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3.6 - Rasterize full species groups.R
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3.6 - Rasterize full species groups.R
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# Supplementary code for Short et al. Part 3.6 - Rasterize the full species spatial data
# Monica Short, August 2020
# Set working directory
setwd("~/Documents/Short")
getwd()
# Install packages to be used
install.packages("tidyverse", dependencies = TRUE)
install.packages("sf", dependencies = TRUE)
install.packages("rgdal", dependencies = TRUE)
install.packages("sp")
install.packages("raster")
install.packages("fasterize")
#load packages
library(tidyverse)
library(sf)
library(sp)
library(rgdal)
library(raster)
library(fasterize)
#create a global 1 degree raster
gr <- raster(nrow = 360, ncol = 360, res = c(1,1))
#read in IUCN table
iucn <- read_csv("~/Documents/Short/Shortdata.csv")
#alter colnames of iucn
iucn <- iucn %>% plyr::rename(c("scientific_name" = "SciName", "kingdom_name" = "Kingdom", "phylum_name" = "Phylum",
"class_name" = "Class", "order_name" = "Order", "family_name" = "Family", "genus_name" = "Genus"))
## ------------------------------------------------------------------------------
## Rasterize each animal group - full species file - includes all species, medicinal or otherwise
## ------------------------------------------------------------------------------
#change working directory
setwd("~/Documents/SpatialData")
#read in range polygon shapefile, change filepath
ranges <- read_sf("./MAMMALS/MAMMALS.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus because we get them from the iucn data
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
mammals <- inner_join(ranges, iucn, by = c("SciName"))
#MAMMALS
st_crs(mammals)
rr <- fasterize(mammals, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "mammalsALLRast", format = "GTiff", overwrite = TRUE)
#CONUS
ranges <- read_sf("./CONUS/CONUS.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
conus <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(conus, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "conusALLRast", format = "GTiff", overwrite = TRUE)
#REPTILES
ranges <- read_sf("./REPTILES/REPTILES.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
reptiles <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(reptiles, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "reptilesALLRast", format = "GTiff", overwrite = TRUE)
#AMPHIBIANS
ranges <- read_sf("./AMPHIBIANS/AMPHIBIANS.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
amphibians <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(amphibians, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "amphibsALLRast", format = "GTiff", overwrite = TRUE)
#LOBSTERS
ranges <- read_sf("./LOBSTERS/LOBSTERS.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
lobs <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(lobs, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "lobsALLRast", format = "GTiff", overwrite = TRUE)
#BIRDS
ranges <- read_sf("./Birds/Birds.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("SCINAME" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
birds <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(birds, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "birdsALLRast", format = "GTiff", overwrite = TRUE)
#FW PART 1
ranges <- read_sf("./FW_GROUPS/FW_GROUPS_PART1.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
fwpt1 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(fwpt1, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "fwpt1ALLRast", format = "GTiff", overwrite = TRUE)
#FW PART 2
ranges <- read_sf("./FW_GROUPS/FW_GROUPS_PART2.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order_, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
fwpt2 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(fwpt2, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "fwpt2ALLRast", format = "GTiff", overwrite = TRUE)
#FW PART 3
ranges <- read_sf("./FW_GROUPS/FW_GROUPS_PART3.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
fwpt3 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(fwpt3, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "fwpt3ALLRast", format = "GTiff", overwrite = TRUE)
#FW PART 4
ranges <- read_sf("./FW_GROUPS/FW_GROUPS_PART4.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
fwpt4 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(fwpt4, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "fwpt4ALLRast", format = "GTiff", overwrite = TRUE)
#FW PART 5
ranges <- read_sf("./FW_GROUPS/FW_GROUPS_PART5.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
fwpt5 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(fwpt5, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "fwpt5ALLRast", format = "GTiff", overwrite = TRUE)
#FW PART 6
ranges <- read_sf("./FW_GROUPS/FW_GROUPS_PART6.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
fwpt6 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(fwpt6, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "fwpt6ALLRast", format = "GTiff", overwrite = TRUE)
#SEACUCS
ranges <- read_sf("./SEACUCUMBERS/SEACUCUMBERS.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
seacucs <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(seacucs, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "seacucsALLRast", format = "GTiff", overwrite = TRUE)
#MARINE FISH PART 1
ranges <- read_sf("./MARINEFISH/MARINEFISH_PART1.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
mfpt1 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(mfpt1, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "mfpt1ALLRast", format = "GTiff", overwrite = TRUE)
#MARINE FISH PART 2
ranges <- read_sf("./MARINEFISH/MARINEFISH_PART2.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
mfpt2 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(mfpt2, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "mfpt2ALLRast", format = "GTiff", overwrite = TRUE)
#MARINE FISH PART 3
ranges <- read_sf("./MARINEFISH/MARINEFISH_PART3.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
mfpt3 <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(mfpt3, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "mfpt3ALLRast", format = "GTiff", overwrite = TRUE)
#SHARKS RAYS CHIMAERAS
ranges <- read_sf("./SHARKS_RAYS_CHIMAERAS/SHARKS_RAYS_CHIMAERAS.shp")
#rename binomial as "SciName" for the join
ranges <- ranges %>% plyr::rename(c("binomial" = "SciName"))
#drop kingdon, phylum, class, order, family, and genus
ranges <- ranges %>% dplyr::select(-c(kingdom, phylum, class, order_, family, genus))
#join ranges and iucn using the scientific name (SciName)
sharksrayschima <- inner_join(ranges, iucn, by = c("SciName"))
rr <- fasterize(sharksrayschima, gr, fun = "sum", background = 0)
plot(rr)
writeRaster(rr, "sharksrayschimaALLRast", format = "GTiff", overwrite = TRUE)
##COMBINE
mammals <- raster("mammalsALLRast.tif")
conus <- raster("conusALLRast.tif")
amphibs <-raster("amphibsALLRast.tif")
lobs <- raster("lobsALLRast.tif")
reptiles <- raster("reptilesALLRast.tif")
seacucs <- raster("seacucsALLRast.tif")
fwpt1 <- raster("fwpt1ALLRast.tif")
fwpt2 <- raster("fwpt2ALLRast.tif")
fwpt3 <- raster("fwpt3ALLRast.tif")
fwpt4 <- raster("fwpt4ALLRast.tif")
fwpt5 <- raster("fwpt5ALLRast.tif")
fwpt6 <- raster("fwpt6ALLRast.tif")
mfpt1 <- raster("mfpt1ALLRast.tif")
mfpt2 <- raster("mfpt2ALLRast.tif")
mfpt3 <- raster("mfpt3ALLRast.tif")
sharksrayschima <- raster("sharksrayschimaALLRast.tif")
birds <- raster("birdsALLRast.tif")
combinelayers <- merge(mammals, conus)
combinelayers2 <- merge(combinelayers, reptiles)
combinelayers3 <- merge(combinelayers2, seacucs)
combinelayers4 <- merge(combinelayers3, fwpt1)
combinelayers5 <- merge(combinelayers4, fwpt2)
combinelayers6 <- merge(combinelayers5, fwpt3)
combinelayers7 <- merge(combinelayers6, fwpt4)
combinelayers8 <- merge(combinelayers7, fwpt5)
combinelayers9 <- merge(combinelayers8, fwpt6)
combinelayers10 <- merge(combinelayers9, mfpt1)
combinelayers11 <- merge(combinelayers10, mfpt2)
combinelayers12 <- merge(combinelayers11, mfpt3)
combinelayers13 <- merge(combinelayers12, sharksrayschima)
combinelayers14 <- merge(combinelayers13, amphibs)
combinelayers15 <- merge(combinelayers14, birds)
combinelayers16 <- merge(combinelayers15, lobs)
plot(combinelayers16)
writeRaster(combinelayers16, "CombinedRastALL", format = "GTiff")