NMDS 2.0 Program Description
Basic Knowledge about the Interface
How to start a NMDS
Dealing with Missing Values (MV)
Dealing with the Temperature Option
This is a usual Power Point Presentation.
Use Mouse-Clicks or the Hyperlinks to proceed.
The Menu of NMDS
The menu of NMDS is very simple
Each topic directly leads to a
window of the application
The Menu of NMDS
The menu of Access calls the
Access data-base that contains the
rank-matrixes. Call this option to import your own matrix.
You, for instance, can simply import any correlation
matrix generated by excel using the access import filter
and visualize the relations using NMDS
The list of all matrixes that are stored in the
Access database are listed in this combo box
The NMDS Rank-Matrix
This is the examle rank-matrix of the example “Staedte” (towns)
This is the classical example in psychological text-books.
The NMDS Rank-Matrix
This is the example rank-matrix based on reaction times (1/100-seconds)
typing several letters with a QWERTY keyboard
The NMDS Rank-Matrix
This is the example rank-matrix based on an imported correlation matrix
produced in EXCEL and imported in ACCESS
The Interface - NMDS Control 1/5
This is the Option Box
where you select the
Rank Matrix you want to
elaborate
If you start NMDS, you
see the following Windows.
This is the Information Line
showing you the actual
Progress of the NMDS
This button loads the
specified rank-matrix
Here you have to adjust whether high values
in the rank-matrix mean
similarity or no-similarity
Here you choose the dimensionality
of the NMDS graph
(since a screen only has a 2D presentation,
usually keep the default)
Here you select how to deal
with missing values
The Interface - NMDS Control 2/5
This option box determines
the temperature for the
NMDS calculation
This option box determines
what is affected by
the temperature
Here you select the Random Algorithm you
want to use for calculation
(usually you*ll keep 0 as default)
This button starts the
NMDS calculation
The Interface - NMDS Control 2/5
This button shows you the
NMDS graph
This option box determines
the size of NMDS graph
This option decides whether the
information in the text-field
is presented on the NMDS graph
Mirroring the NMDS graph
horizontally
Mirroring the NMDS graph
vertically
Rotating the NMDS graph
in steps of 45 degrees
This is the information that is
generated automatically with
each start of the program
In this field you can
specufy how long the
labels are on the NMDS graph
The Interface - NMDS Control 4/5
This button shows you the
Alienus graph
Switching into the
single step mode
(you then have to press a key
for each iteration step)
An information field of the
actual iterations
calculated
An information field of the
actual calculated
alienus
The Interface - NMDS Control 5/5
This button prints the NMDS graph
on the standard printer
This button exports the NMDS
calculation into *.txt files
This button stops
and continues the
NMDS calculation
This button terminates the
NMDS program
The Interface - NMDS Graph
Use right button
to move an item
Click into this window
to refresh the
NMDS drawing
Moving an item manually
is useful to test
certain hypotheses about
relationships of variables
The Interface - Alienus Monitor
The Alienus Monitor shows
the development of the
alienus over time.
It is useful to set the
appropriate temperature
for a give rank matrix
How to Start a NMDS
4. Press here
3. Press here
1. Press here
5. Enter 10 here
6. Press here & wait
2. Press here
To see how NMDS is working just
try the default “Städte” (towns)
How to deal with Missing Values (MV)
NMDS has various options to
deal with Missing Values (MV)
by choosing several options in this
combo-box
How to deal with Missing Values (MV)
Missing-Values can be treated with the following options
• MV set to -1
All MV are set to -1
• MV set to 0
All MV are set to 0
• inverse-single
Optimal Option if the Rank-Matrix contains values from 0 to 1
• positive-double
Optimal Option if the Rank-Matrix contains values from 1 onwards
• negative-double
Option if the Rank-Matrix contains values from 0 to 1
and the MV are to be distinguished very clearly from known values
• inverse-double
Option if the Rank-Matrix contains values from 0 to 1
and the MV are to be distinguished clearly from known values
• all-inverse
Fits to all problems that cannot be treated with means above
The Temperature Option
The temperature Option is a highly efficient option to avoid local minima in
a NMDS calculation.
A temperature of 0 would, for instance lead to about 1%-4% wrong
representations in a simple Example with about 10 varibales and a defined
optimal solution, as “Städte” (towns) in this software package.
Using a temperature of 1.0 for this example reduces this error to zero, i.e. in
all times the optimal minimum is found.
Set the temperature in a way that the calculated points are “shaken” and
cooled down in order to find the best fit of the NMDS graph to your
rank matrix. Consider the following experience-based suggestions:
• For 10 Variables:
• For 30 Variables:
• For 90 Variables:
Temperature set to 0.5 or higher
Temperature set to 1.0 or higher
Temperature set to 3.0 or higher
The Temperature Option
Input the value for the
temperature as you like here.
The most efficient value
for about 10 variables
in terms of time and result-quality
for the temperature is preset.
There are two algorithms implemented
how the temperature
boils the points in the
NMDS graph.
“Dots+Alineation” or “Alineation”
“Dots+Alineation” is more efficient
in finding local minima
“Alineation” is more efficient in terms
of time until the solution is found
.
The Temperature Option
Without the temperature,
a Rank-Matrix may fall
into a local minimum.
This means, the NMDS will
not find the optimal
interrelation of the
variables
In general the Alienus-Monitor
is showing a graph like
the green one if the
temperature has successfully
overcome a local minima
The temperature avoids
that a NMDS graph falls
into a local minimum and
fixes 90% to 100% of all
possible local mimima.
The Temperature Option
Don’t worry, if the NMDS graph
looks like this during the
NMDS calculation.
The temperature cools down
with each iteration so that
an optimum is found after
a certain amount of interations.
The absolute number of
iterations required depends
on the quality of the data as well as the
temperature set
Showdown
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© Oliver Straeter