theBioBucket*: September 2013

16 Sept 2013

R GIS: Polygon Intersection with gIntersection{rgeos}

A short tutorial on doing intersections in R GIS. gIntersection{rgeos} will pick the polygons of the first submitted polygon contained within the second poylgon - this is done without cutting the polygon's edges which cross the clip source polygon. For the function that I use to download the example data, url_shp_to_spdf() please see HERE.

library(rgeos)
library(dismo)

URLs <- c("http://gis.tirol.gv.at/ogd/umwelt/wasser/wis_gew_pl.zip",               # all water bodies in Tyrol
          "http://gis.tirol.gv.at/ogd/umwelt/wasser/wis_tseepeicher_pl.zip")       # only artificial..

y <- lapply(URLs, url_shp_to_spdf)
z <- unlist(unlist(y))
a <- getData('GADM', country = "AT", level = 2)

b <- a[a$NAME_2=="Innsbruck Land", ]                                               # political district's boundaries
c <- spTransform(b, z[[1]]@proj4string)                                            # (a ring polygon)    
z1_c <- gIntersection(z[[1]], c, byid = TRUE)                                      
z2_c <- gIntersection(z[[2]], c, byid = TRUE)

plot(c)
plot(z1_c, lwd = 5, border = "red", add = T)
plot(z2_c, lwd = 5, border = "green", add = T)
plot(z[[1]], border = "blue", add = T)              # I plot this on top, so it will be easier to identify
plot(z[[2]], border = "brown", add = T)

Batch Downloading Zipped Shapefiles with R

Here's a function I use to download multiple zipped shapefiles from url and load them to the workspace:

URLs <- c("http://gis.tirol.gv.at/ogd/umwelt/wasser/wis_gew_pl.zip",
          "http://gis.tirol.gv.at/ogd/umwelt/wasser/wis_tseepeicher_pl.zip")

url_shp_to_spdf <- function(URL) {

  require(rgdal)

  wd <- getwd()
  td <- tempdir()
  setwd(td)

  temp <- tempfile(fileext = ".zip")
  download.file(URL, temp)
  unzip(temp)

  shp <- dir(tempdir(), "*.shp$")
  lyr <- sub(".shp$", "", shp)
  y <- lapply(X = lyr, FUN = function(x) readOGR(dsn=shp, layer=lyr))
  names(y) <- lyr

  unlink(dir(td))
  setwd(wd)
  return(y)
  }

y <- lapply(URLs, url_shp_to_spdf)
z <- unlist(unlist(y))

# finally use it:
plot(z[[1]])

Follow Up on Spatial Overlays with R - Getting Altitude for a Set of Points

A short follow up on a previous post on spatial overlays with R.

library(sp)
library(dismo)

# some addresses in Austria
pts <- geocode(c("Aldrans, Grubenweg", "Wien, Stephansdom", "Salzburg, Mozartplatz"))
 
# make pts spatial
coords <- SpatialPoints(pts[, c("longitude", "latitude")])
spdf_pts <- SpatialPointsDataFrame(coords, pts)

# assign CRS/projection (which is WGS 1984)
crs <- CRS(" +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0") 
proj4string(spdf_pts) <- crs
 
# spatial data to extract (altitude)
alt <- getData('alt', country = "AT")

# convert alt from raster to grid (needed for over::sp)
# and assign CRS (which is the same as spdf_pts, see > alt@crs)
# don't mind warning - the CRS is the same..
spdf_alt <- as(alt, 'SpatialGridDataFrame')
proj4string(spdf_alt) <- crs

# view
plot(alt)
# plot pts on top
plot(spdf_pts, cex = 2, col = 2, add = T)
 
# check data
str(spdf_pts)
str(spdf_alt)
 
# get the raster/pixel/grid data (> ?over):
cbind(spdf_pts$interpretedPlace, over(spdf_pts, spdf_alt))

# result:
#                                       spdf_pts$interpretedPlace AUT_msk_alt
# 1                              Grubenweg, 6071 Aldrans, Austria         736
# 3 Saint Stephen's Vienna, Stephansplatz 1, 1010 Vienna, Austria         183
# 2                           Mozartplatz, 5020 Salzburg, Austria         450

10 Sept 2013

Loading Multiple Shapefiles to the R-Console Simultaneously

A quick tip on how to load multiple shapefiles (point shapefiles, i.e.) to the R console in one go:

library(maptools)

# get all files with the .shp extension from working directory 
setwd("D:/GIS_DataBase/GIS_Tirol/Tirol_Verbreitungskarten/Verbreitungs_Daten")

shps <- dir(getwd(), "*.shp")

# the assign function will take the string representing shp and turn it into a variable
# which holds the spatial points data
for (shp in shps) assign(shp, readShapePoints(shp))
plot(get(shp[1])) # i.e.
# ...done