VocGradSIS eLearning Portal

  • Increase font size
  • Default font size
  • Decrease font size

Assessment 4: Nearest Neighbour Analysis

Print PDF
User Rating: / 0
PoorBest 

Contents

    Introduction
    Research background and data
    Software Requirements
    Establishing a working directory
    Assessment
    Part 1: Calculating Nearest Neighbour Index using ArcGIS
    Part 2: Calculating Nearest Neighbour Index using CrimeState III
    Part 3: Calculating the Kth Order Nearest Neighbour Index using CrimeStat III

Introduction

One of the things a spatial analyst (eg. business manager, biogeographer, demographer, forester, and marketer) might want to do is evaluate the spatial pattern of distribution of a phenomenon (eg. plant species, retail outlets, incidence of disease, settlement of migrants) in a particular area. There are all kinds of techniques that can be used for this sort of "point pattern analysis" problem. This lesson introduces you to nearest neighbour analysis, which is often used to describe a spatial pattern as "clumped", "random", or "uniform." The terms clumped and clustered are used interchangeably throughout this lesson.

The Nearest Neighbour Analysis techniques used in this lesson are based upon a method described by Clark & Evans (1954).  Clark and Evans were botanists who developed the Nearest Neighbour Index (NNI) primarily for analysing botanical field data, but it has been used in a variety of disciplines as a quantitative tool. Often when visually interpreting the geography of a point data set, the personal knowledge and experience of the analyst can lead to bias.  This approach is often referred to as qualitative.  Therefore, by adopting a statistical approach the method may be repeated and compared, certainly one of the principles of good science!

The NNI compares the distances between nearest points and distances that would be expected on the basis of chance. It is an index that is the ratio of two summary measures. First, there is the observed average nearest neighbour distance, Robs. For each point (or incident location, i) in turn, the distance to the closest other point (nearest neighbour, j) is calculated and averaged over all points. The mathematical expression for this is as follows:

Equation 1

Second, the expected average nearest neighbour distance, Rexp, of random points is the density of points within the study area, defined mathematically as follows:

Equation 2

Therefore, the NNI is the ratio of the above two separate statistics as follows:

Equation 3

The total area is the area of the study site.  When R = 1, the points are randomly located.  When R < 1 clustering is suggested and when R > 1 there is a tendency towards dispersion (Rogerson, 2001).

Regular Distribution of Points Random Distribution of Points Clustered Distribution of Points

The above Figures show a regular (R>1), random (R = 1) and clustered (R<1) distribution of points (graphics generated using ArcGIS, Hawth's Tools and IrfanView).

Some differences from 1.0 in the nearest neighbour index would be expected by chance. Clark and Evans (1954) proposed a Z-test to indicate whether the observed average nearest neighbour distance was significantly different from the mean random distance. The test is between the observed nearest neighbour distance and that expected from a random distribution and is given by:

Equation 4

where the standard error of the mean random distance is approximately given by:

Equation 5

with A being the area of a region and N the number of points within that region. There have been other suggested tests for the nearest neighbour distance as well as corrections for edge effects.

Research background and data

This lesson is largely based around the PhD research of Dr. Heather Builth.  While undertaking this research through Flinders University, Healther also Lectured in geography for the School and even took some survey students away to collect some of the data used in this lesson.Archaeological Rock Survey

Please read the following articles to find out more about Heather's research:

For this exercise you will need four shapefiles (courtesy of Dr. Heather Builth):

  • rocks.shp
  • house.shp
  • water.shp
  • bdy.shp

Zip File IconDownload this as a compressed zip file here exercise_data.zip

The shapefile house.shp defines the location of the centres of stone circles over the whole study area.  The shapefile called bdy.shp defines the actual study area survey boundary.   The shapefile called water.shp defines the extent of the floodplain.  The shapefile rocks.shp defines individual rocks that were surveyed accross a small area within the main site.  An image of the rock can be seen above-right.

Further pattern recognition analysis has lent support to a hypothesis that the stone clusters are culturally altered (unnatural) and circular in nature.  The archaeological interpretation is that these rocks are possibly aboriginal stone shelters or eel storage areas.

Software Requirements

You will need several different software applications for this exercise, including:

Please ensure all these programs have been downloaded and installed on the PC you are using for this exercise.

Establish a working directory

For this exercise you will need to establish a working directory.  Create a folder on your computer named NNA (eg. in C:\NNA).  Create two sub folders, one for the Data, another for Software.  Ensure all software has been downloaded into the Software folder and all data downloaded into the Data folder.  If any downloaded files are zipped, then unzip directly into the relevant folders.

Note that you will always get better performance if you use a local disk such as the "C" DRIVE rather than an external hard drive or USB flash drive.  It is preferable if you do not use a flash drive for this lesson. If you wish, you can always copy the working directory to your USB flash drive for transfer to another computer or for backup.

As you work through this exercise, you must ensure that all files created and results obtained are saved into your working directory.

Assessment

You are required to record all results.  Produce a report in scientific journal format. This includes an Introduction, Methods, Results and Discussion.  The focus of your report should be on your results and discussion.

The introduction should include a brief paragraph on NNA, with aims of this exercise clearly summarised. Methods should be kept brief, making reference to the software applications used and options chosen.  Your results section should just include figures and statistical results, and include simple figures of the two study sites from ArcMap.

Your discussion needs to be approximately 3/4 of a page, and include a critical reflection of the techniques used.  In your discussion consider the following:

  1. boundary effects
  2. size and shape of the study area
  3. projections, datums
  4. measurement error of the phenomena being analysed
  5. Application and usefulness of NNA and Kth Order NNA

Part 1: Calculating Nearest Neighbour Index using ArcGIS

Launch ArcMap and remove all toolbars except  Main menu, Standard and Hawth's Tools.  Add all four shapefiles. Within the Table of Contents (TOC) ensure that rocks is above house, which is above water which is above bdy.  Save your ArcMap session to your working directory (eg. C:/NNA/*.mxd) and name it NNA.mxd

For each shapefile, change the symbology as follows:

  • rocks.shp -  Symbol = Circle 1; Fill Colour = Cherrywood Brown; Size = 5.00 
  • house.shp -  Symbol = Circle 1; Fill Colour = Leaf Green; Size = 5.00
  • water.shp -  Fill Colour = Yogo Blue; Outline Width = 0.00; Outline Colour = No Colour
  • bdy.shp - Fill Colour = No Colour; Outline Width = 2.00; Outline Colour = Tuscan Red

Hit the Save button again (or Ctrl + S).

Your ArcMap window should look like the following:

ArcMap window

To perform NNA in ArcGIS you will need to install a VBA macro into the normal.mxt document template.  This is described in detail in the PDF that accompanies the VBA macro.  Read this carefully and install the routine.

NOTE: There is an omission on Pages 6-7 where you are required to load the *.FRM file.  The file is named frmNN (not frmLayerInfo as indicated).  Also, on Page 11 there is a code reference to frmLayerInfo.  Change this to frmNN also.

Use the VBA macro to calculate the NNI for house.shp (the "events") within the bdy.shp study area. Shown below are the input parameters. You should also see that there is an option to use an automatic polygon extent, with or without applying a buffer.  We will come back to this later.

Nearest Neighbour dialog box

You will see in the above figure that the option to Add NN distances & OIDs to feature table is checked. This will add the calculated distance from each event (house point) to its nearest neighbour to the attribute table, and give each event an Object ID (OID) so that the user can reference the points.

Click Calculate.

Record your results. Tip: you can opt to save the results to a text file, which you can the Copy and Paste from into your report.

Open the Attribute table for house.shp and view the results of the NN distances.  Close the Attribute table.

Repeat the Nearest Neighbour statistic for rocks.shp but first you will need to create a Minimum Convex Polygon (MVP) around the sample data.  An effective tool for calculating a MCP around a point data set is found in Hawth's Tools.

Zoom to the full extent of rocks.shp (in the TOC, right-click and select Zoom to Layer).  From the HawthsTools drop down menu, select Animal Movements, then Create Minimum Convex Polygons (shown below):

HawthsTools drop down menu

 

 

 

 

 

 

 

 

 

 

The Point locations layer should be set to rocks, and the output will need to go into your working directory, with the output shapefile named rocks_mcp.shp

HawthsTools MCP options

Click OK when done.

A Minimum Convex Polygon will then be created and added to your map window, which should look very similar to that shown below:

MCP around rocks.shp

Save your ArcMap session.

Run the NNA macro for rocks.shp, using the MCP as the boundary layer.

Record your results.

Repeat the NNA macro and again but this time use the Automatic Polygon Extent option with a Convex Hull, and a buffer of 1.5 metres.  Parameters and results shown below:

Nearest Neighbour dialog box with buffer.

record your results.

Part 2: Calculating Nearest Neighbour Index using CrimeStat III

In this part of the exercise you will repeat the calculation for NNA as for the two examples in Part 1 above.  The purpose of this is two-fold.  Firstly, CrimeStat vIII is an excellent (FREEWARE) spatial statistics package and it is important to be familiar with alternative applications. Secondly, it is often assumed that software is always correct.  By repeating the exercise in CrimeStat vIII you should get the same results, however it is good practice to check results in alternative application where possible.

If CrimeStat has been properly unzipped into your software directory, you should see a list of files as shown below:

CrimeStat directory

Double-click on the crimestat.exe to launch CrimeStat vIII. Accept the license. A "splash screen" appears.  You can click on this to close it and see the CrimeStat application.  The CrimeStat application is shown below:

CrimeStat Application Window

Click on the Select Files button and set the Type: to shapefiles. For the Name: you will need to navigate to your working directory and load house.shp.

CrimeStat Load Files

Click OK.

Next, you need to specify the fields containing the X-coordinates and Y-coordinates, as shown below.

CrimeStat Application Window with data

Also, in the above figure, the Type of coordinate system must be set to Projected (Euclidean) and the Data units set to Meters.

Next, hit the Spatial description tab (the green one!) and the Distance Analysis I tab. Check the box next to Nearest neighbour analysis (Nna). Here you leave the number of neighbours to be computed as 1, and leave the border correction as None.

CrimeStat NNA Tab

When ready, hit the Compute button. Record all results.

Your results should look something like:

    Sample size........: 100
    Measurement type...: Direct
    Start time.........: 11:44:37 PM, 11/17/2008

    Mean Nearest Neighbor Distance ..:  10.73 m
    Standard Dev of Nearest
    Neighbor Distance ...............:  17.95 m
    Minimum Distance ................:  0.00 m
    Maximum Distance ................:  1304.53 m

    Based on Bounding Rectangle:
    Area ............................:  865252.00 sq m
    Mean Random Distance ............:  46.51 m
    Mean Dispersed Distance .........:  99.95 m
    Nearest Neighbor Index ..........:  0.2306
    Standard Error ..................:  2.43 m
    Test Statistic (Z) ..............:  -14.7183
    p-value (one tail) ..............:  0.0001
    p-value (two tail) ..............:  0.0001

             Mean Nearest            Expected Nearest       Nearest
  Order      Neighbor Distance (m)   Neighbor Distance (m)  Neighbor Index
  *****      *********************   *********************  **************
    1                10.7271                46.5095              0.23064
   <-----

Now repeat this process for the rocks.shp. Again, record all results.

Part 3: Calculating the Kth Order Nearest Neighbour Index using CrimeStat III

An extension of the NNI is the Kth-Order Nearest Neighbour Index which compares not only the average distance for the nearest neighbour to an expected random distance, but also the distance between any event and the second, the third…., the Kth nearest neighbour.  The NNI(K) is the ratio of the observed Kth nearest neighbour distance d(KNN) to the Kth mean random distance d(Kran) which is so calculated:

Equation 6

and the index is:

Equation 7

This index can be useful for understanding the overall spatial distributions and for comparing different distributions. For example comparing the values of the index till the, say, 50th order for two distributions A and B and showing the values in a graph we can observe that both the distribution are more concentrated for each of the 50 nearest neighbours than a random distribution (its index is always 1) and that the events of B-distribution are more concentrated than the events of A-distribution.

Now repeat the computation for Nearest Neighbour Analysis for house.shp, however this time we will compute the NN Index to the Nth order, that is, for all orders.  If you return to ArcMap and open the Attribute table for house.shp you will see 100 records, which correspond to 100 points in your map window.  So for the number of nearest neighbours to be computed, enter 100.

Kth Order Nearest Neighbour

Hit the Compute button. Your results will include the information produced above, however,you now have the NNI for all orders.

             Mean Nearest            Expected Nearest       Nearest
  Order      Neighbor Distance (m)   Neighbor Distance (m)  Neighbor Index
  *****      *********************   *********************  **************
    1                10.7271                46.5095              0.23064
    2                17.9109                69.7642              0.25673
    3                25.7180                87.2052              0.29491
    4                34.0131               101.7394              0.33432
    5                43.3604               114.4569              0.37884
    6                53.8606               125.9026              0.42780
    7                60.5486               136.3944              0.44392
    8                74.0338               146.1369              0.50661
    9                80.1829               155.2705              0.51641
   10                91.0217               163.8966              0.55536
   11               100.5076               172.0914              0.58404
   12               104.5308               179.9138              0.58101
   13               108.4723               187.4102              0.57880
   14               122.0274               194.6183              0.62701
   15               125.7757               201.5689              0.62398
   16               130.1702               208.2879              0.62495
   17               138.1151               214.7969              0.64300
   18               140.8884               221.1144              0.63717
   19               145.2627               227.2565              0.63920
   20               148.9154               233.2369              0.63847
   21               152.3298               239.0678              0.63718
   22               159.1417               244.7599              0.65019
   23               163.9953               250.3227              0.65514
   24               174.7052               255.7645              0.68307
   25               182.8329               261.0929              0.70026
   26               185.9819               266.3147              0.69835
   27               205.2012               271.4362              0.75598
   28               213.2770               276.4628              0.77145
   29               223.3628               281.3996              0.79376
   30               228.6277               286.2513              0.79870
   31               231.0114               291.0222              0.79379
   32               239.3908               295.7161              0.80953
   33               244.2553               300.3367              0.81327
   34               266.8836               304.8872              0.87535
   35               282.1031               309.3709              0.91186
   36               287.1416               313.7904              0.91507
   37               291.8088               318.1486              0.91721
   38               302.0245               322.4479              0.93666
   39               316.4744               326.6907              0.96873
   40               324.2783               330.8790              0.98005
   41               388.2331               335.0150              1.15885
   42               395.9717               339.1006              1.16771
   43               402.3153               343.1375              1.17246
   44               408.7465               347.1274              1.17751
   45               411.3775               351.0721              1.17178
   46               417.0142               354.9729              1.17478
   47               419.7722               358.8313              1.16983
   48               424.4844               362.6486              1.17051
   49               463.7489               366.4262              1.26560
   50               475.1212               370.1653              1.28354
   51               525.3238               373.8669              1.40511
   52               537.1146               377.5323              1.42270
   53               539.3531               381.1624              1.41502
   54               542.6058               384.7583              1.41025
   55               544.1922               388.3208              1.40140
   56               545.8260               391.8510              1.39294
   57               549.4378               395.3497              1.38975
   58               554.2567               398.8177              1.38975
   59               597.8323               402.2558              1.48620
   60               604.8910               405.6647              1.49111
   61               626.7347               409.0452              1.53219
   62               634.8238               412.3981              1.53935
   63               642.4786               415.7239              1.54545
   64               645.7652               419.0233              1.54112
   65               716.9444               422.2969              1.69773
   66               723.9547               425.5453              1.70124
   67               727.8668               428.7691              1.69757
   68               738.0152               431.9689              1.70849
   69               744.3959               435.1452              1.71068
   70               747.9839               438.2984              1.70656
   71               759.6643               441.4291              1.72092
   72               763.6157               444.5377              1.71777
   73               815.1231               447.6248              1.82100
   74               818.8826               450.6907              1.81695
   75               821.5413               453.7359              1.81062
   76               822.2031               456.7608              1.80007
   77               824.5873               459.7659              1.79349
   78               836.9893               462.7513              1.80872
   79               840.0427               465.7177              1.80376
   80               844.4218               468.6653              1.80176
   81               847.2045               471.5944              1.79647
   82               850.1759               474.5055              1.79171
   83               861.1361               477.3988              1.80381
   84               862.4848               480.2747              1.79582
   85               863.6894               483.1335              1.78768
   86               865.2495               485.9755              1.78044
   87               871.9266               488.8009              1.78381
   88               875.7699               491.6101              1.78143
   89               890.6080               494.4034              1.80138
   90               895.9462               497.1809              1.80205
   91               898.2094               499.9430              1.79662
   92               900.1293               502.6900              1.79063
   93               936.5883               505.4220              1.85308
   94               943.8823               508.1393              1.85753
   95               957.1726               510.8422              1.87372
   96               963.9898               513.5308              1.87718
   97               969.2317               516.2054              1.87761
   98               983.4022               518.8663              1.89529
   99              1028.2139               521.5136              1.97160
  100                 1.#INF                -1.#IND              1.#INF0


Copy and Paste your results into Notepad.  Delete the column headings (you will add them again in Excel).  Launch Microsoft Excel, import and format the data and plot the NNI (refer figure below).  Label your chart axis and title for inclusion in your report.

Kth Order NNI Plot - House.shp

Repeat for rocks.shp

 

Last Updated on Wednesday, 16 September 2009 03:49