3/11/2010

Spatial Point Patterns

Lecture #1

Point pattern terminology

 Point is the term used for an arbitrary location
 Event is the term used for an observation

 Mapped point pattern: all relevant events in a study

area R have been recorded

 Sampled point pattern: events are recorded from a

sample of different areas within a region

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Objective of point pattern analysis

 Determine if there is a tendency of events to exhibit a
systematic pattern over an area as opposed to being
randomly distributed

 Point data often have attributes, but right now we are

only interested in the location in point pattern analysis

 Does a pattern exhibit clustering or regularity?

 Over what spatial scales do patterns exist?

Types of distributions
 Three general patterns
 Random - any point is equally likely to occur at any location
and the position of any point is not affected by the position of
any other point
 Uniform - every point is as far from all of its neighbors as
possible
 Clustered - many points are concentrated close together, and
large areas that contain very few, if any, points

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Types of distributions

RANDOM UNIFORM CLUSTERED

Methods
 “Exploratory” analysis
 Visualization (maps)
 Estimate how intensity of point pattern varies over an area
 Quadrat analysis, kernel estimation
 Estimate the presence of spatial dependence among events
 Nearest neighbor distances, K-function

 Modeling techniques
 Statistical tests for significant spatial patterns in data, compared
with the null hypothesis of complete spatial randomness (CSR)

 Much of the time we do both!

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How Bailey & Gatrell see it

 Exploring 1st order properties
 Measuring intensity – based on the density (or mean number
of events) in an area
 Quadrat analysis
 Kernel estimation

 Exploring 2nd order properties

 Measuring spatial dependence – based on distances of points
from one another
 Nearest neighbor distances
 K-function

Modeling techniques
 We can conduct statistical tests for significant patterns in
our data
 H0: events exhibit complete spatial randomness (CSR)
 Ha: events are spatially clustered or dispersed

 What is complete spatial randomness?

 What are we comparing our point pattern to?

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Complete spatial randomness

 CSR assumes that points follow a homogeneous Poisson process
over the study area
 The density of points is constant (homogeneous) over the study area
 For a random sample of subregions, the frequency distribution of the
number of points in each region will follow a Poisson distribution
 # of points in an given subregion is the same for all subregions in study area
 # of points in a subregion independent of # of points in any other subregion

Some notes on R
> library(maptools)
> library(rgdal)
> library(shapefiles)
> library(spatstat)
> library(splancs)

> workingDir = "C:/Users/Eroot/Quant/R"

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Splancs and Spatstat in R

 Use different data file formats for analysis
 Both need a set of “points” and a study area “boundary”

 Splancs
> library(shapefiles)
> border <- readShapePoly(paste(workingDir,
"/shapefiles/FLBndy.shp", sep=""))
> flbord <- border@polygons[[1]]@Polygons[[1]]@coords
> str(border)

> flinv<-readShapePoints("C:/Users/Elisabeth
Root/Desktop/Quant/R/shapefiles/FL_Invasive.shp")
> flinvxy<-coordinates(flinv)

Splancs and Spatstat in R

 Spatstat
> library(shapefiles)
> library(maptools)

> flinv<-
readShapePoints("C:/Users/Eroot/Quant/R/shapefiles/
FL_Invasive.shp")
> flpt<-as(flinv,"ppp")

> border <- readShapePoly(paste(workingDir,

"/shapefiles/FLBndy.shp", sep=""))
> flbdry<-as(border,"owin“)

> flppp<-ppp(flpt$x,flpt$y,window=flbdry)

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Sample dataset plot

 Dataset: Location of
Cogon Grass
(invasive species in
FL)

> plot(flppp, axes=T)

Quadrat methods
 Divide the study area into subregions of equal size
 Often squares, but don‟t have to be
 Count the frequency of events in each subregion
 Calculate the intensity of events in each subregion

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Quadrat methods

Quadrat method
 Compare the intensity variation over R

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3 1 2 2 0 0
5 0 2 2 0 0
2 1 2 2 10 10
1 3 2 2 0 0
3 1 2 2 0 0

Quadrat # of Points Quadrat # of Points Quadrat # of Points

# Per Quadrat x^2 # Per Quadrat x^2 # Per Quadrat x^2
1 3 9 1 2 4 1 0 0
2 1 1 2 2 4 2 0 0
3 5 25 3 2 4 3 0 0
4 0 0 4 2 4 4 0 0
5 2 4 5 2 4 5 10 100
6 1 1 6 2 4 6 10 100
7 1 1 7 2 4 7 0 0
8 3 9 8 2 4 8 0 0
9 3 9 9 2 4 9 0 0
10 1 1 10 2 4 10 0 0
20 60 20 40 20 200

Variance 2.222 Variance 0.000 Variance 17.778

Mean 2.000 Mean 2.000 Mean 2.000
Var/Mean 1.111 Var/Mean 0.000 Var/Mean 8.889

N  number of quadrats  10 To test for CSR, calculate the test statistic

for quadrat (2):
Variance 
x 2
 [( x) 2 / N ] m = # of quadrats
(m  1) s 2 s2 = observed variance
N 1  x = observed mean
variance x
Variance mean ratio 
mean Compare to 2 distribution with m-1
degrees of freedom

Quadrats in R
 Done using spatstat package

> qt <- quadrat.test(flppp,

nx = 10, ny = 10)
> qt
Chi-squared test of CSR using
quadrat counts

X-squared = 1239.057, df = 89,

p-value < 2.2e-16

> plot(flppp)
> plot(qt, add = TRUE, cex =
.5)

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Weaknesses of quadrat method

 Quadrat size
 If too small, they may contain only a couple of points
 If too large, they may contain too many points
 Actually a measure of dispersion, and not really pattern,
because it is based primarily on the density of points, and
not their arrangement in relation to one another
 Results in a single measure for the entire distribution, so
variations within the region are not recognized

Kernel estimation
 Believe it or not, we already talked about this with GWR!
 Calculating the density of events within a specified search
radius around each event
 A moving three-dimensional function (the kernel) of a given
radius (bandwidth) „visits‟ each point in the study area
 Use kernel to weight the area surrounding the point
proportionately to its distance to the event
 Sum these individual kernels for the study region
 Produce a smoothed surface

 Variety of different kernels

 Bivariate quartic most common

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Kernel estimation

• Creating a smooth surface for each kernel

• Surface value highest in the center (point location) and
diminishes with distance…reaches 0 at radius distance

Kernel estimation
 s is a location in R (the study area)
 s1…sn are the locations of n events in R

 The intensity at a specific location is estimated by:

distance between
n
1  s  si 
ˆ ( s)   2 k 
point s and si

i 1     bandwidth
(radius of the circle)

kernel
(which is a function of the
distance and bandwidth)
 Summed across all points si within the radius ()

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Different types of kernels

Uniform n
1  s  si 
 ( s)   2 k 
ˆ 
i 1    
Triangular
Each kernel type has a different equation
for the function k, for example:
di
Quartic
Triangular: k  1


3  hi2 
Quartic: k 1  
Gaussian    2 
h2
1  2i 2
Normal: k e
2

Kernel estimation
 The kernel (k) is basically a mathematical function that
calculates how the surface value “falls off” as it reaches
the radius
 There are lots of different kernel functions
 Most researchers believe it doesn‟t really matter which you use
 Most common in GIS is the quartic kernel
2
n
3  d2 
ˆ ( s)   2 1  i2  distance between point s and si
d i     
At point s, the weight is
bandwidth 3/2 and drops smoothly
(radius of the circle) to a value of 0 at 
 Summed for all values of di which are not larger than 

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Kernel estimation
(s)

Adding up the “bumps”

2
n
3  d i2 
 2 1   2 
d i    

Individual “bumps”
2
3  d i2 
1  
 2   2 

A few notes
 Like GWR, we can used fixed and adaptive kernels
 Fixed = bandwidth is a specified distance
 Adaptive = fixed number of points used
 Results are sensitive to change in bandwidth
 When bandwidth is larger, the intensity will appear smooth and
local details obscured
 When bandwidth is small, the intensity appears as local spikes
at event locations
 No agreement on how to select the “best” bandwidth
 prior information about underlying spatial process
 comparison of various bandwidths
 using Mean Square Error (in R)

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Kernel estimation in R
 Can be done in both splancs and spatstat
 splancs = quartic kernel
 spatstat=gaussian kernel

 Mean standard error one way to find “optimal bandwidth”

> mse<-mse2d(flinvxy,flbord, 100, 600)

> plot(mse$h, mse$mse, xlab="Bandwidth", ylab="MSE",

type="l", xlim=c(100,600), ylim=c(-30,50))
> i<-which.min(mse$mse)
> points(mse$h[i], mse$mse[i])

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Kernel estimation in R
 Need to make a grid to “dump” kernel estimates into
 The Sobj_SpatialGrid() function in maptools takes a maxDim=
argument, which indirectly controls the cell resolution
> sG <- Sobj_SpatialGrid(border, maxDim=400)$SG
> grd <- slot(sG, "grid")
> summary(grd)

 Can also create a GridTopology object from scratch:

> poly <- slot(border, "polygons")[[1]]
> poly1 <- slot(poly, "Polygons")[[1]]
> coords <- slot(poly1, "coords")
> min(coords[,1])
> min(coords[,2])
> grd <- GridTopology(cellcentre.offset=c(616593,531501),
cellsize=c(150,150), cells.dim=c(400,400))
> summary(grd)

Kernel estimation in R
 Using splancs
> k0 <- spkernel2d(flinvxy, flbord, h0=400, grd)
> k1 <- spkernel2d(flinvxy, flbord, h0=600, grd)
> k2 <- spkernel2d(flinvxy, flbord, h0=800, grd)
> k3 <- spkernel2d(flinvxy, flbord, h0=1000, grd)
> df <- data.frame(k0=k0, k1=k1, k2=k2, k3=k3)
> kernels <- SpatialGridDataFrame(grd, data=df)
> summary(kernels)
> gp <- grey.colors(5, 0.9, 0.45, 2.2)
> print(spplot(kernels, at=seq(0,.00001,length.out=20),
col.regions=colorRampPalette(gp)(21)))

 Using spatstat
> plot(density(flppp, sigma = 600))

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Nearest neighbor analysis

G-function
 Simplest measure and is similar to the mean
 Examine the cumulative frequency distribution of the
nearest neighbor distances
Nearest
Event x y neighbor rmin
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1 66.22 32.54 10 25.59
3 9 2 22.52 22.39 4 15.64
3 31.01 81.21 5 21.14
5 6 4 9.47 31.02 8 24.81
5 30.78 60.10 3 9.00
8 10
6 75.21 58.93 10 21.14
1
4 7 79.26 7.68 12 21.94
2 8 8.23 39.93 4 9.00
9 98.73 42.53 6 21.94
10 89.78 42.53 6 21.94
12 7 11 65.19 92.08 6 34.63
10 meters 12 54.46 8.48 7 24.81

G-function
Nearest
Event x y neighbor rmin
1 66.22 32.54 10 25.59 1
2 22.52 22.39 4 15.64
3 31.01 81.21 5 21.14 0.75
4 9.47 31.02 8 24.81
5 30.78 60.10 3 9.00
G(r)

0.5
6 75.21 58.93 10 21.14
7 79.26 7.68 12 21.94
8 8.23 39.93 4 9.00 0.25
9 98.73 42.53 6 21.94
10 89.78 42.53 6 21.94
0
11 65.19 92.08 6 34.63
12 54.46 8.48 7 24.81 0 9 15 22 25 26 35
Distance (r)
# [rmin ( si )  r ]
G (r ) 
n
# point pairs where rmin  r

# of points in study area

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G-function
The shape of G-function tells us the way the events
are spaced in a point pattern
1
 Clustered = G increases
rapidly at short distance
0.75
 Evenness = G increases
slowly up to distance where

G(r)
0.5
most events spaced, then
increases rapidly 0.25

 How do we examine
significance (significant 0
0 9 15 22 25 26 35
departure from CSR)? Distance (r)

How do we tell if G is significant?

 The significance of any departures from CSR (either
clustering or regularity) can be evaluated using simulated
“confidence envelopes”
 Simulate many (1000??) spatial point processes and
estimate the G function for each of these
 Rank all the simulations 95th
 Pull out the 5th and 95th G(r) values
 Plot these as the 95% confidence intervals 5th
G(r)

 This is done in R!

radius (r)

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G estimate in R
> r=seq(0,350,by=50)

> G <- envelope(flppp, Gest, r=r, nsim = 59, rank = 2)

> G
Pointwise critical envelopes for G(r)
Edge correction: “km”
Obtained from 59 simulations of CSR
Significance level of pointwise Monte Carlo test: 2/60 = 0.03333
Data: flppp
Entries:
id label description
-- ----- -----------
r r distance argument r
obs obs(r) observed value of G(r) for data pattern
theo theo(r) theoretical value of G(r) for CSR
lo lo(r) lower pointwise envelope of G(r) from simulations
hi hi(r) upper pointwise envelope of G(r) from simulations
> plot(G)

G estimate in R

Clustered pattern (above the envelopes)

Below envelopes = regular pattern

In envelopes = homogeneous
distribution (CSR)

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Nearest neighbor analysis

F-function
 Select a sample of point locations anywhere in the study
region at random
 Determine minimum distance from each point to any event in
the study area

 Three steps:
1. Randomly select m points (p1, p2, …, pn)
2. Calculate dmin(pi, s) as the minimum distance from location pi
to any event in the point pattern s
3. Calculate F(d)

F-function
1

0.75
F(r)

0.5

0.25

0
0 5 10 15 20 25
10 meters
Distance (r)
= randomly chosen point
= event in study area # [d min ( pi , s)  d ]
= dmin
F (d ) 
m
# of point pairs where rmin  r

# sample points

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F-function
 Clustered = F(r) rises
slowly at first, but more
1
rapidly at longer distances
 Evenness = F(r) rises rapidly 0.75
at first, then slowly at longer
distances

F(r)
0.5
 Examine significance by
simulating “envelopes” 0.25

0
0 5 10 15 20 25
Distance (r)

F estimate in R
> r=seq(0,350,by=50)

> F <- envelope(flppp, Fest, r=r, nsim = 59, rank = 2)

> plot(F)
lty col key label meaning
obs 1 1 obs obs(r) observed value of F(r) for data pattern
theo 2 2 theo theo(r) theoretical value of F(r) for CSR
hi 3 3 hi hi(r) upper pointwise envelope of F(r) from simulations
lo 4 4 lo lo(r) lower pointwise envelope of F(r) from simulations

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F estimate in R

Clustered pattern (below the envelopes)

Above envelopes = regular pattern

Within envelopes = CSR

Comparison between G and F

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K function
 Limitation of nearest neighbor distance method is that it
uses only nearest distance
 Considers only the shortest scales of variation
 K function (Ripley, 1976) uses more points
 Provides an estimate of spatial dependence over a wider range
of scales
 Based on all the distances between events in the study area
 Assumes isotropy over the region

K function
 Defined as:
1
K (h)  E (# (events w/in distance h of randomly chosen event)

  = the intensity of events (n/A)

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How do we estimate the K-function

1. Construct a circle of radius h around each point event (i)
2. Count the number of other events (j) that fall inside this
circle
3. Repeat these two steps for all points (i) and sum results
dummy variable
1 if dij ≤ h
area of R
0 otherwise
R I h (d ij )
Kˆ (h)  2
n
 i j wij edge correction
the proportion of circumference of circle
(centered on point i, containing point j)
number of points =1 if whole circle in the study area

4. Increment h by a small amount and repeat the computation

Interpreting the K-function

 K(h) can be plotted against different values of h

 But what should K look like for no spatial dependence?

 Consider what K(h) should look like for a random point
process (CSR)
 The probability of an event at any point in R is independent of
what other events have occurred and equally likely anywhere
in R

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Interpreting the K function

 Under the assumption of CSR, the expected number of
events within distance h of an event is:
The density of events should be
K (h)  h 2 the radius of
the circle
evenly distributed across all circles

 K(h) < h2 if point pattern is regular

 K(h) > h2 if point pattern is clustered

 Now we can compare K(h) to h2

 How do we do this?

Interpreting K with L
 This L-function is nothing more than a standardized
version of the K function
 Transforms the K function so we can easily interpret it
 Compare it to 0 uniform

Kˆ (h) random
Lˆ (h)  h

L(h)

clustered
 L(h) = 0 if point process is random
 Peaks of positive values = clustering
 Troughs of negative values = regularity radius (h)

 Significance of any departures from L=0 evaluated using

simulated “confidence envelopes”

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K function in R
> L <- envelope(flppp, Lest, nsim = 59, rank = 2, global=TRUE)
> L
Simultaneous critical envelopes for L(r)
Edge correction: “iso”
Obtained from 59 simulations of CSR
Significance level of Monte Carlo test: 1/60 = 0.0166667
Data: flppp
Entries:
id label description
-- ----- -----------
r r distance argument r
obs obs(r) observed value of L(r) for data pattern
theo theo(r) theoretical value of L(r) for CSR
lo lo(r) lower critical boundary for L(r)
hi hi(r) upper critical boundary for L(r)
> plot(L)

K function in R

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Real world situations

 In the real world, the location of events is often related to
underlying patterns
 Population centers
 Events that may not seem to cluster in space, but cluster in
space time

 There are many (many many) variations of point pattern

analysis

 Often called “multivariate point pattern” analysis

 Comparing distributions of multiple sets of points

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