maprich returns the same output as mapocc!

[jgsaulsbury]

This can be seen from the example on the front of the github - if you compare the output of maprich and mapocc for testudinata, side-by-side, you can see they are exactly the same. I imagine it should not be too hard to change it so that maprich counts only unique occurrences?

[jgsaulsbury]

I implemented a goofy fix by modifying .rank_filter. There are undoubtedly better ways of doing this (this one is implemented just for maps of species richness):

.rank_filter <- function(r, data, res, rank) {
  if (rank=="species") {
    #save all fossil occurrences where the rank is species
    rank.df <- base::subset(data, !is.na(data$species))
  }
  if (rank=="genus") {
    #save all fossil occurrences where there is a known genus
    rank.df <- base::subset(data, !is.na(data$genus))
  }
  if (rank=="family") {
    #save all fossil occurrences where there is a known family
    rank.df <- base::subset(data, !is.na(data$family))
  }
  if (rank=="order") {
    #save all fossil occurrences where there is a known order
    rank.df <- base::subset(data, data$order!="NA")
  }
  if (rank=="class") {
    #save all fossil occurrences where there is a known class
    rank.df <- base::subset(data, data$class!="NA")
  }
  if (rank=="phylum") {
    #save all fossil occurrences where there is a known phylum
    rank.df <- base::subset(data, data$order!="NA")
  }
  rank.df <- stats::setNames(split(rank.df, seq(nrow(rank.df))), rank.df$species)
  rankraster <- base::lapply(rank.df, function(y) {
    #split off paleolat and paleolng
    latlng <- base::split(y, base::paste(y$paleolng, y$paleolat))
    latlngmatrix <- base::as.matrix(base::do.call(base::rbind,base::lapply(latlng,function(x)c(x$paleolng[1],
                                                                                               x$paleolat[1],1))))

    latlngmatrix <- base::rbind(latlngmatrix[1,], latlngmatrix)
    latlngras <- raster::rasterize(latlngmatrix[,1:2], r, latlngmatrix[,3])
  })
  splist <- list()
  for(i in 1:base::length(base::unique(base::names(rankraster)))){
    print(paste("generating raster for species",i))
    suppressWarnings(rs <- raster::subset(rankraster,names(rankraster)==base::unique(base::names(rankraster))[i])
    rs <- raster::calc(raster::stack(rs), function(x) base::sum(x,na.rm=TRUE))
    #creates a presence/absence matrix for this species
    rs[rs>0] <- 1
    splist <- c(splist, rs)
  }
  rankraster <- raster::calc(raster::stack(splist), function(x) base::sum(x,na.rm=TRUE))
  raster::values(rankraster)[raster::values(rankraster)==0]<-NA
  return(rankraster)
}

[SaraVarela]

Hi! Thank you very much for the feedback and for your help! this library is not finished and it might have some more issues. A student will finish it in the next months, so I will let him decide what to do with this issue :-) abrazos, Sara