Reviewers: Sarah Newman
This tutorial will review how to import spatial points stored in
Separated Value) format into
R as a spatial object - a
SpatialPointsDataFrame. We will also
reproject data imported in a shapefile format, and export a shapefile from an
R spatial object and plot raster and vector data as
layers in the same plot.
R Skill Level: Intermediate - you’ve got the basics of
Goals / Objectives
After completing this activity, you will:
- Be able to import .csv files containing x,y coordinate locations into
- Know how to convert a .csv to a spatial object.
- Understand how to project coordinate locations provided in a Geographic Coordinate System (Latitude, Longitude) to a projected coordinate system (UTM).
- Be able to plot raster and vector data in the same plot to create a map.
Things You’ll Need To Complete This Tutorial
You will need the most current version of
R and, preferably,
on your computer to complete this tutorial.
Install R Packages
- More on Packages in R - Adapted from Software Carpentry.
Data to Download
These vector data provide information on the site characterization and infrastructure at the National Ecological Observatory Network’s Harvard Forest field site. The Harvard Forest shapefiles are from the Harvard Forest GIS & Map archives. US Country and State Boundary layers are from the US Census Bureau.
The LiDAR and imagery data used to create this raster teaching data subset were collected over the National Ecological Observatory Network’s Harvard Forest and San Joaquin Experimental Range field sites and processed at NEON headquarters. The entire dataset can be accessed by request from the NEON Airborne Data Request Page on the NEON website.
Set Working Directory: This lesson assumes that you have set your working
directory to the location of the downloaded and unzipped data subsets. An overview
of setting the working directory in
R can be found here.
R Script & Challenge Code: NEON data lessons often contain challenges that reinforce
learned skills. If available, the code for challenge solutions is found in the
R script of the entire lesson, available in the footer of each lesson page.
Spatial Data in Text Format
HARV_PlotLocations.csv file contains
x, y (point) locations for study
plot where NEON collects data on
vegetation and other ecological metrics.
We would like to:
- Create a map of these plot locations.
- Export the data in a
shapefileformat to share with our colleagues. This shapefile can be imported into any GIS software.
- Create a map showing vegetation height with plot locations layered on top.
Spatial data are sometimes stored in a text file format (
the text file has an associated
y location column, then we can
convert it into an
R spatial object which in the case of point data,
will be a
allows us to store both the
x,y values that represent the coordinate location
of each point and the associated attribute data - or columns describing each
feature in the spatial object.
Data Tip: There is a
SpatialPoints object (not
R that does not allow you to store associated
We will use the
raster libraries in this tutorial.
# load packages library(rgdal) # for vector work; sp package should always load with rgdal. library (raster) # for metadata/attributes- vectors or rasters # set working directory to data folder # setwd("pathToDirHere")
To begin let’s import
.csv file that contains plot coordinate
locations at the NEON Harvard Forest Field Site (
R. Note that we set
stringsAsFactors=FALSE so our data import as a
character rather than a
# Read the .csv file plot.locations_HARV <- read.csv("NEON-DS-Site-Layout-Files/HARV/HARV_PlotLocations.csv", stringsAsFactors = FALSE) # look at the data structure str(plot.locations_HARV) ## 'data.frame': 21 obs. of 15 variables: ## $ easting : num 731405 731934 731754 731724 732125 ... ## $ northing : num 4713456 4713415 4713115 4713595 4713846 ... ## $ geodeticDa: chr "WGS84" "WGS84" "WGS84" "WGS84" ... ## $ utmZone : chr "18N" "18N" "18N" "18N" ... ## $ plotID : chr "HARV_015" "HARV_033" "HARV_034" "HARV_035" ... ## $ stateProvi: chr "MA" "MA" "MA" "MA" ... ## $ county : chr "Worcester" "Worcester" "Worcester" "Worcester" ... ## $ domainName: chr "Northeast" "Northeast" "Northeast" "Northeast" ... ## $ domainID : chr "D01" "D01" "D01" "D01" ... ## $ siteID : chr "HARV" "HARV" "HARV" "HARV" ... ## $ plotType : chr "distributed" "tower" "tower" "tower" ... ## $ plotSize : int 1600 1600 1600 1600 1600 1600 1600 1600 1600 1600 ... ## $ elevation : num 332 342 348 334 353 ... ## $ soilTypeOr: chr "Inceptisols" "Inceptisols" "Inceptisols" "Histosols" ... ## $ plotdim_m : int 40 40 40 40 40 40 40 40 40 40 ...
Also note that
plot.locations_HARV is a
data.frame that contains 21
locations (rows) and 15 variables (attributes).
Next, let’s identify explore
data.frame to determine whether it contains
columns with coordinate values. If we are lucky, our
.csv will contain columns
- “X” and “Y” OR
- Latitude and Longitude OR
- easting and northing (UTM coordinates)
Let’s check out the column
names of our file.
# view column names names(plot.locations_HARV) ##  "easting" "northing" "geodeticDa" "utmZone" "plotID" ##  "stateProvi" "county" "domainName" "domainID" "siteID" ##  "plotType" "plotSize" "elevation" "soilTypeOr" "plotdim_m"
Identify X,Y Location Columns
View the column names, we can see that our
data.frame that contains several
fields that might contain spatial information. The
plot.locations_HARV$northing columns contain coordinate values.
# view first 6 rows of the X and Y columns head(plot.locations_HARV$easting) ##  731405.3 731934.3 731754.3 731724.3 732125.3 731634.3 head(plot.locations_HARV$northing) ##  4713456 4713415 4713115 4713595 4713846 4713295 # note that you can also call the same two columns using their COLUMN NUMBER # view first 6 rows of the X and Y columns head(plot.locations_HARV[,1]) ##  731405.3 731934.3 731754.3 731724.3 732125.3 731634.3 head(plot.locations_HARV[,2]) ##  4713456 4713415 4713115 4713595 4713846 4713295
So, we have coordinate values in our
data.frame but in order to convert our
data.frame to a
SpatialPointsDataFrame, we also need to know the CRS
associated with those coordinate values.
There are several ways to figure out the CRS of spatial data in text format.
- We can check the file metadata in hopes that the CRS was recorded in the data. For more information on metadata, check out the Why Metadata Are Important: How to Work with Metadata in Text & EML Format tutorial.
- We can explore the file itself to see if CRS information is embedded in the file header or somewhere in the data columns.
northing columns, there is a
geodeticDa and a
utmZone column. These appear to contain CRS information
projection). Let’s view those next.
# view first 6 rows of the X and Y columns head(plot.locations_HARV$geodeticDa) ##  "WGS84" "WGS84" "WGS84" "WGS84" "WGS84" "WGS84" head(plot.locations_HARV$utmZone) ##  "18N" "18N" "18N" "18N" "18N" "18N"
It is not typical to store CRS information in a column. But this particular
file contains CRS information this way. The
contain the information that helps us determine the CRS:
geodeticDa: WGS84 – this is geodetic datum WGS84
When Vector Data Don’t Line Up - Handling Spatial Projection & CRS in R
we learned about the components of a
proj4 string. We have everything we need
to now assign a CRS to our data.frame.
To create the
proj4 associated with
UTM Zone 18 WGS84 we could look up the
projection on the
spatial reference website
which contains a list of CRS formats for each projection:
- This link shows the proj4 string for UTM Zone 18N WGS84.
However, if we have other data in the
UTM Zone 18N projection, it’s much
easier to simply assign the
proj4 format from that object to our
new spatial object. Let’s import the roads layer from Harvard forest and check
out its CRS.
# Import the line shapefile lines_HARV <- readOGR( "NEON-DS-Site-Layout-Files/HARV/", "HARV_roads") ## OGR data source with driver: ESRI Shapefile ## Source: "NEON-DS-Site-Layout-Files/HARV/", layer: "HARV_roads" ## with 13 features ## It has 15 fields # view CRS crs(lines_HARV) ## CRS arguments: ## +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs +ellps=WGS84 ## +towgs84=0,0,0 # view extent extent(lines_HARV) ## class : Extent ## xmin : 730741.2 ## xmax : 733295.5 ## ymin : 4711942 ## ymax : 4714260
Exploring the data above, we can see that the lines shapefile is in
UTM zone 18N. We can thus use the CRS from that spatial object to convert our
data.frame into a
Next, let’s create a
crs object that we can use to define the CRS of our
SpatialPointsDataFrame when we create it
# create crs object utm18nCRS <- crs(lines_HARV) utm18nCRS ## CRS arguments: ## +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs +ellps=WGS84 ## +towgs84=0,0,0 class(utm18nCRS) ##  "CRS" ## attr(,"package") ##  "sp"
.csv to R SpatialPointsDataFrame
Next, let’s convert our
data.frame into a
SpatialPointsDataFrame. To do
this, we need to specify:
- The columns containing X (
easting) and Y (
northing) coordinate values
- The CRS that the column coordinate represent (units are included in the CRS) -
stored in our
- optional: the other columns stored in the data frame that you wish to append as attributes to your spatial object
We will use the
SpatialPointsDataFrame() function to perform the conversion.
# note that the easting and northing columns are in columns 1 and 2 plot.locationsSp_HARV <- SpatialPointsDataFrame(plot.locations_HARV[,1:2], plot.locations_HARV, #the R object to convert proj4string = utm18nCRS) # assign a CRS # look at CRS crs(plot.locationsSp_HARV) ## CRS arguments: ## +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs +ellps=WGS84 ## +towgs84=0,0,0
Plot Spatial Object
We now have a spatial
R object, we can plot our newly created spatial object.
# plot spatial object plot(plot.locationsSp_HARV, main="Map of Plot Locations")
Define Plot Extent
Open and Plot Shapefiles in R
we learned about spatial object
extent. When we plot several spatial layers in
R, the first layer that is plotted, becomes the extent of the plot. If we add
additional layers that are outside of that extent, then the data will not be
visible in our plot. It is thus useful to know how to set the spatial extent of
a plot using
Let’s first create a SpatialPolygon object from the
NEON-DS-Site-Layout-Files/HarClip_UTMZ18 shapefile. (If you have completed
Vector 00-02 tutorials in this
Introduction to Working with Vector Data in R
series, you can skip this code as you have already created this object.)
# create boundary object aoiBoundary_HARV <- readOGR("NEON-DS-Site-Layout-Files/HARV/", "HarClip_UTMZ18") ## OGR data source with driver: ESRI Shapefile ## Source: "NEON-DS-Site-Layout-Files/HARV/", layer: "HarClip_UTMZ18" ## with 1 features ## It has 1 fields
To begin, let’s plot our
aoiBoundary object with our vegetation plots.
# plot Boundary plot(aoiBoundary_HARV, main="AOI Boundary\nNEON Harvard Forest Field Site") # add plot locations plot(plot.locationsSp_HARV, pch=8, add=TRUE)
# no plots added, why? CRS? # view CRS of each crs(aoiBoundary_HARV) ## CRS arguments: ## +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs +ellps=WGS84 ## +towgs84=0,0,0 crs(plot.locationsSp_HARV) ## CRS arguments: ## +proj=utm +zone=18 +datum=WGS84 +units=m +no_defs +ellps=WGS84 ## +towgs84=0,0,0
When we attempt to plot the two layers together, we can see that the plot locations are not rendered. We can see that our data are in the same projection, so what is going on?
# view extent of each extent(aoiBoundary_HARV) ## class : Extent ## xmin : 732128 ## xmax : 732251.1 ## ymin : 4713209 ## ymax : 4713359 extent(plot.locationsSp_HARV) ## class : Extent ## xmin : 731405.3 ## xmax : 732275.3 ## ymin : 4712845 ## ymax : 4713846 # add extra space to right of plot area; # par(mar=c(5.1, 4.1, 4.1, 8.1), xpd=TRUE) plot(extent(plot.locationsSp_HARV), col="purple", xlab="easting", ylab="northing", lwd=8, main="Extent Boundary of Plot Locations \nCompared to the AOI Spatial Object", ylim=c(4712400,4714000)) # extent the y axis to make room for the legend plot(extent(aoiBoundary_HARV), add=TRUE, lwd=6, col="springgreen") legend("bottomright", #inset=c(-0.5,0), legend=c("Layer One Extent", "Layer Two Extent"), bty="n", col=c("purple","springgreen"), cex=.8, lty=c(1,1), lwd=6)
The extents of our two objects are different.
much larger than
aoiBoundary_HARV. When we plot
uses the extent of that object to as the plot extent. Thus the points in the
plot.locationsSp_HARV object are not rendered. To fix this, we can manually
assign the plot extent using
ylims. We can grab the extent
values from the spatial object that has a larger extent. Let’s try it.
plotLoc.extent <- extent(plot.locationsSp_HARV) plotLoc.extent ## class : Extent ## xmin : 731405.3 ## xmax : 732275.3 ## ymin : 4712845 ## ymax : 4713846 # grab the x and y min and max values from the spatial plot locations layer xmin <- plotLoc.extent@xmin xmax <- plotLoc.extent@xmax ymin <- plotLoc.extent@ymin ymax <- plotLoc.extent@ymax # adjust the plot extent using x and ylim plot(aoiBoundary_HARV, main="NEON Harvard Forest Field Site\nModified Extent", border="darkgreen", xlim=c(xmin,xmax), ylim=c(ymin,ymax)) plot(plot.locationsSp_HARV, pch=8, col="purple", add=TRUE) # add a legend legend("bottomright", legend=c("Plots", "AOI Boundary"), pch=c(8,NA), lty=c(NA,1), bty="n", col=c("purple","darkgreen"), cex=.8)
Challenge - Import & Plot Additional Points
We want to add two phenology plots to our existing map of vegetation plot locations.
Import the .csv:
R and do the following:
- Find the X and Y coordinate locations. Which value is X and which value is Y?
- These data were collected in a geographic coordinate system (WGS84). Convert
- Plot the new points with the plot location points from above. Be sure to add
a legend. Use a different symbol for the 2 new points! You may need to adjust
the X and Y limits of your plot to ensure that both points are rendered by
If you have extra time, feel free to add roads and other layers to your map!
HINT: Refer to When Vector Data Don’t Line Up - Handling Spatial Projection & CRS in R for more on working with geographic coordinate systems. You may want to “borrow” the projection from the objects used in that tutorial!
Export a Shapefile
We can write an
R spatial object to a shapefile using the
rgdal. To do this we need the following arguments:
- the name of the spatial object (
- the directory where we want to save our shapefile
current = getwd()or you can specify a different path)
- the name of the new shapefile (
- the driver which specifies the file format (ESRI Shapefile)
We can now export the spatial object as a shapefile.
# write a shapefile writeOGR(plot.locationsSp_HARV, getwd(), "PlotLocations_HARV", driver="ESRI Shapefile")