R/pfPublication.R

In paleofire: Analysis of Charcoal Records from the Global Charcoal Database

#' Get citations for charcoal sites
#'
#' @author O. Blarquez
#' @param x A "pfSiteSel" object
#' @param output Defines the output as a "list" or a "data.frame" (default).
#' @return A list or data frame with citation informations related to charcoal sites.
#' @examples
#' x=pfSiteSel(id_site %in% c(1:4))
#' pfPublication(x,output="list")


pfPublication <- function(x, output="data.frame") {
  pub_key <- pub <- NULL
  data(pub, envir = environment())
  data(pub_key, envir = environment())



  ## data.frame output
  if (output == "data.frame") {
    a <- b <- id_pub_list <- list()
    for (i in 1:length(x$id_site)) {
      id_pub_list[[i]] <- pub_key[pub_key[, 1] == x$id_site[i], 2]
      a[[i]] <- rep(x$id_site[i], length(pub_key[pub_key[, 1] == x$id_site[i], 2]))
      b[[i]] <- rep(x$site_name[i], length(pub_key[pub_key[, 1] == x$id_site[i], 2]))
    }

    c <- cbind(unlist(a), unlist(b), unlist(id_pub_list))
    for (i in 1:nrow(c))
      c[i, 3] <- c(as.character(pub[pub[, 1] == c[i, 3], 2]))

    colnames(c) <- c("id_site", "site_name", "citation")
    pub_frame <- data.frame(c)
    return(pub_frame)
  } else {
    ## List output
    pub_list <- NULL
    for (i in 1:length(x$id_site)) {
      pub_list[[i]] <- list(
        id_site = x$id_site[i],
        site_name = x$site_name[i],
        citation = as.character(
          pub[pub[, 1] %in% pub_key[pub_key[, 1] == x$id_site[i], 2], 2]
        )
      )
    }
    return(pub_list)
  }
}