Extract taxonomic data from a set of sites.
#' @description From a sites object,
#' @param object A \code{sites} object.
#' @returns A \code{data.frame} reporting the taxa/data objects, units,
#' elements and other features within a set of records.
#' @examples \donttest{
#' somesites <- get_sites(datasettype = "diatom", limit = 3) %>%
#'   get_downloads()
#' diatomtaxa <- taxa(somesites)
#' common_taxa <- diatomtaxa %>%
#'   dplyr::filter(sites == 3)
#'   }
#'
setMethod(f = "taxa",
          signature = "sites",
          definition = function(object) {
            output <- purrr::map(object@sites, function(y) taxa(y)) %>%
              dplyr::bind_rows() %>%
                group_by(units,
                context,
                element,
                taxonid,
                symmetry,
                taxongroup,
                elementtype,
                variablename,
                ecologicalgroup) %>%
              summarise(samples = sum(samples),
                        sites = sum(sites), .groups = "keep")
            if(nrow(output) == 0){
              warnsite <- sprintf("No assigned samples. Did you run get_downloads()?")
              warning(warnsite)
            }
            return(output)
          }
)

#' @title Extract taxonomic data from a single site.
#' @param object A \code{site} object.
#' @returns A \code{data.frame} reporting the taxa/data objects, units,
#' elements and other features within a set of records.
#' @examples \donttest{
#' somesites <- get_sites(datasettype = "pollen", limit = 3) %>%
#'   get_downloads()
#' diatomtaxa <- taxa(somesites[[1]])
#' }
setMethod(f = "taxa",
          signature = "site",
          definition = function(object) {
            samples <- samples(object)
            tx_table <- samples %>%
              group_by(units,
                       context,
                       element,
                       taxonid,
                       symmetry,
                       taxongroup,
                       elementtype,
                       variablename,
                       ecologicalgroup,
                       siteid) %>%
              summarise(samples = n(), .groups = "keep") %>%
              group_by(units,
                       context,
                       element,
                       taxonid,
                       symmetry,
                       taxongroup,
                       elementtype,
                       variablename,
                       ecologicalgroup) %>%
              summarise(sites = n(), samples = sum(samples), .groups = "keep")
            return(tx_table)
          })

#' @title Extract taxonomic data from a set of sites.
#' @param object A \code{collunits} object.
#' @returns A \code{data.frame} reporting the taxa/data objects, units,
#' elements and other features within a set of records.
setMethod(f = "taxa",
          signature = "collunits",
          definition = function(object) {
            samples <- samples(object)
            tx_table <- samples %>%
              group_by(units,
                       context,
                       element,
                       taxonid,
                       symmetry,
                       taxongroup,
                       elementtype,
                       variablename,
                       ecologicalgroup,
                       siteid) %>%
              summarise(samples = n(), .groups = "keep") %>%
              group_by(units,
                       context,
                       element,
                       taxonid,
                       symmetry,
                       taxongroup,
                       elementtype,
                       variablename,
                       ecologicalgroup) %>%
              summarise(sites = n(), samples = sum(samples), .groups = "keep")
            return(tx_table)
          })

#' @title Extract taxonomic data from a set of sites.
#' @param object A \code{collunit} object.
#' @returns A \code{data.frame} reporting the taxa/data objects, units,
#' elements and other features within a set of records.
setMethod(f = "taxa",
          signature = "collunit",
          definition = function(object) {
            samples <- samples(object)
            tx_table <- samples %>%
              group_by(units,
                       context,
                       element,
                       taxonid,
                       symmetry,
                       taxongroup,
                       elementtype,
                       variablename,
                       ecologicalgroup,
                       siteid) %>%
              summarise(samples = n(), .groups = "keep") %>%
              group_by(units,
                       context,
                       element,
                       taxonid,
                       symmetry,
                       taxongroup,
                       elementtype,
                       variablename,
                       ecologicalgroup) %>%
              summarise(sites = n(), samples = sum(samples), .groups = "keep")
            return(tx_table)
          })