R/Range Intersections.R

In gfalbery/SpRanger:

IntersectGet <-
  function(Rasterstack, PairList, Names = "All"){

    library(raster); library(tidyverse); library(Matrix)

    t1 <- Sys.time()
    print("Getting the grid values")

    if(class(Rasterstack)=="RasterBrick"){

      Valuedf <- data.frame(raster::getValues(Rasterstack)) %>% as.matrix

    }else{

      Valuedf <- lapply(1:length(Rasterstack), function(a){

        getValues(Rasterstack[[a]])

      }) %>% bind_cols %>% as.data.frame()

    }

    colnames(Valuedf) <- names(Rasterstack)

    Valuedf[is.na(Valuedf)] <- 0
    Valuedf <- Valuedf %>% as.matrix() %>% as("dgCMatrix")

    print(paste0("Data frame size = ", dim(Valuedf)))

    if (Species != "All"){
      Valuedf <- Valuedf[, Species]
    }

    if (any(Matrix::colSums(Valuedf) == 0)) {
      print("Removing some species with no ranging data :(")
      Valuedf <- Valuedf[, -which(Matrix::colSums(Valuedf) == 0)]
    }

    if(length(intersect(c(PairList[,1], PairList[,2]), colnames(Valuedf)))<ncol(Valuedf)){
      print("Removing some species in the PairList but with no rasters :(")

      Species <- intersect(c(PairList[,1], PairList[,2]), colnames(Valuedf))

      Valuedf <- Valuedf[,Species]
      PairList <- PairList[PairList[,1]%in%Species&PairList[,2]%in%Species,]

    }

    print(paste0("Data frame size = ", dim(Valuedf)))

    lapply(1:nrow(PairList), function(b){

      Sp1 <- PairList[b,1]
      Sp2 <- PairList[b,2]

      Vector1 <- Valuedf[,Sp1]
      Vector1[Valuedf[,Sp2]==0] <- 0

      Vector1 %>% return

    }) -> ValuesVectors

    names(ValuesVectors) <- paste(PairList[,1],
                                  PairList[,2],
                                  sep = ".")

    return(ValuesVectors)

  }