R/get_DES_input.R

In thauffe/simDES: Simulate fossil biogeography

get_DES_input <- function(SimDfBinned, Time, BinSize, Distribution = "state", DataInArea)
{
  BinnedTime <- seq(0, Time + BinSize, by = BinSize)
  Nspecies <- max(SimDfBinned$Species)
  DesInput <-  data.frame(scientificName = paste0("SP_", 1:Nspecies),
                          as.data.frame(matrix(NA_integer_,
                                               nrow = Nspecies,
                                               ncol = length(BinnedTime))))
  colnames(DesInput)[-1] <- rev(BinnedTime)
  for(i in 1:Nspecies){
    Species <- SimDfBinned[SimDfBinned$Species == i, ]
    SpeciesState <- Species[, Distribution]
    S <- SpeciesState[-length(SpeciesState)]
    if(any(S > 1))
    {
      From <- min(which(SpeciesState > 1))
      Species <- Species[From:nrow(Species), ]
      DesInput[i, 2 + Species$BinnedTimeIndex] <- Species[, Distribution] - 1 # 1:4 -> 0:3
    }
  }
  DesInputTrim <- DesInput[, -c(1, 2, ncol(DesInput))]
  if (is.null(DataInArea))
  {
    Keep <- rowSums(DesInputTrim, na.rm = TRUE) > 0
    DesInput <- DesInput[Keep, ]
  } else
  {
    Keep <- apply(DesInputTrim, 1, function(x) any(x == 3, na.rm = TRUE))
    DesInput <- DesInput[Keep, ]
    DesInput <- DesInput[, -1]
  }
  return(DesInput)
}