04_Spatial.R

#' ---
#' title: "Working with Spatial Data"
#' ---
#' 
#' 
#' [<i class="fa fa-file-code-o fa-3x" aria-hidden="true"></i> The R Script associated with this page is available here](`r output`).  Download this file and open it (or copy-paste into a new script) with RStudio so you can follow along.  
#' 
#' # Setup
#' 
#' ## Load packages
## ----messages=F,warning=F, results="hide"--------------------------------
library(sp)
library(rgdal)
library(ggplot2)
library(dplyr)
library(tidyr)
library(maptools)

#' 
#' # Point data
#' 
#' ## Generate some random data
## ------------------------------------------------------------------------
coords = data.frame(
  x=rnorm(100),
  y=rnorm(100)
)
str(coords)

#' 
#' 
#' 
## ------------------------------------------------------------------------
plot(coords)

#' 
#' 
#' 
#' ## Convert to `SpatialPoints`
## ------------------------------------------------------------------------
sp = SpatialPoints(coords)
str(sp)

#' 
#' 
#' 
#' ## Create a `SpatialPointsDataFrame`
#' 
#' First generate a dataframe (analagous to the _attribute table_ in a shapefile)
## ------------------------------------------------------------------------
data=data.frame(ID=1:100,group=letters[1:20])
head(data)

#' 
#' 
#' 
#' Combine the coordinates with the data
## ------------------------------------------------------------------------
spdf = SpatialPointsDataFrame(coords, data)
spdf = SpatialPointsDataFrame(sp, data)

str(spdf)

#' Note the use of _slots_ designated with a `@`.  See `?slot` for more. 
#' 
#' 
#' ## Promote a data frame with `coordinates()`
## ------------------------------------------------------------------------
coordinates(data) = cbind(coords$x, coords$y) 

#' 
## ------------------------------------------------------------------------
str(spdf)

#' 
#' ## Subset data
#' 
## ------------------------------------------------------------------------
subset(spdf, group=="a")

#' 
#' Or using `[]`
## ------------------------------------------------------------------------
spdf[spdf$group=="a",]

#' 
#' Unfortunately, `dplyr` functions do not directly filter spatial objects.
#' 
#' 
#' <div class="well">
#' ## Your turn
#' 
#' Convert the following `data.frame` into a SpatialPointsDataFrame using the `coordinates()` method and then plot the points with `plot()`.
#' 
## ------------------------------------------------------------------------
df=data.frame(
  lat=c(12,15,17,12),
  lon=c(-35,-35,-32,-32),
  id=c(1,2,3,4))

#' 
#' 
#' <button data-toggle="collapse" class="btn btn-primary btn-sm round" data-target="#demo1">Show Solution</button>
#' <div id="demo1" class="collapse">
#' 
#' 
#' </div>
#' </div>
#' 
#' ## Examine topsoil quality in the Meuse river data set
#' 
## ------------------------------------------------------------------------
## Load the data
data(meuse)
str(meuse)

#' 
#' <div class="well">
#' ## Your turn
#' _Promote_ the `meuse` object to a spatial points data.frame with `coordinates()`.
#' 
#' <button data-toggle="collapse" class="btn btn-primary btn-sm round" data-target="#demo2">Show Solution</button>
#' <div id="demo2" class="collapse">
#' 
#' 
#' </div>
#' </div>
#' 
#' Plot it with ggplot:
## ---- fig.height=4-------------------------------------------------------
  ggplot(as.data.frame(meuse),aes(x=x,y=y))+
    geom_point(col="red")+
    coord_equal()

#' 
#' Note that `ggplot` works only with data.frames.  Convert with `as.data.frame()` or `fortify()`.
#' 
#' # Lines
#' 
#' ### A `Line` is a single chain of points.
#' 
## ------------------------------------------------------------------------
L1 = Line(cbind(rnorm(5),rnorm(5)))
L2 = Line(cbind(rnorm(5),rnorm(5)))
L3 = Line(cbind(rnorm(5),rnorm(5)))
L1

#' 
#' 
## ------------------------------------------------------------------------
plot(coordinates(L1),type="l")

#' 
#' 
#' 
#' ### A `Lines` object is a list of chains with an ID
#' 
## ------------------------------------------------------------------------
Ls1 = Lines(list(L1),ID="a")
Ls2 = Lines(list(L2,L3),ID="b")
Ls2

#' 
#' 
#' 
#' ### A `SpatialLines` is a list of Lines
#' 
## ------------------------------------------------------------------------
SL12 = SpatialLines(list(Ls1,Ls2))
plot(SL12)

#' 
#' 
#' 
#' ### A `SpatialLinesDataFrame` is a `SpatialLines` with a matching `DataFrame`
#' 
## ------------------------------------------------------------------------
SLDF = SpatialLinesDataFrame(
  SL12,
  data.frame(
  Z=c("road","river"),
  row.names=c("a","b")
))
str(SLDF)

#' 
#' 
#' # Polygons
#' 
#' ## Getting complicated
#' 
#' <img src="04_assets/polygons.png" alt="alt text" width="75%">
#' 
#' ### Issues
#' 
#' * Multipart Polygons
#' * Holes
#' 
#' Rarely construct _by hand_...
#' 
#' # Importing data
#' 
#' But, you rarely construct data _from scratch_ like we did above.  Usually you will import datasets created elsewhere.  
#' 
#' ## Geospatial Data Abstraction Library ([GDAL](gdal.org))
#' 
#' `rgdal` package for importing/exporting/manipulating spatial data:
#' 
#' * `readOGR()` and `writeOGR()`: Vector data
#' * `readGDAL()` and `writeGDAL()`: Raster data
#' 
#' Also the `gdalUtils` package for reprojecting, transforming, reclassifying, etc.
#' 
#' List the file formats that your installation of rgdal can read/write with `ogrDrivers()`:
## ---- echo=F-------------------------------------------------------------
knitr::kable(ogrDrivers())

#' 
#' Now as an example, let's read in a shapefile that's included in the `maptools` package.  You can try 
## ------------------------------------------------------------------------
## get the file path to the files
file=system.file("shapes/sids.shp", package="maptools")
## get information before importing the data
ogrInfo(dsn=file, layer="sids")

## Import the data
sids <- readOGR(dsn=file, layer="sids")
summary(sids)
plot(sids)

#' 
#' 
#' ### Maptools package
#' The `maptools` package has an alternative function for importing shapefiles that can be a little easier to use (but has fewer options).
#' 
#' * `readShapeSpatial`
#' 
## ------------------------------------------------------------------------
sids <- readShapeSpatial(file)

#' 
#' ### Raster data
#' 
#' We'll deal with raster data in the next section.
#' 
#' # Coordinate Systems
#' 
#' * Earth isn't flat
#' * But small parts of it are close enough
#' * Many coordinate systems exist
#' * Anything `Spatial*` (or `raster*`) can have one
#' 
#' ## Specifying the coordinate system
#' 
#' ### The [Proj.4](https://trac.osgeo.org/proj/) library
#' Library for performing conversions between cartographic projections. 
#' 
#' See [http://spatialreference.org](http://spatialreference.org) for information on specifying projections. For example, 
#' 
#' 
#' #### Specifying coordinate systems 
#' 
#' **WGS 84**:
#' 
#' * proj4: <br><small>`+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs`</small>
#' * .prj / ESRI WKT: <small>`GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",`<br>`
#' SPHEROID["WGS_1984",6378137,298.257223563]],`<br>`
#' PRIMEM["Greenwich",0],UNIT["Degree",0.017453292519943295]]`</small>
#' * EPSG:`4326`
#' 
#' 
#' 
#' Note that it has no projection information assigned (since it came from a simple data frame).  From the help file (`?meuse`) we can see that the projection is EPSG:28992.  
#' 
## ------------------------------------------------------------------------
proj4string(sids) <- CRS("+proj=longlat +ellps=clrk66")
proj4string(sids)

#' 
#' ## Spatial Transform
#' 
#' Assigning a CRS doesn't change the projection of the data, it just indicates which projection the data are currently in.  
#' So assigning the wrong CRS really messes things up.
#' 
#' Transform (_warp_) projection from one to another with `spTransform`
#' 
#' 
#' Project the `sids` data to the US National Atlas Equal Area (Lambert azimuthal equal-area projection):
## ------------------------------------------------------------------------
sids_us = spTransform(sids,CRS("+proj=laea +lat_0=45 +lon_0=-100 +x_0=0 +y_0=0 +a=6370997 +b=6370997 +units=m +no_defs"))

#' 
#' Compare the _bounding box_:
## ------------------------------------------------------------------------
bbox(sids)
bbox(sids_us)

#' 
#' And plot them:
#' 
## ------------------------------------------------------------------------
# Geographic
ggplot(fortify(sids),aes(x=long,y=lat,order=order,group=group))+
  geom_polygon(fill="white",col="black")+
  coord_equal()
# Equal Area
ggplot(fortify(sids_us),aes(x=long,y=lat,order=order,group=group))+
  geom_polygon(fill="white",col="black")+
  coord_equal()+
  ylab("Northing")+xlab("Easting")

#' 
#' # RGEOS
#' 
#' Interface to Geometry Engine - Open Source (GEOS) using a C API for topology operations (e.g. union, simplification) on geometries (lines and polygons).
#' 
## ------------------------------------------------------------------------
library(rgeos)

#' 
#' ## RGEOS package for polygon operations
#' 
#' * Area calculations (`gArea`)
#' * Centroids (`gCentroid`)
#' * Convex Hull (`gConvexHull`)
#' * Intersections (`gIntersection`)
#' * Unions (`gUnion`)
#' * Simplification (`gSimplify`)
#' 
#' If you have trouble installing `rgeos` on OS X, look [here](http://dyerlab.bio.vcu.edu/2015/03/31/install-rgeos-on-osx/)
#' 
#' 
#' ## Example: gSimplify
#' 
#' Make up some lines and polygons:
## ------------------------------------------------------------------------
p = readWKT(paste("POLYGON((0 40,10 50,0 60,40 60,40 100,50 90,60 100,60",
 "60,100 60,90 50,100 40,60 40,60 0,50 10,40 0,40 40,0 40))"))
l = readWKT("LINESTRING(0 7,1 6,2 1,3 4,4 1,5 7,6 6,7 4,8 6,9 4)")

#' 
#' 
#' ### Simplication of lines
#' 
## ------------------------------------------------------------------------
par(mfrow=c(1,4))  # this sets up a 1x4 grid for the plots
plot(l);title("Original")
plot(gSimplify(l,tol=3));title("tol: 3")
plot(gSimplify(l,tol=5));title("tol: 5")
plot(gSimplify(l,tol=7));title("tol: 7")

#' 
#' 
#' ### Simplification of polygons
## ------------------------------------------------------------------------
par(mfrow=c(1,4))  # this sets up a 1x4 grid for the plots
plot(p);title("Original")
plot(gSimplify(p,tol=10));title("tol: 10")
plot(gSimplify(p,tol=20));title("tol: 20")
plot(gSimplify(p,tol=25));title("tol: 25")

#' 
#' 
#' ##  Use `rgeos` functions with real spatial data
#' 
#' Load the `sids` data again
## ------------------------------------------------------------------------
file = system.file("shapes/sids.shp", package="maptools")
sids = readOGR(dsn=file, layer="sids")

#' 
#' ## Simplify polygons with RGEOS
#' 
## ------------------------------------------------------------------------
sids2=gSimplify(sids,tol = 0.2,topologyPreserve=T)

#' 
#' ### Plotting vectors with ggplot
#' 
#' `fortify()` in `ggplot` useful for converting `Spatial*` objects into plottable data.frames.  
#' 
## ------------------------------------------------------------------------
sids%>%
  fortify()%>%
  head()

#' 
#' To use `ggplot` with a `fortify`ed spatial object, you must specify `aes(x=long,y=lat,order=order, group=group)` to indicate that each polygon should be plotted separately.  
#' 
## ------------------------------------------------------------------------
ggplot(fortify(sids),aes(x=long,y=lat,order=order, group=group))+
  geom_polygon(lwd=2,fill="grey",col="blue")+
  coord_map()

#' 
#' Now let's overlay the simplified version to see how they differ.
#' 
## ------------------------------------------------------------------------
ggplot(fortify(sids),aes(x=long,y=lat,order=order, group=group))+
  geom_polygon(lwd=2,fill="grey",col="blue")+
  geom_polygon(data=fortify(sids2),col="red",fill=NA)+
  coord_map()

#' 
#' How does changing the tolerance (`tol`) affect the map?
#' 
#' ## Calculate area with `gArea`
#' 
## ------------------------------------------------------------------------
sids$area=gArea(sids,byid = T)

#' 
#' 
#' ### Plot a chloropleth of area
#' 
#' From [Wikipedia](https://en.wikipedia.org/wiki/Choropleth_map):
#' 
#' > A **choropleth** (from Greek χώρο ("area/region") + πλήθος ("multitude")) is a thematic map in which areas are shaded or patterned in proportion to the measurement of the statistical variable being displayed on the map, such as population density or per-capita income.
#' 
#' By default, the rownames in the dataframe are the unique identifier (e.g. the **FID**) for the polygons.  
#' 
## ---- fig.height=4-------------------------------------------------------
## add the ID to the dataframe itself for easier indexing
sids$id=as.numeric(rownames(sids@data))
## create fortified version for plotting with ggplot()
fsids=fortify(sids,region="id")

ggplot(sids@data, aes(map_id = id)) +
    expand_limits(x = fsids$long, y = fsids$lat)+
    scale_fill_gradientn(colours = c("grey","goldenrod","darkgreen","green"))+
    coord_map()+
    geom_map(aes(fill = area), map = fsids)

#' 
#' ## Union
#' 
#' Merge sub-geometries (polygons) together with `gUnionCascaded()`
#' 
## ------------------------------------------------------------------------
sids_all=gUnionCascaded(sids)

#' 
#' 
## ------------------------------------------------------------------------
ggplot(fortify(sids_all),aes(x=long,y=lat,group=group,order=order))+
  geom_path()+
  coord_map()

#' 
#' 
#' ## Colophon
#' See also:  `Raster` package for working with raster data
#' 
#' Sources:
#' 
#' * [UseR 2012 Spatial Data Workshop](http://www.maths.lancs.ac.uk/~rowlings/Teaching/UseR2012/index.html) by Barry Rowlingson
#' 
#' Licensing: 
#' 
#' * Presentation: [CC-BY-3.0 ](http://creativecommons.org/licenses/by/3.0/us/)
#' * Source code: [MIT](http://opensource.org/licenses/MIT) 
#'