0.

!
!

1 km

Occupied Psilon
Colonized Psilon

0.5

0.5

1 km

1 km

2008

Section 2

Section 9

Section 6
!

1 plant

0.5

1 km

Why use R?
Simplicity

ArcGIS is hard to learn

The simplest map requires no data les
More control over features
R help is amazing

Why use R?
Simplicity

ArcGIS is hard to learn

The simplest map requires no data les
More control over features
R help is amazing

Repeatability
Run the same script and produce the same map
ArcGIS version incompatibilities

Why use R?
Simplicity

ArcGIS is hard to learn

The simplest map requires no data les
More control over features
R help is amazing

Repeatability
Run the same script and produce the same map
ArcGIS version incompatibilities

FREE!
No licenses or complications, available wherever you are

Created with ArcMap r

Powerful, but messy if you dont know what you are doing

23

260

520

1,040
Kilometers

East
West

Made with ArcGIS

Dicult to control what appears in the legend
Annoying lines if you tell points to not overlap

Sampled Populations

23

260

520

1,040
Kilometers

East
West

CNA
EEU
WNA
ENA

WEU
0

260

520

1,040
Kilometers

Not easily reproducible

Bits of Canada above Maine now missing
Legend forgotten
Text and shading added via photoshop

Sampled Populations

23

260

520

1,040
Kilometers

East
West

CNA
Sampled
Populations

EEU

WNA
ENA

WEU
0

260

520

1,040
Kilometers

CNA
WNA

EEU
ENA

WEU
0

300 600

1,200
Kilometers

Created with R
library(maps)
library(mapdata)
map("worldHires","Canada,
xlim=c(-141,-53),
ylim=c(40,85),
col="gray90",
fill=TRUE)

Only three lines of code!

Created with R
library(maps)
library(mapdata)
library(mapproj)
map("worldHires","Canada,
xlim=c(-141,-53),
ylim=c(40,85),
col="gray90",
fill=TRUE,
projection="conic",
param=35))

Tools of the Trade

library(sp)
data

#classes and methods for spatial

library(scales)

#for transparency

library(mapplots)

#data visualization on maps

library(mapdata)
#contains basic data to go along
with 'maps' (topographic and geologic)

library(RgoogleMaps)
tiles in R

#overlays on Google map

library(sfsmisc)
#utilities from Seminar fuer
Statistik ETH Zurich

library(plotGoogleMaps) # plot SP data as HTML map

mashup over Google Maps

library(mapproj)

#for creating projected maps

library(ggmap)
#a package for spatial
visualization with Google Maps and OpenStreetMap

library(raster)

#tools to deal with raster maps

library(maptools)
#tools for reading and handling
spatial objects
gpclibPermit()
#allow general polygon clipping
library for R - library(gpclib)
library(maps)

#for creating geographical maps

library(rgeos)
#interface to geometry engine - open
source (GEOS)
library(rgdal)
#bindings for the geospatial data
abstraction library

library(GEOmap)
mapping

#topographic and geologic

library(plotrix)

#various plotting functions

Tools of the Trade

(Optional) Tools of the Trade

Shapeles
Used for adding additional layers of data: roads, cities,
waterways, species ranges, temperature or precipitation
gradients..

These do not come with R

A good amount of GIS data is freely available online
ESRI, USGS, GeoBC, GeoGratis

Google is your best friend

Getting started
1. Load libraries
2. Read in data
3. Plot data

Getting started
1. Load libraries
2. Read in data
3. Plot data
library(maps)
library(mapdata)

map("worldHires","Canada, xlim=c(-141,-53), ylim=c(40,85), col="gray90, fill=TRUE)

Getting started
1. Load libraries

Load libraries
(in this case that loads our data as well)

2. Read in data
3. Plot data
library(maps)
library(mapdata)

map("worldHires","Canada, xlim=c(-141,-53), ylim=c(40,85), col="gray90, fill=TRUE)

Getting started
1. Load libraries

Load libraries
(in this case that loads our data as well)

2. Read in data
3. Plot data
library(maps)
library(mapdata)

The map
function draws
the map

map("worldHires","Canada, xlim=c(-141,-53), ylim=c(40,85), col="gray90, fill=TRUE)

Getting started
1. Load libraries
2. Read in data
3. Plot data

Load libraries
(in this case that loads our data as well)
Draw this data: draw the country of
Canada, out of the database worldHires

library(maps)
library(mapdata)

The map
function draws
the map

map("worldHires","Canada, xlim=c(-141,-53), ylim=c(40,85), col="gray90, fill=TRUE)

Getting started
1. Load libraries
2. Read in data
3. Plot data

Load libraries
(in this case that loads our data as well)
Draw this data: draw the country of
Canada, out of the database worldHires
Draw the map to cover this area: from
longitude -53 to -141 and latitude 40 to 85

library(maps)
library(mapdata)

The map
function draws
the map

*Note the order!

xlim is for LONGITUDE
ylim is for LATITUDE

map("worldHires","Canada, xlim=c(-141,-53), ylim=c(40,85), col="gray90, fill=TRUE)

Getting started
1. Load libraries
2. Read in data
3. Plot data

Load libraries
(in this case that loads our data as well)
Draw this data: draw the country of
Canada, out of the database worldHires
Draw the map to cover this area: from
longitude -53 to -141 and latitude 40 to 85

library(maps)
library(mapdata)

The map
function draws
the map

Make the
map gray

Fill the map

with gray
(rather than an
empty outline
of gray)

map("worldHires","Canada, xlim=c(-141,-53), ylim=c(40,85), col="gray90, fill=TRUE)

library(maps)
library(mapdata)
map("worldHires","Canada, xlim=c(-141,-53), ylim=c(40,85), col="gray90, fill=TRUE)

You could stop here and throw everything else on with powerpoint
But we wont do that, onward with R!

A more involved example:

1. Load libraries
library(sp)

#classes and methods for spatial data

library(maptools)

#tools for reading and handling

gpclibPermit()

#allow general polygon clipping library for R - library(gpclib)

library(maps)

#for creating geographical maps

library(mapdata)

#contains basic data to go along with 'maps' (topographic and geologic)

library(sfsmisc)

#utilities from Seminar fuer Statistik ETH Zurich

library(mapproj)

#for creating projected maps

library(raster)

#tools to deal with raster maps

library(rgeos)

#interface to geometry engine - open source (GEOS)

library(rgdal)

#bindings for the geospatial data abstraction library

library(scales)

#for transparency

spatial objects

2. Read in data: shapeles and GPS points

readShapePoly read in a polygon shape layer

This means the layer is of type polygon

i.e. not lines, such as roads or rivers

readShapeLines ; readShapePoints read in a line or point shape layer

pcontorta <- readShapePoly("~/Documents/My Documents/UBC/Research/LodgepoleData/pinucont/pinucont.shp)
roads2011 <- readShapeLines("/Users/Kim/Documents/My Documents/Taylor Lab/SideProject/R_Analyses/Maps/
MiscGISdata/VA_2011_PriSecRoads/tl_2011_51_prisecroads.shp")

2. Read in data: shapeles and GPS points

readShapePoly read in a polygon shape layer

This means the layer is of type polygon

i.e. not lines, such as roads or rivers

readShapeLines ; readShapePoints read in a line or point shape layer

pcontorta <- readShapePoly("~/Documents/My Documents/UBC/Research/LodgepoleData/pinucont/pinucont.shp)
roads2011 <- readShapeLines("/Users/Kim/Documents/My Documents/Taylor Lab/SideProject/R_Analyses/Maps/
MiscGISdata/VA_2011_PriSecRoads/tl_2011_51_prisecroads.shp")

Read in your data, as you would any other .csv le

For GPS points, must have columns individually for latitude and longitude
Must be in decimal degrees
samps <- read.csv("~/Documents/My Documents/UBC/Research/FieldWork/Summer2012/
FieldData_2012.csv", header=TRUE, stringsAsFactors=T, strip.white=TRUE, na.strings=c("NA",
"na", "nan", "inf", "", "."))

3. Create the Map

Several steps:
1. Plot the base map
This will be the nal shape and size of your full map

2. Plot layers or data onto this map

Add your shape les or data points
Plotting occurs in order, unless you use transparency, you will
cover things up

3. Add any nal touches youd like

*Remember to use add=TRUE for every step after the rst

Lets map the range of lodgepole pine and some sample sites:

1. Plot Map
map("worldHires",
"Canada",
xlim=c(-140,-110),
ylim=c(48,64),
col="gray90",
fill=TRUE)

1. Plot Map
map("worldHires",
"usa",
xlim=c(-140,-110),
ylim=c(48,64),
col="gray95",
fill=TRUE,
add=TRUE)

2. Add layers
plot(pcontorta,
add=TRUE,
xlim=c(-140,-110),
ylim=c(48,64),
col=alpha("darkgreen",
0.6),
border=FALSE)

2. Add layers
points(samps$Long,
samps$Lat,
pch=19,
col="red",
cex=1)

!
!
!
!
!

3. Add extras
map.scale(-127, 63.5,
ratio=FALSE,
relwidth=0.2,
cex=1.2)

*Note: This is an unprojected map,

placement of the scale bar is important,
as it will change size north to south

200

400 km

!
!
!
!
!

Zoomed In
#plot map
map("worldHires","Canada", xlim=c(-123.5,-120.5),ylim=c(49,50.8), col="gray90", fill=TRUE)
map("worldHires","usa", xlim=c(-140,-110),ylim=c(48,64), col="gray95", fill=TRUE, add=TRUE)
Cache Creek

#plot species range

plot(pcontorta, add=TRUE,
xlim=c(-140,-110),
ylim=c(48,64), col=alpha("darkgreen",
0.6), border=FALSE)

Ashcroft
Lillooet

20

40

60 km
Logan Lake
!

#map cities
map.cities(country="Canada",
label=TRUE, cex=1, xlim=c(-140,-110),
ylim=c(48,64),
pch=20)

Pemberton
!

Whistler

Merritt

#plot field data

points(samps$Long, samps$Lat, pch=4,
col="red", cex=0.8)
Squamish

#put a scale on the map

map.scale(-123.3, 50.7, ratio=FALSE,
relwidth=0.2, cex=1.2)
box()

Lions Bay
Gibsons

Princeton

Hope

!
!

Vancouver
Kent

Walnut Grove

Chilliwack

Aldergrove
Abbotsford Cultus Lake
White Rock Fort Langley
!

Create a Projected Map More Realistic

Unprojected

map(database="world", xlim=c
(-170,-10),ylim=c
(45,83),resolution=0,
col="grey80,
fill=TRUE)

Projected
library(mapproj)
map(database="world",xlim=c
(-170,-20), ylim=c(65,83),
projection="gilbert",
fill=T,col="grey80",
orientation=c(90,0,225),
resolution=0)

Plotting points on a projected map

#plotting the map, note the 'orientation' which appears to be necessary for
points and map to match up.
map(database="world",ylim=c(45,90),xlim=c(-160,-50),
projection="gilbert", fill=T,col="grey80", orientation=c(90,0,225),
resolution=0, lwd=0.5)
lon<-c(-72,-66,-107,-154) #fake longitude vector
lat<-c(81.7,64.6,68.3,60) #fake latitude vector

Plotting points on a projected map

#plotting the map, note the 'orientation' which appears to be necessary for
points and map to match up.
map(database="world",ylim=c(45,90),xlim=c(-160,-50),
projection="gilbert", fill=T,col="grey80", orientation=c(90,0,225),
resolution=0, lwd=0.5)
lon<-c(-72,-66,-107,-154) #fake longitude vector
lat<-c(81.7,64.6,68.3,60) #fake latitude vector
#converting your points
to projected lat/lon
coord<-mapproject(
lon,lat,
proj="gilbert",
orientation=c(90,0,225))
points(coord,
pch=21,cex=1.2)
#plot converted points
onto map

Plotting points on a projected map

#plotting the map, note the 'orientation' which appears to be necessary for
points and map to match up.
map(database="world",ylim=c(45,90),xlim=c(-160,-50),
projection="gilbert", fill=T,col="grey80", orientation=c(90,0,225),
resolution=0, lwd=0.5)
lon<-c(-72,-66,-107,-154) #fake longitude vector
lat<-c(81.7,64.6,68.3,60) #fake latitude vector
#converting your points
to projected lat/lon
coord<-mapproject(
lon,lat,
proj="gilbert",
orientation=c(90,0,225))
points(coord,
pch=21,cex=1.2)
#plot converted points
onto map

*Note: there is currently no

capability to plot a scale bar
on a projected map, but grid
lines can be plotted

map("state", add=TRUE, col="gray")

map("state","Virginia", add=TRUE, col="black")
points(-80.523326, 37.375409, pch="*", col="red", cex=3)

Can create insets

See layout in the graphics package

Adding Text and Detail

#main roads, Virginia
plot(roads2011, add=TRUE, xlim=c(-80.69,-80.341),ylim=c(37.215,37.45), col="light gray", lwd=0.8)
#Giles county roads
plot(gilesdetail2, add=TRUE, xlim=c(-80.69,-80.341),ylim=c(37.215,37.45), col="light gray", lwd=0.8)
#Craig county roads
plot(craigdetail, add=TRUE, xlim=c(-80.69,-80.341),ylim=c(37.215,37.45), col="light gray", lwd=0.8)
#Giles county line
plot(gilessub, add=TRUE, xlim=c(-80.69,-80.341),ylim=c(37.215,37.45), col="dark gray", lwd=2)
#Craig county line
plot(craigsub, add=TRUE, xlim=c(-80.69,-80.341),ylim=c(37.215,37.45), col="dark gray", lwd=2)

text(-80.496,37.377, "Mountain Lake", cex=1.6)

text(-80.496,37.3705, "Biological Station", cex=1.6)
text(-80.415,37.36, "Craig County", cex=1.7)
text(-80.6,37.36, "Giles County", cex=1.7)

Giles County

Mountain Lake
Biological Station

Craig County

!!
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Giles County

Mountain Lake
Biological Station

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Scaled Point Sizes and Types

points(pops2$W, pops2$N, pch=20, col="red3", cex=sqrt(pops2$Plants))
points(pops2$W, pops2$N, pch=20, col=as.numeric(pops2$Subsection),
cex=sqrt(pops2$Plants))
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Biological Station

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Using Transparency
library(scales) #for transparency
points(slat08$Long, slat08$Lat, pch=pch20, col=c(alpha(slat08$col2,0.6), alpha
(slat08$col2,0.8)), cex=sqrt(slat08$GenoPop))

0.5

!
!

1 km

0.5

0.5

1 km

1 km

2008

Occupied Psilon
Colonized Psilon

Section 2
!

0.5

1 km

1 plant

! 10 plants

! 20 plants
0

2010

Section 9

Section 6

0.5

1 km

0.5

1 km

Plotting Pie Charts

Libraries: mapplots or plotrix
Functions: add.pie or oating.pie (respectively)

Plotting Pie Charts

Libraries: plotrix or mapplots
Functions: oating.pie or add.pie (respectively)
floating.pie(5, 48, x=c(0.001,5), radius=5, col=c("orange", "blue"))

x position
(longitude)

y position
(latitude)

values for sectors

of the pie chart

radius of the pie chart

(i.e. scale by this size)

*Note: oating.pie cannot

accept zeros (when one pie
chart is of only one type)

Plotting Pie Charts

Libraries: mapplots or plotrix
Functions: add.pie or oating.pie (respectively)
add.pie(x=2, y=48, z=c(4,10), radius=5)

x position
(longitude)

y position
(latitude)

values for sectors

of the pie chart

radius of the pie chart

(i.e. scale by this size)

Plotting Pie Charts

Libraries: mapplots or plotrix
Functions: add.pie or oating.pie (respectively)
floating.pie(5, 48, x=c(0.001,5), radius=5, col=c("orange", "blue"))
add.pie(x=2, y=48, z=c(4,10), radius=5)

1000

2000 km

Final Touches
Print to a .pdf, arrange layout, create a border edge
pdf("~/Documents/My_Documents/UBC/Research/FieldWork/Summer2012/
SamplingMap_PcontRange.pdf")
Make the map here
Can use layout settings to plot multiple maps together
box() #put a box around the map
dev.off()

RgoogleMaps
A package in R to plot data onto maps from Google

Im still new at RgoogleMaps

Two main functions:
GetMap()
GetMap.bbox()
The second one takes care of some of the overhead

Plots straight to an output le

Not sure about shapeles yet

Another map of BC
#define our map's range
lat <- c(48,64)
lon <- c(-140,-110)
#tell what point to center on
center = c(mean(lat), mean(lon))
#zoom: 1 = furthest out (entire globe),
larger numbers = closer in
zoom <- 5
terrmap <- GetMap(
center=center,
zoom=zoom,
maptype= "terrain",
destfile = "terrain.png")

#lots of visual options for maptype, just like

google maps: "roadmap", "mobile", "satellite",
"terrain", "hybrid", "mapmaker-roadmap",
"mapmaker-hybrid

Add our data

samps <- read.csv("~/Documents/My Documents/UBC/Research/FieldWork/Summer2012/
FieldData_2012.csv", header=TRUE, stringsAsFactors=T, strip.white=TRUE, na.strings=c("NA", "na",
"nan", "inf", "", "."))
#want to make a data frame of just points and their visualizations
samps$size <- "small
samps$col <- "red
samps$char <- "
mymarkers <- cbind.data.frame(samps$lat, samps$lon, samps$size, samps$col, samps$char)
names(mymarkers) <- c("lat", "lon", "size", "col", "char")
mymarkers <- mymarkers[c(1:18,50:64),] #taking a subset because it craps out when I use all of
the data

Plot our data

samps <- read.csv("~/Documents/My Documents/UBC/Research/FieldWork/Summer2012/
FieldData_2012.csv", header=TRUE, stringsAsFactors=T, strip.white=TRUE, na.strings=c("NA", "na",
"nan", "inf", "", "."))
#want to make a data frame of just points and their visualizations
samps$size <- "small
samps$col <- "red
samps$char <- "
mymarkers <- cbind.data.frame(samps$lat, samps$lon, samps$size, samps$col, samps$char)
names(mymarkers) <- c("lat", "lon", "size", "col", "char")
mymarkers <- mymarkers[c(1:18,50:64),] #taking a subset because it craps out when I use all of
the data
lat <- c(48,60)
lon <- c(-140,-110)
center = c(mean(lat), mean(lon))
zoom <- 5

satclose <- GetMap.bbox(lonR= range(lon),

latR= range(lat),
center= c(50, -122),
destfile= "satclose.png",
markers= mymarkers,
zoom=8,
maptype="satellite")

Plot our data

samps <- read.csv("~/Documents/My Documents/UBC/Research/FieldWork/Summer2012/
FieldData_2012.csv", header=TRUE, stringsAsFactors=T, strip.white=TRUE, na.strings=c("NA", "na",
"nan", "inf", "", "."))
#want to make a data frame of just points and their visualizations
samps$size <- "small
samps$col <- "red
samps$char <- "
mymarkers <- cbind.data.frame(samps$lat, samps$lon, samps$size, samps$col, samps$char)
names(mymarkers) <- c("lat", "lon", "size", "col", "char")
mymarkers <- mymarkers[c(1:18,50:64),] #taking a subset because it craps out when I use all of
the data
lat <- c(48,60)
lon <- c(-140,-110)
center = c(mean(lat), mean(lon))
zoom <- 5

satclose <- GetMap.bbox(lonR= range(lon),

latR= range(lat),
center= c(50, -122),
destfile= "satclose.png",
markers= mymarkers,
zoom=8,
maptype="satellite")

Another version
samps$size <- "large

lat <- c(48,60)

lon <- c(-140,-110)
center = c(mean(lat), mean(lon))
zoom <- 5

terrfar <- GetMap.bbox(

lonR= range(lon),
latR= range(lat),
center= c(51, -122),
destfile= "terrfar.png",
markers= mymarkers2,
zoom=7,
maptype="terrain")

And the best part about R,

there will be more every day!