R/occCitePrint.R

In occCite: Querying and Managing Large Biodiversity Occurrence Datasets

#' @title Print occCite citation object
#'
#' @description Prints formatted citations for occurrences and main
#' packages used (i.e. base, occCite, rgbif, and/or BIEN).
#'
#' @param x An object of class \code{\link{occCiteCitation}}
#'
#' @param ... Additional arguments affecting how the formatted
#' citation document is produced
#'
#' @return A text string with formatted citations
#'
#' @import bib2df
#' @importFrom stats na.omit
#'
#' @examples
#'
#' # Print citations for all species together
#' data(myOccCiteObject)
#' print(myOccCiteObject)
#'
#' # Print citations for each species individually
#' data(myOccCiteObject)
#' print(myOccCiteObject, bySpecies = TRUE)
#' @export
#'
print.occCiteCitation <- function(x, ...) {
  args <- list(...)

  if ("bySpecies" %in% names(args)) {
    bySpecies <- args$bySpecies
  } else {
    bySpecies <- FALSE
  }

  stopifnot(is(x, "occCiteCitation"))

  if (!requireNamespace("RefManageR", quietly = TRUE)) {
    stop(paste0(
      "Package \"RefManageR\" needed for this\n",
      "function to work. Please install it."
    ),
    call. = FALSE
    )
  }

  # Utility function for making a citation list
  refManMCL <- function(x) {
    rval <- list()
    for (i in seq_along(x)) {
      if (!is.null(x[[i]])) {
        rval <- c(rval, unclass(x[[i]]))
      }
    }
    class(rval) <- c("BibEntry", "bibentry")
    rval
  }
  # Function to generate package citations
  packageCitations <- function(packagesUsed) {
    pkg.bib <- lapply(packagesUsed, function(pkg) {
      refs <- RefManageR::as.BibEntry(utils::citation(pkg))
      if (length(refs)) {
        names(refs) <- make.unique(rep(pkg, length(refs)))
      }
      refs
    })
    pkg.bib <- refManMCL(pkg.bib)
    RefManageR::WriteBib(pkg.bib, "temp.bib")

    # this works
    temp <- bib2df::bib2df("temp.bib", separate_names = T)

    packageCitations <- vector(mode = "character", length = nrow(temp))
    for (j in 1:nrow(temp)) {
      i <- temp[j, ]
      if ("R Core Team" %in% i$AUTHOR[[1]]["full_name"]) {
        packageCitations[j] <- paste0(
          i$AUTHOR[[1]]["full_name"],
          ". ", "(", i$YEAR, "). ",
          i$TITLE, ". ",
          i$ORGANIZATION, ", ",
          i$ADDRESS, ". ",
          i$URL, "."
        )
      } else if (i$CATEGORY == "ARTICLE") {
        packageCitations[j] <- paste0(
          paste(apply(i$AUTHOR[[1]],
            MARGIN = 1,
            FUN = function(x) {
              paste0(
                x[4], ", ",
                substring(x[2], 1, 1), ".",
                if (!is.na(x[3])) {
                  paste0(substring(x[3], 1, 1), ".")
                }
              )
            }
          ),
          collapse = ", "
          ),
          " (", i$YEAR, "). ",
          i$TITLE, ". ",
          i$JOURNAL, if (!any(
            is.na(i$VOLUME),
            is.na(i$PAGES)
          )) {
            paste0(" ")
          },
          if (!is.na(i$VOLUME)) {
            paste0(i$VOLUME, ": ")
          },
          if (!is.na(i$PAGES)) {
            paste0(i$PAGES)
          },
          "."
        )
      } else if (grepl("R package", i$NOTE)) {
        packageCitations[j] <- paste0(
          paste(apply(i$AUTHOR[[1]],
            MARGIN = 1,
            FUN = function(x) {
              paste0(
                x[4], ", ",
                substring(x[2], 1, 1), ".",
                if (!is.na(x[3])) {
                  paste0(substring(x[3], 1, 1), ".")
                }
              )
            }
          ),
          collapse = ", "
          ),
          " (", i$YEAR, "). ",
          i$TITLE, ". ",
          i$NOTE, ". ",
          i$URL, "."
        )
      } else {
        packageCitations[j] <- paste0(
          paste(apply(i$AUTHOR[[1]],
            MARGIN = 1,
            FUN = function(x) {
              paste0(
                x[4], ", ",
                substring(x[2], 1, 1), ".",
                if (!is.na(x[3])) {
                  paste0(substring(x[3], 1, 1), ".")
                }
              )
            }
          ),
          collapse = ", "
          ),
          " (", i$YEAR, "). ",
          i$TITLE, ". ",
          i$ORGANIZATION, ", ",
          i$ADDRESS, ". ",
          i$URL, "."
        )
      }
    }

    file.remove("temp.bib")
    packageCitations <- sort(packageCitations)
    return(packageCitations)
  }

  # Combine citations
  if (bySpecies) {
    for (i in 1:length(x$occCitationResults)) {
      # Get list of packages used and get citations
      packCit <- c("base", "occCite", "RefManageR")
      packages <- unique(x$occCitationResults[[i]]$occSearch)
      if ("GBIF" %in% packages) packCit <- c(packCit, "rgbif")
      if ("BIEN" %in% packages) packCit <- c(packCit, "BIEN")
      packCit <- packageCitations(packCit)

      # Print results
      cat(paste("Species:", names(x$occCitationResults)[[i]], "\n\n"))
      singleSpRecord <- x$occCitationResults[[i]]
      singleSpRecord <- singleSpRecord[order(singleSpRecord$Citation), ]
      if (nrow(singleSpRecord[!is.na(singleSpRecord$Citation), ]) > 0) {
        recordCitations <- paste0(
          singleSpRecord$Citation,
          " Accessed via ", singleSpRecord$occSearch,
          " on ", singleSpRecord$`Accession Date`, "."
        )
        allCitations <- sort(c(packCit, recordCitations))
        cat(allCitations, sep = "\n")
      } else {
        cat("NOTE: No occurrences to cite.\n\n")
        cat(packCit, sep = "\n")
      }
      cat(paste("\n"))
    }
  } else {
    recordCitations <- do.call(rbind, x$occCitationResults)
    recordCitations <- recordCitations[!is.na(recordCitations$Citation), ]

    # Get list of packages used and get citations
    packCit <- c("base", "occCite")
    packages <- unique(recordCitations$occSearch)
    if ("GBIF" %in% packages) packCit <- c(packCit, "rgbif")
    if ("BIEN" %in% packages) packCit <- c(packCit, "BIEN")
    packCit <- packageCitations(packCit)

    # Print results
    recordCitations <- recordCitations[order(recordCitations$Citation), ]
    recordCitations <- unique(recordCitations[, c(
      "occSearch",
      "Citation",
      "Accession Date"
    )])
    recordCitations <- paste0(
      recordCitations$Citation,
      " Accessed via ", recordCitations$occSearch,
      " on ", recordCitations$`Accession Date`, "."
    )
    allCitations <- sort(c(packCit, recordCitations))
    cat(allCitations, sep = "\n")
    cat(paste("\n"))
  }
}