R/taxaaccum.R

In SCAR/biotaxa: Visualising the growth and prediction of taxonomic diversity and identifying taxonomic incompleteness and imprecision

#'Report the accumulative numbers of a rank of a given taxa overtime
#'
#' @param taxa A string.
#' @param rank A string.
#' @return accumulation curve of \code{rank} of a \code{taxa}
#' @import data.table
#' @import ggplot2
#'@examples
#'\dontrun{
#'taxaaccum("Animalia", "Phylum")
#'}
#'@export

taxaaccum <- function(taxa, rank) {
  df <- subset(data_m, Kingdoms == taxa | Phyla == taxa | Classes == taxa | Orders == taxa | Families == taxa | Genera == taxa)
  dt = as.data.table(unique(df))
  setkey(dt, "year")
  if (rank == "Phylum") {
    dt[, id := as.numeric(factor(Phyla, levels = unique(Phyla)))]
    ranklabel = "phyla"
  } else if (rank == "Class") {
    dt[, id := as.numeric(factor(Classes, levels = unique(Classes)))]
    ranklabel = "classes"
  } else if (rank == "Order") {
    dt[, id := as.numeric(factor(Orders, levels = unique(Orders)))]
    ranklabel = "orders"
  } else if (rank == "Family") {
    dt[, id := as.numeric(factor(Families, levels = unique(Families)))]
    ranklabel = "families"
  } else if (rank == "Genus") {
    dt[, id := as.numeric(factor(Genera, levels = unique(Genera)))]
    ranklabel = "genera"
  } else if (rank == "Species") {
    dt[, id := as.numeric(factor(AphiaIDs, levels = unique(AphiaIDs)))]
    ranklabel = "species"
  }
  setkey(dt, "year", "id")
  dt.out <- dt[J(unique(year)), mult = "last"]#[, Phylum := NULL]
  dt.out[, id := cummax(id)]
  numtaxa <- cummax(as.numeric(factor(dt$id)))
  taxa_dt <- aggregate(numtaxa, list(year = dt$year), max )
  colnames(taxa_dt) <- c("year", "taxacount")
  minx <- min(as.vector(taxa_dt$year))
  maxx <- max(as.vector(taxa_dt$year))
  ylab = paste("Number of", ranklabel, sep = " ")
  p <- ggplot(taxa_dt, aes(x = year, y = taxacount, colour = "#FF9999")) + geom_point(colour = "cornflowerblue")
  p <- p + labs(x = "Year", y = ylab) + ggtitle(taxa) + scale_x_discrete(breaks = c(seq(minx, maxx, 25))) + theme(legend.position = "none", axis.text.x = element_text(angle = 60, hjust = 1), axis.text.y = element_text(angle = 60, hjust = 1), axis.title.y = element_text(margin = margin(t = 0, r = 20, b = 0, l = 0)))

  p

}