R/occSum.R

In occCite: Querying and Managing Large Biodiversity Occurrence Datasets

#' @title Summary for occCite data objects
#'
#' @description Displays a summary of relevant stats about a query
#'
#' @param object An object of class \code{\link{occCiteData}}
#'
#' @param ... Additional arguments affecting the summary produced
#'
#' @examples
#'
#' data(myOccCiteObject)
#' summary(myOccCiteObject)
#' @method summary occCiteData
#' @export
#'
summary.occCiteData <- function(object, ...) {
  x <- object

  stopifnot(inherits(x, "occCiteData"))

  if (!is.null(x@occCiteSearchDate)) {
    cat(
      "\t\n",
      sprintf(
        "OccCite query occurred on: %s\n",
        format(as.Date(x@occCiteSearchDate),
          format = "%d %B, %Y"
        )
      )
    )
  }

  if (!is.null(x@userQueryType)) {
    cat(
      "\t\n",
      sprintf("User query type: %s\n", x@userQueryType)
    )
  }

  if (!is.null(x@userSpecTaxonomy)) {
    cat(
      "\t\n",
      sprintf(
        "Sources for taxonomic rectification: %s\n",
        paste0(x@userSpecTaxonomy, collapse = ", ")
      ), "\t\n"
    )
  }

  if (!is.null(x@cleanedTaxonomy)) {
    cat(
      "\t\n",
      sprintf("Taxonomic cleaning results: %s\n", "\t\n")
    )
    print(x@cleanedTaxonomy)
  }

  if (!is.null(x@occResults)) {
    if (length(x@occResults) > 0) {
      cat(
        "\t\n",
        sprintf(
          "Sources for occurrence data: %s\n",
          paste0(x@occSources, collapse = ", ")
        ), "\t\n"
      )
      # Tabulate search results
      occurrenceCountGBIF <- vector(
        mode = "numeric",
        length = length(x@occResults)
      )
      occurrenceCountBIEN <- vector(
        mode = "numeric",
        length = length(x@occResults)
      )
      sourceCountGBIF <- vector(
        mode = "numeric",
        length = length(x@occResults)
      )
      sourceCountBIEN <- vector(
        mode = "numeric",
        length = length(x@occResults)
      )

      for (i in 1:length(x@occResults)) {
        # GBIF counts
        if (any(all(x@occSources == "bien", length(x@occSources) == 1),
          is.null(x@occResults[[i]]$GBIF$OccurrenceTable),
          nrow(x@occResults[[i]]$
            GBIF$OccurrenceTable[!is.na(x@occResults[[i]]$
            GBIF$OccurrenceTable$
            datasetKey), ]) == 0,
          na.rm = T
        )) {
          occurrenceCountGBIF[[i]] <- 0
          sourceCountGBIF[[i]] <- 0
        } else {
          occurrenceCountGBIF[[i]] <- nrow(
            x@occResults[[i]]$GBIF$OccurrenceTable
          )
          sourceCountGBIF[[i]] <- length(
            unique(x@occResults[[i]]$GBIF$OccurrenceTable$datasetKey)
          )
        }
        # BIEN counts
        if (any(all(x@occSources == "gbif", length(x@occSources) == 1),
          is.null(x@occResults[[i]]$BIEN$OccurrenceTable),
          na.rm = T
        )) {
          occurrenceCountBIEN[[i]] <- 0
          sourceCountBIEN[[i]] <- 0
        } else {
          occurrenceCountBIEN[[i]] <- nrow(
            x@occResults[[i]]$BIEN$OccurrenceTable
          )
          sourceCountBIEN[[i]] <- length(
            unique(x@occResults[[i]]$BIEN$OccurrenceTable$datasetKey)
          )
        }
      }
      sumTab <- as.data.frame(cbind(
        names(x@occResults),
        (occurrenceCountGBIF + occurrenceCountBIEN),
        (sourceCountGBIF + sourceCountBIEN)
      ))
      colnames(sumTab) <- c(
        "Species", "Occurrences",
        "Sources"
      )
      print(sumTab)
    }
  }

  if ("gbif" %in% x@occSources) {
    if (length(x@occResults) > 0) {
      cat(
        "\t\n",
        sprintf("GBIF dataset DOIs: %s\n", "\t\n")
      )

      # Tabulate DOIs
      GBIFdoi <- vector(mode = "numeric", length = length(x@occResults))
      GBIFaccessDate <- vector(mode = "numeric", length = length(x@occResults))
      for (i in 1:length(x@occResults)) {
        if (as.numeric(sumTab$Occurrences[[i]]) > 0) {
          GBIFdoi[[i]] <- x@occResults[[i]]$GBIF$Metadata$doi
          GBIFaccessDate[[i]] <- strsplit(
            x@occResults[[i]]$GBIF$Metadata$modified,
            "T"
          )[[1]][1]
        } else {
          GBIFdoi[[i]] <- NA
          GBIFaccessDate[[i]] <- NA
        }
      }
      doiTab <- as.data.frame(cbind(
        names(x@occResults),
        GBIFaccessDate, GBIFdoi
      ))
      colnames(doiTab) <- c("Species", "GBIF Access Date", "GBIF DOI")
      print(doiTab)
    }
  }
}