Spatial Analysis For Ecologists
Help File for SAFE-v01
Commands: File ... Convert ... Display ... Calc ...
(NB. If you are viewing this file online, you may like to
save it to disk for future reference)
SAFE combines some simple
GIS capabilities with more specialised functions of exploratory data analysis
that might be useful to ecologists dealing with spatially explicit data.
SAFE-v01 is the first version, therefore many of the features are only
partially developed in order to illustrate what might be possible. (See Conditions
of Use and Future
Developments).
There are also a number of known bugs. In particular, the program may crash if you enter
illogical or out-of-range values into certain input boxes. Please bear with me
and let me know what needs fixing, and what else you would like to be included.
SAFE accepts two basic
forms of spatially explicit data: point files and grid files.
Point Files are a list of
points with their x and y co-ordinates.
Each row of the file should
consist of three comma-separated values: point-ID, x-coordinate, y-coordinate
E.g.
1,23,45
2,36,78
3,54,21
4,11,63
Data files can be created
and read by Excel by "saving as" .csv format. Alternatively they can
be typed directly into a text editor such as Notepad, or Word (remembering to
"save as" .txt).
If you have trouble reading
in a file make sure that the data starts on the first line and that there are
no extra commas after the y-coordinates, and no blank lines at the bottom of
the file.
Notes
In display, each point is
represented by a red square of 1 mapunit by 1 mapunit.
The GB Display option
assumes that the map units are kilometres
The text box to the upper
left of the main window will display the data that has been read in. Two
information boxes above the text box will also display the name of the data
file and the number of records read. You should verify that this is correct.
Grid Files are used to
represent raster data. i.e. the sort of data captured by satellites. The values
of each grid cell may represent a spatially continuous variables (such as
density or elevation), categorical data (such as land cover types) or binary
data ( such presence/absence).
The grid data files
contains one row of comma-separated values for each row of the grid, starting
with the northern-most row and finishing with the southern-most one. The number
of columns is determined by the number of values per row.
E.g. a grid of 5 rows by 6
columns:
5, 0, 3, 2, 1, 0
6, 2, 3, 1, 0, 0
4, 5, 2, 0, 0, 0
3, 2, 1, 1, 0, 1
1, 0, 0, 1, 2, 4
As with point files, grid
files can be created and read by Excel by "saving as" .csv format.
Alternatively they can be typed directly into a text editor such as Notepad, or
Word (remembering to "save as" .txt).
If you have trouble reading
in a file make sure that the data starts on the first line and that there are
no extra commas after the y-coordinates, and no blank lines at the bottom of
the file.
Notes
You should know ahead of
loading how many rows and columns are in your data file, and the size of each
cell (although a default size of one can be used).
Interface Layout
The main interface has a
command bar at the top with three fixed windows below.
1. The "Map
Window" is the large square window with a blue background to the right. It
is used to provide a visual display of the data and/or analysis. At any time
one can zoom-in on the map display by highlighting a square sub-section of the
window.
2. The "Text
Window" is the white window to the upper left. It has vertical and
horizontal scroll bars. It displays text information to keep the user informed
of what is going on. e.g. it displays the contents of data files that have been
imported
3. The "Graph
Window" is the white window to the lower left. In later versions it will
display graphs relating to the current analysis.
Import Point
File
Select a point file to load
as the current point file. See Data file Structure - Point
Files. The imported file will replace any
previously loaded point file, but will not affect the current grid file.
Import Grid
File
Select a point file to load
as the current point file. See Data file Structure - Grid Files. The imported file will replace any previously loaded grid
file, but will not affect the current point file. You will be prompted to enter
the number of rows and columns in your data file, as well as the cell size
(i.e. resolution) and style of your data. It is up to you to decide on the
units being used, but the result of all analyses will be expressed in terms of
these map units. In future, different types of data (continuous, categorical
and binary) will display differently.
Convert Point
to Grid
As the name suggests, this
command will convert a point file into a grid file. You will be prompted to
supply a file name and location, the number of rows and columns in the grid, a
point of origin and the cell size.
A suite of commands for
altering the extent and magnification of the file in view. Shortcuts are
provided in combination with the Control key.
Clear Screen
Clears the screen.
Full Extent
Calculates the minimum
extent required to display all of the data and then jumps to this magnification
and central location. This is the default when a data file is imported.
Select Area
Use the cursor to select a
square area on the map window. (Click on one corner of the area using the left
mouse button, then drag across to the diagonally opposite corner and release.)
The display will zoom-in on this area.
GB View
Calculates Sets the map
window to display an area from (0,0) mapunits at the lower left corner to
(1000,1000) mapunits at the upper right. This encompasses all of Great Britain
if the mapunits are kilometres.
Zoom In / Zoom
Out
Increases or decreases the
magnification by a factor of two, located around the current central position.
Pan Left / Pan
Right / Pan Up / Pan Down
Pan left, right, up or down
by three-quarters of a screen. Magnification remains the same.
Interpoint
Distances
Calculates the euclidean
distance between every pair of points in a point file. You will be prompted to
save the interpoint distance matrix to a text file.
Connected
Clusters
Firstly, this command will
display links between sites that are not further apart (and not closer
together) than certain specified distances. Based upon these links there is an
option to calculate how many distinct clusters or networks of sites there are.
A binary matrix is appended to the text box display, which shows which sites
are in the same cluster.
Neighbourhood
Analysis
There are two sub-options
which operate in almost exactly the same way.
Counts in
circles
This function centres a
circle of radius r around every point and calculates how many other
points fall within the circle. The result is then averaged across all points
and displayed in a message box. The process is then repeated for a different
length radius (different scale). You will be prompted to enter nine different
radius values.
Counts in
squares
This function centres a
square of side length s around every point and calculates how many other
points fall within the square. The result is then averaged across all points
and displayed in a message box. The process is then repeated for a different
side length (different scale). You will be prompted to enter nine different
values for (s / 2), i.e. the equivalent of a radius.
Notes
Both of the above commands
give you the option of saving the results to a .csv file that can be read by
excel. The output file has one row for each point, with column headers
indicating the Id, easting, northing, numer of points within distance1,
distance2 etc. If you select the "continuous" option you will not see
any graphical output and will not be prompted to continue for each scale, but
the results can still be written to file.
Fractal analysis
These commands are still
under development.
The file testdata.csv
contains 60 points with x-coordinate values ranging from 265 to 415 and
y-coordinate values ranging from 195 to 316 map units. (It can be thought of as
a hypothetical species distribution, concentrated in the south-east of Britain,
using map units of kilometres referenced according to the GB National Grid).
This software may be
distributed freely for non-commercial academic use only. Whilst every effort
has been made to create an acceptable working version, no responsibility is
accepted for consequential loss or damage of hardware or data caused by use of
this software.
The program will usually
crash if you enter letters where numbers are required, or if you fail to enter
a number or file name when required.
Please e-mail me details of
additional bugs not reported here.
Calculate the mass fractal
dimension of points and grids.
Patch-occupancy analyses
Correlation between two
grids, with appropriate adjustment for spatial autocorrelation
Enable SAFE to read D-Map
files. I.e. Convert National Grid alphanumeric coordinates to numeric only
coordinates (e.g. SE 224 679 = 422.4, 467.9 km)
Please e-mail me with
further suggestions