Spatial

Outline Types of Spatial Data R Spatial packages S4 R objects Projections Spatial methods SpatialPoints SpatialLines/SpatialPolygons SpatialPixels SpatialPoints - Sample Dataset Importing/Exporting Spatial information and slots Displaying SpatialPolygons - Sample Dataset Reprojecting SpatialPixels - Sample Dataset Importing/Exporting rasters Deriving Thematic rasters (importing, spatial info, reclassing) Temporary files

Spatial Data in R ## Types of Spatial Data Points - a set of single point locations Lines - an ordered set of points, connected by straight line segments Polygons – an area, with enclosed lines, possibly containing holes Rasters – a collection of points or rectangular cells, in grid format ## R Spatial packages sp Basic R classes for handling geospatial data maptools Read and write shapefiles. Cannot read the projection file. rgeos Interface to spatial geometry for sp objects rgdal Supports GDAL raster formats and OGR vector formats.. Retains projection information when reading and writing (PROJ.4 library) raster Spatial data analysis for rasters. ## Help links for spatial tools in R # Summary of tools for Spatial data analysis http://cran.r-project.org/web/views/Spatial.html

Spatial Data in R # Set working directory # Load libraries path <- "W:/Techniques/Projects/Peru/Rworkshop" setwd(path) # Load libraries library(sp) library(maptools) library(rgeos) library(rgdal) library(raster)

Spatial Data in R ## Spatial classes (sp package) Bivand, et al. 2008 getClass("Spatial") Bivand, et al. 2008

Spatial Data in R ## S4 R objects New-style classes with formal definitions that specify the name and type of the object's components, called slots. ## The Spatial class has 2 pre-defined slots bbox – The bounding box, consisting of a matrix of coordinates defining the extent of the spatial object. proj4string – The class object defining the coordinate reference system (CRS) CRS contains datum and projection datum – a surface that represents the shape of the earth projection – renders the surface of an ellipsoid as a plane

Spatial Data in R ## Projections # rgdal package PROJ.4 - Cartographic Projections Library A library of projection functions to perform respective forward and inverse transformation of cartographic data. # Format of projection string (proj4string) "+proj=prj +ellps=GRS80 +datum=datum +no_defs” # List of common projections http://www.remotesensing.org/geotiff/proj_list/ # More proj4string options.. " +proj=longlat +ellps=GRS80 +datum=NAD83 +no_defs" " +proj=utm +zone=13 +datum=NAD83" " +proj=utm +ellps=WGS84 +datum=WGS84 +zone=11, +units=m +towgs84=0,0,0" " +proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +datum=NAD83 +units=m" " +no_defs +ellps=GRS80 +towgs84=0,0,0"

Spatial Data in R ## Spatial methods (sp package) ## Common attributes of R objects: # method - a function associated with a particular type of object (ex. summary, print) ## Spatial methods (sp package) Bivand, et al. 2008

SpatialPoints Bivand, et al. 2008

SpatialLines/Polygons Lists of List Objects List of Objects Object Bivand, et al. 2008

SpatialPixels Similar to SpatialPoints with regularly spaced coordinates. Bivand, et al. 2008

Sample Dataset Utah, USA

Sample Dataset Uinta Mountains, Utah,USA Highest East-West oriented mountain range in the contiguous U.S. - up to 13,528 ft (4,123 m) High Uinta Wilderness ## Vegetation 5 different life zones: shrub-montane aspen lodgepole pine spruce-fir alpine

SpatialPoints

SpatialPoints - Importing/Exporting Sample Dataset SpatialPoints - Importing/Exporting ## Import data frame with X/Y coordinates ## (FIA plot data with fuzzed/swapped coordinates) plt <- read.csv("PlotData/plt.csv", header=TRUE, stringsAsFactors=FALSE) ## Generate SpatialPoints x <- "LON" y <- "LAT" prj <- "longlat" datum <- "NAD83" prj4str <- "+proj=longlat +ellps=GRS80 +datum=NAD83 +no_defs" ptshp <- SpatialPointsDataFrame(plt[,c(x,y)], plt, proj4string = CRS(prj4str)) class(ptshp) # Export SpatialPoints help(writeOGR) writeOGR(ptshp, "Outfolder", "ptshp", driver="ESRI Shapefile")

SpatialPoints – Spatial Info Sample Dataset SpatialPoints – Spatial Info ## Get spatial information for ptshp summary(ptshp) # General info and summary statistics for attribute # data of ptshp mode(ptshp) # Get mode of ptshp class(ptshp) # Get class of ptshp is.projected(ptshp) # Check if ptshp has projection information proj4string(ptshp) # Set or get projection information str(ptshp) # Structure of ptshp

Sample Dataset SpatialPoints - Slots ## Get slot names and access slots for SpatialPoints slotNames(ptshp) # Get name of ptshp components (slots) ptshp@data # Get data frame attributes of ptshp ptshp@coords # Get coordinates of ptshp ptshp@bbox # Get extent of ptshp ptshp@proj4string # Get projection information head(ptshp@data) # Get first 6 rows of data frame of ptshp dim(ptshp) # Get dimensions of data frame of ptshp

SpatialPoints - Displaying Sample Dataset SpatialPoints - Displaying ## Display ptshp plot(ptshp) # Display ptshp points with red dots, half size plot(ptshp, col="RED", pch=16, cex=0.5) # Display subsets of ptshp plot(ptshp[ptshp$INVYR==2002,], col="BLUE") plot(subset(ptshp, INVYR==2003), col="RED", add=TRUE) # pch codes # Colors colors() ## Help for point graphics http://127.0.0.1:11789/library/graphics/html/points.html

Sample Dataset ## Exercise 1 Exercise ## 1.1 Get the min and max coordinates of the boundary of ptshp. ## 1.2 Display points where elevation (ELEVM) are >= 3000 in dark green. ## 1.3 Add points where elevation (ELEVM) are < 3000 in yellow. ## 1.4 Overlay the point with the maximum elevation (ELEVM) in red.

SpatialPolygons

Sample Dataset SpatialPolygons # SpatialPolygons – file names # Area of Interest (AOI) boundary (Uinta Mountains, UT) aoifn <- "uintaN_aoi.shp" # National Forest System boundary within AOI nfsfn <- "uintaN_nfs.shp" # High Uinta Wilderness boundary within AOI wildfn <- "uintaN_wild.shp"

SpatialPolygons - Importing/Exporting Sample Dataset SpatialPolygons - Importing/Exporting ## Importing shapefiles using OGR drivers (rgdal) ## OGR functions From the Geospatial Data Abstraction Library (GDAL), interfaced through rgdal. Reads spatial data, including the spatial reference. readOGR – reads OGR data source and layer into an R Spatial object writeOGR – writes data out using supported drivers Note: There are 2 main arguments.. that may take different forms, depending on the available drivers. dsn – data source name layer – the name of the layer Note: A driver is a software component loaded on demand to enable a device to work with a computer's operating system. ogrDrivers() help(readOGR)

SpatialPolygons - Import Sample Dataset SpatialPolygons - Import ## Importing polygon shapefiles ## (AOI boundary, NFS boundary, Wilderness boundary) # dsn – data source name (folder with layers) # layer – the name of the layer (no extension) ## Set dsn dsn <- "SpatialData" ## Spatial layer names aoinm <- "uintaN_aoi" nfsnm <- "uintaN_nfs" wildnm <- "uintaN_wild" ## Import shapefiles bndpoly <- readOGR(dsn=dsn, layer=aoinm, stringsAsFactors=FALSE) nfspoly <- readOGR(dsn=dsn, layer=nfsnm, stringsAsFactors=FALSE) wildpoly <- readOGR(dsn=dsn, layer=wildnm, stringsAsFactors=FALSE)

SpatialPolygons – Spatial Info Sample Dataset SpatialPolygons – Spatial Info ## Get spatial information for bndpoly bndpoly # Get general information of polygon summary(bndpoly) # Summary information for polygon mode(bndpoly) # Get mode of bndpoly typeof(bndpoly) # Get typeof class(bndpoly) # Get class of bndpoly proj4string(bndpoly) # Set or get projection information of bndpoly bbox(bndpoly) # Get extent of bndpoly dim(bndpoly) # Get dimension of bndpoly str(bndpoly) # Get structure of bndpoly

SpatialPolygons - slots Sample Dataset SpatialPolygons - slots (1) (2) (3) # Get slot names for class SpatialPolygons (1) getClass("SpatialPolygons") slotNames(bndpoly) @polygons # the list of Polygons objects @plotOrder # the order to plot the Polygons @bbox # bounding box slot @proj4string # coordinate reference system slot @data # associated data frame (for class SpatialPolygonsDataFrame objects)

SpatialPolygons – Displaying Sample Dataset SpatialPolygons – Displaying ## Display bndpoly plot(bndpoly) # Display polygon shapefile plot(bndpoly, col="blue") # Display polygon with blue fill color plot(bndpoly, border="red", lwd=3) # red outline and line width=3 plot(bndpoly, col="blue", border="red", lwd=3) # blue fill plot(bndpoly, col="blue", border="red", lwd=3, bg="black", axes=TRUE) # with background colored and axes labels

SpatialPolygons – Spatial Info Sample Dataset SpatialPolygons – Spatial Info # Get spatial information for nfspoly nfspoly # Get general information of nfspoly summary(nfspoly) # Summary information for nfspoly dim(nfspoly) # Dimensions of nfspoly str(nfspoly) # Get structure of nfspoly

SpatialPolygons - slots Sample Dataset SpatialPolygons - slots (1) (2) (3) # Get slot names for class SpatialPolygons (1) getClass("SpatialPolygons") slotNames(nfspoly) @polygons # the list of Polygons objects @plotOrder # the order to plot the Polygons @bbox # bounding box slot @proj4string # coordinate reference system slot @data # associated data frame (for class SpatialPolygonsDataFrame objects)

SpatialPolygons - slots Sample Dataset SpatialPolygons - slots (1) (2) (3) # Get slot names for class Polygons (2) getClass("Polygons") slotNames(nfspoly@polygons[[1]]) # First feature @polygons[[1]]@Polygons # a list of rings (islands/holes) that make up the feature @polygons[[1]]@plotOrder # the order to plot the feature @polygons[[1]]@labpt # label point coordinates of the feature @polygons[[1]]@ID # unique identifier of the feature @polygons[[1]]@area # area of the feature (in units of feature projection)

SpatialPolygons - slots Sample Dataset SpatialPolygons - slots (1) (2) (3) # Get slot names for class Polygon (3) getClass("Polygon") slotNames(slot(nfspoly@polygons[[1]], "Polygons")[[1]]) @polygons[[1]]@Polygons[[1]] # first ring of feature - class 'Polygon' @polygons[[1]]@Polygons[[1]]@labpt # label point coordinates of the feature ring @polygons[[1]]@Polygons[[1]]@area # area of the feature ring @polygons[[1]]@Polygons[[1]]@coords # coordinates of the feature ring

SpatialPolygons - slots Sample Dataset SpatialPolygons - slots # Accessing slots of SpatialPolygons nfspoly@data # Data frame attributes of shp nfspoly@polygons # Get info of each polygon within Spatial Polygons nfspoly@plotOrder # Get order of polygons within Spatial Polygons nfspoly@bbox # Get extent of bndpoly # Accessing slots of Polygons slot(nfspoly, "polygons") # (2)slots slotsPolygons <- slot(nfspoly, "polygons") # (2)slots typeof(slotsPolygons) length(slotsPolygons) sapply(slotsPolygons, function(x)slot(x, "ID")) # (2)slots sapply(slotsPolygons, function(x)slot(x, "area")) # (2)slots slotsPolygon <- slot(nfspoly@polygons[[1]], "Polygons") # (3)slots slotsPolygon <- slot(nfspoly@polygons[[2]], "Polygons") # (3)slots

SpatialPolygons - Displaying Sample Dataset SpatialPolygons - Displaying ## Display nfspoly and wildpoly plot(bndpoly, col="dark blue") plot(nfspoly, border="yellow", add=TRUE, lwd=2) plot(wildpoly, add=TRUE, border="green") # Add points – in red plot(ptshp, add=TRUE, col="red", pch=16, cex=0.5)

SpatialPolygons - Reprojecting Sample Dataset SpatialPolygons - Reprojecting ## Notice, the point layer did not display. Check the projections. projection(bndpoly) projection(ptshp) ## Reproject ptshp to projection of bndpoly polyprj <- projection(bndpoly) ptshpprj <- spTransform(ptshp, CRSobj=CRS(polyprj)) projection(ptshpprj) # Add points – in red plot(ptshpprj, add=TRUE, col="red", pch=16, cex=0.5) # Add thicker boundary line plot(bndpoly, lwd=3, add=TRUE) # Add labels for nfspoly text(nfspoly, nfspoly$FORESTNAME, cex=0.75, pos=3, col="white")

Sample Dataset ## Exercise 2 Exercise ## 2.1 Get projection of nfspoly. ## 2.2 Display the area of interest boundary (bndpoly) with no color fill. ## 2.3 Add the wilderness boundary (wildpoly) with green fill and with no outline. ## 2.4 Get total sum of area of nfspoly.

SpatialPixels

Sample Dataset # Elevation (m) SpatialPixels # National Elevation Dataset (NED) in meters elevfn <- "SpatialData/uintaN_elevm.img" # Elevation (m)

Sample Dataset # Forest/Nonforest map SpatialPixels fnffn <- "SpatialData/uintaN_fnf.img"

SpatialPixels - Importing/Exporting Sample Dataset SpatialPixels - Importing/Exporting ## Importing SpatialPixels (raster) files help(raster) elev <- raster("SpatialData/uintaN_elevm.img") elev dim(elev) class(elev) ## Importing a raster stack help(stack) rstack <- stack("SpatialData/uintaN_elevm.img", "SpatialData/uintaN_fnf.img") rstack dim(rstack) class(rstack) ## Exporting a raster help(writeRaster) writeRaster(rstack, filename="Outfolder/rstack1.img") # Add integer datatype and notice size of file writeRaster(rstack, filename="Outfolder/rstack2.img", datatype="INT1U", overwrite=TRUE)

SpatialPixels - Spatial Info Sample Dataset SpatialPixels - Spatial Info ## Get spatial information for elev elev class(elev) inMemory(elev) # Checks if raster is stored in memory (RAM) unique(elev) # Get unique values of raster extent(elev) # Get extent of raster boxplot(elev) # Display boxplot of raster values dim(elev) # Get dimensions of raster res(elev) # Get the resolution of raster (x y) ncell(elev) # Number of cells of raster maxValue(elev) # Get Maximum value in raster freq(elev) # Get frequency table of raster ## Overview of functions in raster package http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/raster/html/raster-package.html

Sample Dataset SpatialPixels - slots ## Get slot names for class SpatialPixels getClass("SpatialPixels") slotNames(elev) str(elev) # @file the source (file name) of raster # @data list of attributes of raster # @legend the legend features of raster, if exist # @title the title of raster, if exists # @extent the bounding box of raster # @ncols number of columns of raster # @nrows number of rows of raster # @crs coordinate reference system slot ## Get slot names for class SpatialPixels slots slotNames(elev@file) elev@file@name elev@file@nbands slotNames(elev@data) elev@data@min

SpatialPixels - Displaying Sample Dataset SpatialPixels - Displaying ## Display rasters plot(elev) # Display with terrain colors – 4 classes plot(elev, col=terrain.colors(n=4)) # Display with terrain colors – 20 classes plot(elev, col=terrain.colors(n=20)) # Exclude axis labels plot(elev, col=terrain.colors(n=4), axes=FALSE) # Get help with other colors for continuous data help(terrain.colors) # Display elevation data with contours contour(elev)

SpatialPixels - Deriving Sample Dataset SpatialPixels - Deriving ## Derive new rasters # Generate slope and aspect and hillshade from elevation dataset slp <- terrain(elev, opt=c('slope'), unit='radians') asp <- terrain(elev, opt=c('aspect'), unit='radians') hill <- hillShade(slope, asp) # Generate hillshade # Display hillshade in grey scale plot(hill, col=grey(0:100/100), legend=FALSE) # Classify raster elevcl <- cut(elev, breaks=5) # 5 classes plot(elevcl) # Display classified raster cols <- c("brown", "palegreen", "orange1", "dark green", "snow") plot(elevcl, col=cols, breaks=c(0:5)) # Converts raster from meters to feet elevft <- elev * 3.28084 summary(elev) summary(elevft)

Sample Dataset SpatialPixels - fnf ## Get spatial information for fnf (thematic raster) fnf <- raster("SpatialData/uintaN_fnf.img") unique(fnf) # Get unique values of raster extent(fnf) # Get extent of raster barplot(fnf) # Display barplot of raster values ## Display fnf fnfvals <- sort(unique(fnf)) plot(fnf, breaks=fnfvals, col=c("green", "brown", "blue"), legend=TRUE) ## Overview of functions in raster package http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/raster/html/raster-package.html

Sample Dataset reclass raster ## Reclass raster layer to 2 categories help(reclassify) fromvect <- c(0,1,2,3) tovect <- c(2,1,2,2) rclmat <- matrix(c(fromvect, tovect), 4, 2) fnfrcl <- reclassify(x=fnf, rclmat) fnfrcl unique(fnfrcl) freq(fnfrcl) ## To save to file help(writeRaster) stratrcl <- reclassify(x=fnf, rclmat, datatype='INT2U', filename="SpatialData/uintaN_fnfrcl.img", overwrite=TRUE) ## Plot new reclassed raster fnfrclvals <- c(0, unique(fnfrcl)) plot(fnfrcl, breaks=fnfrclvals, col=c("green","brown"), legend=TRUE) barplot(fnfrcl)

Temporary Files ## Note: Functions in raster package create temporary files if the values of an output RasterLayer cannot be stored in memory (RAM). This can happen when no filename is provided to a function an in functions where you cannot provide a filename. Temporary files are automatically removed at the start of each session. ## During session: showTmpFiles() removeTmpFiles() ## You can change where the temporary folder is in the Rprofile.site file. ## (C:\Program Files\R\R-3.0.0\etc\Rprofile.site) # Added options(scipen=6) options(rasterTmpDir='c:/Temp/') rasterOptions() rasterOptions(chunksize = 1e+04, maxmemory = 1e+06)

Sample Dataset ## Exercise 3 Exercise ## 3.1 Get the minimum value of elev ## 3.2 Display elev raster with heat colors and 10 classes ## 3.3 Generate slope (in degrees) ## 3.4 Classify the slope raster from 3.3 into 4 classes ## 3.5 Display the classified slope raster with unique colors. Use colors() to select color choices. Exclude axes labels.

Spatial Help Links # Summary of tools for Spatial data analysis http://cran.r-project.org/web/views/Spatial.html # Presentation – Introduction to representing spatial objects in R – Roger Bivand http://geostat-course.org/system/files/monday_slides.pdf # List of common projections http://www.remotesensing.org/geotiff/proj_list/ ## Help for point graphics http://127.0.0.1:11789/library/graphics/html/points.html ## Overview of functions in raster package http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/raster/html/raster-package.html