Load libraries:
require(rgdal)
require(rgeos)
require(sp)
require(ggplot2)
require(raster)
library(maps)
library(maptools)
require(devtools)
library(spatialEco)
library(terra)
Example data extraction code
Set working directory, load functions, import files
Calculate 25th percenitle for each raster in the stack. Here we are only doing this for the 25th percentile, but you can run the full code to estimate 50th and 10th percentinles, too. (Or any other percentile). These will compute for both spring and autumn where availalbe. To get annual exposure, will have to sum seasonal values. To get exposure from area near Gulf of Mexico, have to clip shp files by relevant polygons near Gulf of Mexico
setwd("/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters")
#Loop to extract 25 percentile for each raster in spat.rast stack
for (i in 1:length(rlist)) {
#aggregate rasters/resample
r <- aggregate(spat.rast[[i]], fact=2)
#create rasters
#vol50<-raster.vol(r, p=.50)
vol25<-raster.vol(r, p=.25)
#vol10<-raster.vol(r, p=.10)
#raster to polygon
#vol50<-raster(vol50)
vol25<-raster(vol25)
#vol10<-raster(vol10)
# vol50shp<-rasterToPolygons(vol50, fun=function(x) {x==1}, dissolve=TRUE)
vol25shp<-rasterToPolygons(vol25, fun=function(x) {x==1}, dissolve=TRUE)
# vol10shp<-rasterToPolygons(vol10, fun=function(x) {x==1}, dissolve=TRUE)
#save as shapefile
# writeOGR(vol50shp, dsn = '.', layer=paste(rlist[i],"_vol50", sep=""), driver='ESRI Shapefile', overwrite_layer= TRUE)
writeOGR(vol25shp, dsn = '.', layer=paste(rlist[i],"_vol25", sep=""), driver='ESRI Shapefile', overwrite_layer= TRUE)
# writeOGR(vol10shp, dsn = '.', layer=paste(rlist[i],"_vol10", sep=""), driver='ESRI Shapefile', overwrite_layer= TRUE)
}
Load raster data
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setwd("/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/MigrationRiskFactors")
envrastlist=list.files(getwd(), pattern="tif$", full.names=FALSE)
for(i in envrastlist) { assign(unlist(strsplit(i,"[.]"))[1], raster(i)) }
Load risk factor data (rasters)
#load all rasters
setwd("/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/MigrationRiskFactors")
TurbineRast<-raster("TurbineRastR.tif")
HurrPtsRast<-raster("HurrPtsRastR.tif")
TotalTorn<-raster("TotalTornRastR.tif")
TotalTowers<-raster("TotalTowersRastR.tif")
CropCov<-raster("CropCovresfix.tif")
ForestShrubCov<-raster("ForestShrubCovresfix.tif")
HFootP<-raster("HFootPresfix.tif")
Forest2010<-raster("Forest_2010Hyde.tif")
Forest2000<-raster("Forest_2000Hyde.tif")
OVERALL2<-raster("OVERALL2.tif")
#turn NAs into zeros
TurbineRast<-reclassify(TurbineRast, cbind(NA, NA, 0), right=TRUE)
HurrPtsRast<-reclassify(HurrPtsRast, cbind(NA, NA, 0), right=TRUE)
TotalTorn<-reclassify(TotalTorn, cbind(NA, NA, 0), right=TRUE)
TotalTowers<-reclassify(TotalTowers, cbind(NA, NA, 0), right=TRUE)
CropCov<-reclassify(CropCov, cbind(NA, NA, 0), right=TRUE)
ForestShrubCov<-reclassify(ForestShrubCov, cbind(NA, NA, 0), right=TRUE)
HFootP<-reclassify(HFootP, cbind(NA, NA, 0), right=TRUE)
OVERALL2<-reclassify(OVERALL2, cbind(NA, NA, 0), right=TRUE)
Can also load future risk-factor exposure, too. But this takes some time and is easier to deal with afterward if it is kept relatively simple (fewer factors, single spatial scale, single season, etc.)
# setwd("/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/MigrationRiskFactors")
# BioFuels<-raster("BiofuelsThreat2030Clip.tif")
# Coal<-raster("CoalThreatClip.tif")
# Mining<-raster("MiningThreatClip.tif")
# OilGasDev<-raster("OilGasDevThreatClip.tif")
# SolarThreat<-raster("SolarThreatClip.tif")
# UnconvOilGas<-raster("UnconvOilGasClip.tif")
# UrbanThreat<-raster("UrbanThreatClip.tif")
# WindThreat<-raster("WindThreatClip.tif")
#replace NAs with zeros
# BioFuels<-reclassify(BioFuels, cbind(NA, NA, 0), right=TRUE)
# Coal<-reclassify(Coal, cbind(NA, NA, 0), right=TRUE)
# Mining<-reclassify(Mining, cbind(NA, NA, 0), right=TRUE)
# OilGasDev<-reclassify(OilGasDev, cbind(NA, NA, 0), right=TRUE)
# SolarThreat<-reclassify(SolarThreat, cbind(NA, NA, 0), right=TRUE)
# UnconvOilGas<-reclassify(UnconvOilGas, cbind(NA, NA, 0), right=TRUE)
# UrbanThreat<-reclassify(UrbanThreat, cbind(NA, NA, 0), right=TRUE)
# WindThreat<-reclassify(WindThreat, cbind(NA, NA, 0), right=TRUE)
# AgAgThreat<-reclassify(AgThreat, cbind(NA, NA, 0), right=TRUE)
Extract risk factors from core-use areas
setwd("/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters")
#get subset of file name x characters from right
substrRight <- function(x, n){
substr(x, nchar(x)-n+1, nchar(x))
}
shplist=list.files("/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters", pattern="shp$", full.names=FALSE)
#set up dataframe
shpdata<-data.frame()[1:length(shplist), ]
shpdata$num<-as.numeric(1:length(shplist))
#get layer name and scale as separate columns
shpname<-gsub('.shp','',shplist)
shpscale<-substrRight(shpname, 2)
#extract layers. Here we only do it for one layer because it can take a long time.
#can uncomment any subset of factors and extract data for those variables.
for (i in 1:length(shplist)) {
#load shapefile
x<-readOGR(shplist[i])
#add entries based on shapefile characteristics
shpdata$ID[i]<-paste(shpname[i])
shpdata$scale[i]<-shpscale[i]
#Migration risk factors
shpdata$Turbine[i]<-raster::extract(TurbineRast, x, fun=sum)
# shpdata$Hurr[i]<-raster::extract(HurrPtsRast, x, fun=sum)
# shpdata$TotalTorn[i]<-raster::extract(TotalTorn, x, fun=sum)
# shpdata$TotalTowers[i]<-raster::extract(TotalTowers, x, fun=sum)
# shpdata$CropCov[i]<-raster::extract(CropCov, x, fun=sum)
# shpdata$ForestShrubCov[i]<-raster::extract(ForestShrubCov, x, fun=sum)
# shpdata$HFootP[i]<-raster::extract(HFootP, x, fun=sum)
# shpdata$Forest2010[i]<-raster::extract(Forest2010, x, fun=sum)
# shpdata$Forest2000[i]<-raster::extract(Forest2000, x, fun=sum)
# shpdata$OVERALL2[i]<-raster::extract(OVERALL2, x, fun=sum)
# #Future threat layers, can uncomment these and run to extract those layers.
# shpdata$BioFuels[i]<-raster::extract(BioFuels, x, fun=sum)
# shpdata$Coal[i]<-raster::extract(Coal, x, fun=sum)
# shpdata$Mining[i]<-raster::extract(Mining, x, fun=sum)
# shpdata$AgThreat[i]<-raster::extract(AgThreat, x, fun=sum)
# shpdata$OilGasDev[i]<-raster::extract(OilGasDev, x, fun=sum)
# shpdata$SolarThreat[i]<-raster::extract(SolarThreat, x, fun=sum)
# shpdata$UnconvOilGas[i]<-raster::extract(UnconvOilGas, x, fun=sum)
# shpdata$UrbanThreat[i]<-raster::extract(UrbanThreat, x, fun=sum)
# shpdata$WindThreat[i]<-raster::extract(WindThreat, x, fun=sum)
# shpdata$AgThreat[i]<-raster::extract(AgThreat, x, fun=sum)
#Data layers for breeding/nonbreeding factors
#These are extracted from raw raster layers available from the data references
#These are not resampled and are at the original layers' resolution. All factors are scaled prior to statistical modeling and resampled vs. raw data Eare extremely strongly correlated (r = 0.98).
#Extractions are completed using 100-km vector buffers around breeding and nonbreeding point estimates.
# shpdata$ForestShrubCov[i]<-raster::extract(ForestShrubCov, x, fun=sum)
# shpdata$HFootP[i]<-raster::extract(HFootP, x, fun=sum)
# shpdata$Forest2010[i]<-raster::extract(Forest2010, x, fun=sum)
# shpdata$Forest2000[i]<-raster::extract(Forest2000, x, fun=sum)
}
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B1_fall_vol25.shp", layer: "B1_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B1_spring_vol25.shp", layer: "B1_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B10_fall_vol25.shp", layer: "B10_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B10_spring_vol25.shp", layer: "B10_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B11_fall_vol25.shp", layer: "B11_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B11_spring_vol25.shp", layer: "B11_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B12_fall_vol25.shp", layer: "B12_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B12_spring_vol25.shp", layer: "B12_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B13_fall_vol25.shp", layer: "B13_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B13_spring_vol25.shp", layer: "B13_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B14_fall_vol25.shp", layer: "B14_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B14_spring_vol25.shp", layer: "B14_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B15_fall_vol25.shp", layer: "B15_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B15_spring_vol25.shp", layer: "B15_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B16_fall_vol25.shp", layer: "B16_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B16_spring_vol25.shp", layer: "B16_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B17_fall_vol25.shp", layer: "B17_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B17_spring_vol25.shp", layer: "B17_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B18_fall_vol25.shp", layer: "B18_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B18_spring_vol25.shp", layer: "B18_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B19_spring_vol25.shp", layer: "B19_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B2_fall_vol25.shp", layer: "B2_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B2_spring_vol25.shp", layer: "B2_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B20_fall_vol25.shp", layer: "B20_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B20_spring_vol25.shp", layer: "B20_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B3_fall_vol25.shp", layer: "B3_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B3_spring_vol25.shp", layer: "B3_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B4_fall_vol25.shp", layer: "B4_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B4_spring_vol25.shp", layer: "B4_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B5_fall_vol25.shp", layer: "B5_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B5_spring_vol25.shp", layer: "B5_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B6_fall_vol25.shp", layer: "B6_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B6_spring_vol25.shp", layer: "B6_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B7_fall_vol25.shp", layer: "B7_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B7_spring_vol25.shp", layer: "B7_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B8_fall_vol25.shp", layer: "B8_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B8_spring_vol25.shp", layer: "B8_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B9_fall_vol25.shp", layer: "B9_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/B9_spring_vol25.shp", layer: "B9_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/DMG03_fall_vol25.shp", layer: "DMG03_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/ILB04_fall_vol25.shp", layer: "ILB04_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/ILB04_spring_vol25.shp", layer: "ILB04_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/ILB06_fall_vol25.shp", layer: "ILB06_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/ILB06_spring_vol25.shp", layer: "ILB06_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/ILB08_fall_vol25.shp", layer: "ILB08_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/ILB08_spring_vol25.shp", layer: "ILB08_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/ILB18_fall_vol25.shp", layer: "ILB18_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/ILB18_spring_vol25.shp", layer: "ILB18_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/KYB14_fall_vol25.shp", layer: "KYB14_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MAB05_fall_vol25.shp", layer: "MAB05_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MAB05_spring_vol25.shp", layer: "MAB05_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MAB06_fall_vol25.shp", layer: "MAB06_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MAB06_spring_vol25.shp", layer: "MAB06_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MAB09_fall_vol25.shp", layer: "MAB09_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MAB09_spring_vol25.shp", layer: "MAB09_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MAB12_fall_vol25.shp", layer: "MAB12_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MAB12_spring_vol25.shp", layer: "MAB12_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MIB02_fall_vol25.shp", layer: "MIB02_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/MIB02_spring_vol25.shp", layer: "MIB02_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
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## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TN13_2015_spring_vol25.shp", layer: "TN13_2015_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TN13_fall_vol25.shp", layer: "TN13_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TN13_spring_vol25.shp", layer: "TN13_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TN16_fall_vol25.shp", layer: "TN16_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TN16_spring_vol25.shp", layer: "TN16_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TNB03_fall_vol25.shp", layer: "TNB03_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TNB09_fall_vol25.shp", layer: "TNB09_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TNB09_spring_vol25.shp", layer: "TNB09_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TNG13_fall_vol25.shp", layer: "TNG13_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/TNG13_spring_vol25.shp", layer: "TNG13_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/VAG01_fall_vol25.shp", layer: "VAG01_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/VAG01_spring_vol25.shp", layer: "VAG01_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/VAG02_fall_vol25.shp", layer: "VAG02_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/VAG02_spring_vol25.shp", layer: "VAG02_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIB05_fall_vol25.shp", layer: "WIB05_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIB05_spring_vol25.shp", layer: "WIB05_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIB11_2016_fall_vol25.shp", layer: "WIB11_2016_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIB11_2016_spring_vol25.shp", layer: "WIB11_2016_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIB11_2017_fall_vol25.shp", layer: "WIB11_2017_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIB11_2017_spring_vol25.shp", layer: "WIB11_2017_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIB19_fall_vol25.shp", layer: "WIB19_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIB19_spring_vol25.shp", layer: "WIB19_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIG01_fall_vol25.shp", layer: "WIG01_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIG01_spring_vol25.shp", layer: "WIG01_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIG02_fall_vol25.shp", layer: "WIG02_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIG02_spring_vol25.shp", layer: "WIG02_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIH03_2016_fall_vol25.shp", layer: "WIH03_2016_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIH03_2016_spring_vol25.shp", layer: "WIH03_2016_spring_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIH03_2017_fall_vol25.shp", layer: "WIH03_2017_fall_vol25"
## with 1 features
## It has 1 fields
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/gunnarkramer/Desktop/FINAL DATA FOR DRUM LAND ECOL/Final_rasters/SeasonalMigrationRasters/WIH03_2017_spring_vol25.shp", layer: "WIH03_2017_spring_vol25"
## with 1 features
## It has 1 fields
#save extracted data
write.csv(shpdata, "TESTriskfactorextraction_25_data.csv")
# write.csv(shpdata, "riskfactorextraction_10_data.csv") # can run 10 and 50 percentile core use areas separately
# write.csv(shpdata, "riskfactorextraction_50_data.csv")# can run 10 and 50 percentile core use areas separately
#################################
After extracting these data, there is still some work to do to combine spring and fall exposures by indivdiual. See the “Data4LassoXX_data.csv” files for 10, 25, and 50 percentile data compiled. See VermThreat4R.csv for threat data.